@article{pmid7536111,

title = {Antibody-antigen interactions: new structures and new conformational changes},

author = {I A Wilson and R L Stanfield},

doi = {10.1016/0959-440x(94)90267-4},

issn = {0959-440X},

year  = {1994},

date = {1994-12-01},

journal = {Curr Opin Struct Biol},

volume = {4},

number = {6},

pages = {857--867},

abstract = {During the past year, many new antibody structures have been determined, increasing our understanding of these immunologically important molecules. Of special interest are new catalytic antibodies, antibody-peptide and antibody-virus complexes, NMR structures, and structures illustrating conformational changes and antibody cross-reactivity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8071992,

title = {Structural analysis of antibody specificity. Detailed comparison of five Fab'-steroid complexes},

author = {J H Arevalo and C A Hassig and E A Stura and M J Sims and M J Taussig and I A Wilson},

doi = {10.1006/jmbi.1994.1543},

issn = {0022-2836},

year  = {1994},

date = {1994-09-01},

journal = {J Mol Biol},

volume = {241},

number = {5},

pages = {663--690},

abstract = {Structures of the Fab' fragment of the anti-progesterone antibody DB3 in complex with five cross-reactive steroids (aetiocholanolone, 5 beta-androstane-3,17-dione, 5 alpha-pregnane-20-one-3 beta-ol-hemisuccinate, progesterone-11 alpha-ol-hemisuccinate and progesterone) have been determined by X-ray crystallography to a maximum resolution of 2.7 A. These different steroids compete with progesterone binding with affinities in the nanomolar range despite substantial differences in their three-dimensional structures. Comparison of the unliganded DB3 Fab' and these five steroid-Fab' complexes reveals that all the steroid ligands bind to an "open" conformation of the Fab' as defined by the orientation of the indole side-chain of TrpH100, whereas in the unliganded or "closed" form the binding site is occluded by TrpH100. Small but significant conformational changes take place in the antibody to maximize the physical and chemical complementarity with each ligand. The various cross-reactive ligands are accommodated in the binding site in two distinct orientations. We term these binding modes syn and anti, as they are defined by the orientation of the steroid beta face relative to TrpH50. In all cases, the steroid D ring is inserted into a hydrophobic cavity formed mainly by TrpH50, TyrH97, TrpH100 and PheH100b; a hydrogen bond interaction with AsnH35 to the keto group at position C17 or C20 orients the steroid in the pocket. The AsnH35 hydrogen bond and the interaction with TrpH50 account for the restricted heavy chain response to immunization with progesterone-like steroids derivatized at the 11 alpha position. Cross-reactivity of the antibody with different steroids is explained by alternative binding pockets for the A ring, which generates different ligand orientations in the binding site. This study suggests which factors are most likely to contribute to the observed antibody specificity, such as linker position and the paucity of functional groups on the immunogenic hapten.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid7520084,

title = {Crystal structure of a peptide complex of anti-influenza peptide antibody Fab 26/9. Comparison of two different antibodies bound to the same peptide antigen},

author = {M E Churchill and E A Stura and C Pinilla and J R Appel and R A Houghten and D H Kono and R S Balderas and G G Fieser and U Schulze-Gahmen and I A Wilson},

doi = {10.1006/jmbi.1994.1530},

issn = {0022-2836},

year  = {1994},

date = {1994-08-01},

journal = {J Mol Biol},

volume = {241},

number = {4},

pages = {534--556},

abstract = {The three-dimensional structure of the complex of a second anti-peptide antibody (Fab 26/9) that recognizes the same six-residue epitope of an immunogenic peptide from influenza virus hemagglutinin (HA1; 75-110) as Fab 17/9 with the peptide has been determined at 2.8 A resolution. The amino acid sequence of the variable region of the 26/9 antibody differs in 24 positions from that of 17/9, the first antibody in this series for which several ligand-bound and free structures have been determined and refined. Comparison of the 26/9-peptide with the 17/9-peptide complex structures shows that the two Fabs are very similar (r.m.s.d. 0.5 to 0.8 A) and that the peptide antigen (101-107) has virtually the same conformation (r.m.s.d. 0.3 to 0.8 A) when bound to both antibodies. A sequence difference in the 26/9 binding pocket (L94; His in 26/9, Asn in 17/9) results in an interaction with a bound water molecule that is not seen in the 17/9 structures. Epitope mapping shows that the relative specificity of 26/9 and 17/9 antibodies for individual positions of the peptide antigen are slightly different. Amino acid substitutions in the peptide, particularly at position SerP107, are tolerated to different extents by 17/9 and 26/9. Structural and sequence analysis suggests that amino acid differences near the peptide-binding site are responsible for altering slightly the specificity of 26/9 for three peptide residues and illustrates how amino acid substitutions can modify antibody-antigen interactions and thereby modulate antibody specificity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15299400,

title = {Reverse screening},

author = {E A Stura and A C Satterthwait and J C Calvo and D C Kaslow and I A Wilson},

doi = {10.1107/S0907444994001794},

issn = {0907-4449},

year  = {1994},

date = {1994-07-01},

journal = {Acta Crystallogr D Biol Crystallogr},

volume = {50},

number = {Pt 4},

pages = {448--455},

abstract = {Major emphasis has been placed in recent years on kits for screening crystallization conditions of macromolecules. Such approaches have undoubtedly speeded up the initial screening and, to a certain extent, helped in reducing the amount of protein required for the initial survey. Factorial screening techniques, either full-factorial or sparse-matrix approaches, have proved successful in the crystallization of many proteins. However, in cases where the amount of protein is limited a systematic approach based on an a priori choice of precipitants may be preferable to an extensive search. The approach described here targets such situations. The approach consists of the determination of the solubility characteristics of the macromolecule under study as a function of precipitant and macromolecule concentrations to define a working range for these parameters. Conditions under which the protein is highly supersaturated, and hence more conducive to nucleation, are established so as to favor the formation of an initial stable nucleus which can be one of the dominant problems that hinders successful crystallization of proteins. Later, changes in solubility as a function of pH and as a result of the introduction of additives are evaluated. In addition, when ligands are available for the formation of macromolecular complexes, screening of different complexes is used as a means to increase the probability of obtaining crystals. Solubility information derived from one, or more, complexes that have been screened can be used for comparison and to aid in the crystallization of other complexes. Cross-seeding between complexes is an intrinsic part of the method and provides an efficient way of obtaining crystals when spontaneous nucleation is hard to achieve. In the example presented here, reverse screening has enabled the production of crystals of several peptide complexes with an anti-malaria antibody.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid7765075,

title = {Antigen-induced conformational changes in antibodies: a problem for structural prediction and design},

author = {R L Stanfield and I A Wilson},

doi = {10.1016/0167-7799(94)90139-2},

issn = {0167-7799},

year  = {1994},

date = {1994-07-01},

journal = {Trends Biotechnol},

volume = {12},

number = {7},

pages = {275--279},

abstract = {Recent work has shown that large conformational changes in antibodies can accompany antigen binding. These structural changes can alter dramatically the size, shape and charge distribution in the antigen-binding pocket, and may present problems for accurate modeling of antibody structures.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid7922033,

title = {Covalently linked ligand stabilizes expression of heterodimeric receptor},

author = {I A Wilson},

doi = {10.1016/s0969-2126(00)00056-3},

issn = {0969-2126},

year  = {1994},

date = {1994-06-01},

journal = {Structure},

volume = {2},

number = {6},

pages = {561--562},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid7511253,

title = {Crystal structure of the principal neutralization site of HIV-1},

author = {J B Ghiara and E A Stura and R L Stanfield and A T Profy and I A Wilson},

doi = {10.1126/science.7511253},

issn = {0036-8075},

year  = {1994},

date = {1994-04-01},

journal = {Science},

volume = {264},

number = {5155},

pages = {82--85},

abstract = {The crystal structure of a complex between a 24-amino acid peptide from the third variable (V3) loop of human immunodeficiency virus-type 1 (HIV-1) gp 120 and the Fab fragment of a broadly neutralizing antibody (59.1) was determined to 3 angstrom resolution. The tip of the V3 loop containing the Gly-Pro-Gly-Arg-Ala-Phe sequence adopts a double-turn conformation, which may be the basis of its conservation in many HIV-1 isolates. A complete map of the HIV-1 principal neutralizing determinant was constructed by stitching together structures of V3 loop peptides bound to 59.1 and to an isolate-specific (MN) neutralizing antibody (50.1). Structural conservation of the overlapping epitopes suggests that this biologically relevant conformation could be of use in the design of synthetic vaccines and drugs to inhibit HIV-1 entry and virus-related cellular fusion.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8303271,

title = {Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart},

author = {M R Haynes and E A Stura and D Hilvert and I A Wilson},

doi = {10.1126/science.8303271},

issn = {0036-8075},

year  = {1994},

date = {1994-02-01},

journal = {Science},

volume = {263},

number = {5147},

pages = {646--652},

abstract = {The three-dimensional structure of a catalytic antibody (1F7) with chorismate mutase activity has been determined to 3.0 A resolution as a complex with a transition state analog. The structural data suggest that the antibody stabilizes the same conformationally restricted pericyclic transition state as occurs in the uncatalyzed reaction. Overall shape and charge complementarity between the combining site and the transition state analog dictate preferential binding of the correct substrate enantiomer in a conformation appropriate for reaction. Comparison with the structure of a chorismate mutase enzyme indicates an overall similarity between the catalytic mechanism employed by the two proteins. Differences in the number of specific interactions available for restricting the rotational degrees of freedom in the transition state, and the lack of multiple electrostatic interactions that might stabilize charge separation in this highly polarized metastable species, are likely to account for the observed 10(4) times lower activity of the antibody relative to that of the natural enzymes that catalyze this reaction. The structure of the 1F7 Fab'-hapten complex provides confirmation that the properties of an antibody catalyst faithfully reflect the design of the transition state analog.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8142304,

title = {Monoclonal antibodies against progesterone: effect of steroid-carrier coupling position on antibody specificity},

author = {M Gani and J Coley and J Piron and A S Humphreys and J Arevalo and I A Wilson and M J Taussig},

doi = {10.1016/0960-0760(94)90156-2},

issn = {0960-0760},

year  = {1994},

date = {1994-02-01},

journal = {J Steroid Biochem Mol Biol},

volume = {48},

number = {2-3},

pages = {277--282},

abstract = {Monoclonal anti-progesterone antibodies were raised by immunizing mice with progesterone coupled through either the C3, C6 or C11 positions to protein carrier (bovine serum albumin, BSA). The specificity of four antibodies for a range of steroids related to progesterone, some carrying substitutions at various ring positions, was studied by competitive inhibition in an ELISA system. The results demonstrated that the ring coupling position has a determining effect on the cross-reactivity of the antibodies obtained. The patterns of cross-reaction were interpreted in the light of the structure of the combining site of an anti-progesterone antibody (DB3) recently determined by X-ray crystallography, and inferences drawn about the orientation of steroid in the combining sites of the antibodies studied. Specifically, in two antibodies raised against progesterone-11-BSA, the orientation of steroid resembled that of the progesterone-DB3 complex, with positions C11 and C3 exposed and C6 and C20 buried; an antibody raised against progesterone-6-BSA bound steroid in an apparently similar disposition, except that C6 was exposed and C11 buried; finally, in an antibody raised against progesterone-3-BSA, all steroid positions other than C3 were apparently buried in the steroid-antibody complex.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8159668,

title = {Crystallization and preliminary structural studies of a chorismate mutase catalytic antibody complexed with a transition state analog},

author = {M R Haynes and E A Stura and D Hilvert and I A Wilson},

doi = {10.1002/prot.340180211},

issn = {0887-3585},

year  = {1994},

date = {1994-02-01},

journal = {Proteins},

volume = {18},

number = {2},

pages = {198--200},

abstract = {The Fab' fragment of a catalytic antibody with chorismate mutase activity has been crystallized as a complex with the transition-state analog hapten. The complex was crystallized by the vapor diffusion method using ammonium sulfate as the precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions a = 37.1 A, b = 63.3 A, c = 178.5 A, and there is one Fab' molecule per asymmetric unit. The crystals diffract X-rays to at least 3.0 A and are suitable for X-ray crystallographic studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid7812653,

title = {Immune recognition of viral antigens},

author = {I A Wilson and R L Stanfield and D A Jewell and J B Ghiara and D H Fremont and E A Stura},

issn = {1056-2044},

year  = {1994},

date = {1994-01-01},

journal = {Infect Agents Dis},

volume = {3},

number = {2-3},

pages = {155--162},

abstract = {The response exhibited by the immune system to viral and other foreign antigens consists of antibody-mediated and T cell-mediated immunity. Structural and molecular biological studies have shown that the antibody response is tailored to provide exquisite specificity by generating binding pockets that are complementary in shape as well as in charge to the antigen. On the other hand, the cellular response uses T-cell receptors (TCRs) and the major histocompatibility complex (MHC) antigens. Structural information on the TCRs is not yet available, but the crystal structures of several MHC class I molecules have shown how one MHC molecule can bind many different peptide sequences that share only the common anchor residue positions that determine allele specificity. MHC class I interactions with the peptide backbone at the N and C termini explain the high specificity of the binding groove for peptide ligands and suggest a universal mode of recognition for peptides to MHC class I molecules. Peptide-MHC class II interactions are less well understood, although recent structural work has shown important differences in the binding clefts of MHC class I and II that lead to longer peptides being bound to class II molecules. Detailed analysis at the molecular level has indicated that conformational changes in both antibodies and MHC molecules occur upon antigen binding.(ABSTRACT TRUNCATED AT 250 WORDS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8008973,

title = {Structure of anti-peptide antibody complexes},

author = {I A Wilson and J B Ghiara and R L Stanfield},

doi = {10.1016/s0923-2494(94)80049-9},

issn = {0923-2494},

year  = {1994},

date = {1994-01-01},

journal = {Res Immunol},

volume = {145},

number = {1},

pages = {73--78},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8263915,

title = {Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes},

author = {U Schulze-Gahmen and J M Rini and I A Wilson},

doi = {10.1006/jmbi.1993.1663},

issn = {0022-2836},

year  = {1993},

date = {1993-12-01},

journal = {J Mol Biol},

volume = {234},

number = {4},

pages = {1098--1118},

abstract = {A new orthorhombic crystal form of Fab 17/9 has been determined in complex with a 7-mer peptide from influenza virus hemagglutinin (HA1 101-107, acetylated and amidated). The three-dimensional structure was resolved to 2.8 A with an improved refinement and better geometry than two previously determined Fab 17/9-peptide (HA1 100-108) complexes, facilitating a detailed description of the Fab-peptide interactions. The binding pockets and the peptide antigen are structurally similar in all three peptide complexes of Fab 17/9. The peptide adopts an extended conformation (residues 100 to 103) and a type I reverse turn (residues 104 to 107). Additionally, the antigenic determinant described here correlates well with previous epitope mapping studies. The structures of the free and antigen bound Fab illustrate the role of induced fit as a mechanism for antibody-antigen recognition. Fab 17/9 undergoes a large conformational change, mainly in the H3 loop, upon peptide binding. As a result, the shape of the binding pocket changes substantially in the liganded Fab. However, the backbone conformations of the other hypervariable loops (L2, L3, H1 and H2) show no significant difference between free and bound structures. The conformation of the L1 loop is also maintained in all structures, but its position relative to the framework varies in different crystal environments. The availability of three X-ray structures of an Fab-peptide complex in three different space groups makes it possible to clearly distinguish between crystal packing and antigen binding as the cause of structural differences. Two distinct H3-loop conformations, free and bound, are observed with no evidence otherwise for multiple conformations of the hypervariable loops (CDRs) or increased flexibility in either the free or bound forms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8413674,

title = {Molecular basis of crossreactivity and the limits of antibody-antigen complementarity},

author = {J H Arevalo and M J Taussig and I A Wilson},

doi = {10.1038/365859a0},

issn = {0028-0836},

year  = {1993},

date = {1993-10-01},

journal = {Nature},

volume = {365},

number = {6449},

pages = {859--863},

abstract = {Two major unanswered questions concerning the specificity of antibodies are: how do structurally different antigens bind with high affinity to the same antibody, and what are the limits of the antibody combining site complementarity and flexibility that contribute to such crossreactivity? We report here a comparative analysis of the X-ray structures of five conformationally different steroids in complex with the Fab' fragment of an anti-progesterone antibody DB3 at 2.7 A. This antibody is unable to complement completely the shape of the hydrophobic antigen so that crossreactivity occurs with other ligands without major structural rearrangements of the binding site. Antigen specificity can be explained through conserved interactions of DB3 with the steroid D-ring, whereas some of the crossreactivity is realized through different binding orientations of the steroid skeleton that place the A-ring into alternative pockets on the antibody surface. The restricted gene usage of the VGAM3.8 family in the generation of anti-progesterone monoclonal antibodies may be explained by the specific interaction of VH hallmark residues with the steroid D-ring. This first detailed structure of steroid interactions with a protein could be applied to the understanding of general mechanisms of steroid recognition as well as in the design of specific binding sites for small hydrophobic ligands.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8069628,

title = {Major antigen-induced domain rearrangements in an antibody},

author = {R L Stanfield and M Takimoto-Kamimura and J M Rini and A T Profy and I A Wilson},

doi = {10.1016/0969-2126(93)90024-b},

issn = {0969-2126},

year  = {1993},

date = {1993-10-01},

journal = {Structure},

volume = {1},

number = {2},

pages = {83--93},

abstract = {BACKGROUND: Recent structural results have shown that antibodies use an induced fit mechanism to recognize and bind their antigens. Here we present the crystallographically determined structure of an Fab directed against an HIV-1 peptide (Fab 50.1) in the unliganded state and compare it with the peptide-bound structure. We perform a detailed analysis of the components that contribute to enhanced antigen binding and recognition.nnRESULTS: Induced fit of Fab 50.1 to its peptide antigen involves a substantial rearrangement of the third complementarity determining region loop of the heavy chain (H3), as well as a large rotation of the variable heavy (VH) chain relative to the variable light (VL) chain. Analysis of other Fab structures suggests that the extent of the surface area buried at the VL-VH interface correlates with the ability to alter antibody quaternary structure by reorientation of the VL-VH domains.nnCONCLUSION: Fab 50.1 exhibits the largest conformational changes yet observed in a single antibody. These can be attributed to the flexibility of the variable region. Comparisons of new data with previous examples lend to the general conclusion that a small VL-VH interface, due in part to a short H3 loop, permits substantial alterations to the antigen-binding pocket. This has major implications for the prediction, engineering and design of antibody-combining sites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8327513,

title = {Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen},

author = {J M Rini and R L Stanfield and E A Stura and P A Salinas and A T Profy and I A Wilson},

doi = {10.1073/pnas.90.13.6325},

issn = {0027-8424},

year  = {1993},

date = {1993-07-01},

journal = {Proc Natl Acad Sci U S A},

volume = {90},

number = {13},

pages = {6325--6329},

abstract = {The crystal structure of the Fab fragment of a human immunodeficiency virus type 1 (HIV-1) neutralizing monoclonal antibody Fab has been determined at 2.8 A resolution in complex with a linear 16-residue peptide from the third hypervariable region (V3) of gp120. The first 9 residues of the peptide are ordered in the electron density maps, and their conformation is in partial agreement with the beta-strand-type II beta-turn structure predicted for this portion of the V3 loop. Notably, several of the peptide residues that are well conserved among different HIV-1 isolates contact a nonpolar 25-A-long groove in the antibody-combining site. The largely extended structure of the peptide differs from the beta-turns seen as the primary determinants in other published anti-peptide Fab structures. Analysis of the specific Fab-peptide interactions only partially explains the MN isolate specificity shown by this antibody.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8496956,

title = {Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex},

author = {J H Arevalo and E A Stura and M J Taussig and I A Wilson},

doi = {10.1006/jmbi.1993.1260},

issn = {0022-2836},

year  = {1993},

date = {1993-05-01},

journal = {J Mol Biol},

volume = {231},

number = {1},

pages = {103--118},

abstract = {The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorphous and belong to the hexagonal space group, P6(4)22, with unit cell dimensions of a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab' have been determined by X-ray crystallography at 2.7 A resolution using molecular replacement techniques. Progesterone is bound in a hydrophobic pocket formed mainly by the interaction of three complementarity determining regions L1, H2 and H3. The orientation of the ligand in the binding site was aided by both crystallographic and biochemical analyses of substituted steroids. The indole side-chain of TrpH100 of the DB3 has two different conformations, inter-converting "open" and "closed" forms of the antibody combining site. The TrpH100 indole thus appears to be acting as an antibody-derived surrogate ligand for its own hydrophobic binding pocket. These structures provide the first atomic view of how a steroid interacts with a protein and offer a structural explanation for the restriction of the anti-progesterone response to the VGAM3.8 family of VH genes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8504218,

title = {Structural analysis of MHC class I molecules with bound peptide antigens},

author = {I A Wilson and D H Fremont},

doi = {10.1006/smim.1993.1011},

issn = {1044-5323},

year  = {1993},

date = {1993-04-01},

journal = {Semin Immunol},

volume = {5},

number = {2},

pages = {75--80},

abstract = {Three-dimensional structures of human and murine MHC class I molecules in complex with peptide antigens have begun to elucidate the mechanism of peptide binding. The MHC molecule has a highly conserved structure in which important variation occurs only in the residues lining the central polymorphic portion of the peptide binding cleft. Peptides bind in extended conformations deep within the cleft and have highly specific and conserved interactions at their amino and carboxyl termini and divergent interactions in the middle. Peptides longer than the canonical length for a given allele appear to bulge in the middle but maintain their interactions at their ends. One or more anchor residues are used by the peptide to establish tight and enduring presentation to T cells. Peptide-associated conformational differences in the MHC molecule itself may contribute to the T cell recognition process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid8419939,

title = {Crystal structure of phospholipase A2 from Indian cobra reveals a trimeric association},

author = {D H Fremont and D H Anderson and I A Wilson and E A Dennis and N H Xuong},

doi = {10.1073/pnas.90.1.342},

issn = {0027-8424},

year  = {1993},

date = {1993-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {90},

number = {1},

pages = {342--346},

abstract = {Phospholipase A2 (PLA2) from Indian cobra venom (Naja naja naja) was crystallized from ethanol in space group P4(3)2(1)2 in the presence of Ca2+. The x-ray crystal structure was determined to 2.3-A resolution by molecular replacement techniques using a theoretical model constructed from homologous segments of the bovine pancreatic, porcine pancreatic, and rattlesnake venom crystal structures. The structure was refined to an R value of 0.174 for 17,542 reflections between 6.0- and 2.3-A resolution (F > 2 sigma), including 148 water molecules. The 119-amino acid enzyme has an overall architecture strikingly similar to the other known PLA2 structures with regions implicated in catalysis showing the greatest structural conservation. Unexpectedly, three monomers were found to occupy the asymmetric unit and are oriented with their catalytic sites facing the pseudo-threefold axis with approximately 15% of the solvent accessible surface of each monomer buried in trimer contacts. The majority of the interactions at the subunit interfaces are made by residues unique to PLA2 sequences from cobra and krait venoms. The possible relevance of this unique trimeric structure is considered.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1438187,

title = {Crystallization, sequence, and preliminary crystallographic data for an antipeptide Fab 50.1 and peptide complexes with the principal neutralizing determinant of HIV-1 gp120},

author = {E A Stura and R L Stanfield and G G Fieser and S Silver and M Roguska and L M Hincapie and H K Simmerman and A T Profy and I A Wilson},

doi = {10.1002/prot.340140410},

issn = {0887-3585},

year  = {1992},

date = {1992-12-01},

journal = {Proteins},

volume = {14},

number = {4},

pages = {499--508},

abstract = {X-ray quality crystals of an Fab fragment from an antipeptide monoclonal antibody (R/V3-50.1) that recognizes the principal neutralizing determinant (PND) of the gp120 glycoprotein of human immunodeficiency virus type 1 (HIV-1) (MN isolate) were grown as uncomplexed and peptide complexed forms. Crystals of the free Fab grew from high salt in orthorhombic space groups P2(1)2(1)2(1) and I222 and from polyethylene glycol in space groups P1 and P2(1). Seeds from either the P1 and P2(1) native (uncomplexed) Fab crystals induced nucleation of crystals of the Fab complexed to a 16-residue synthetic peptide corresponding to the PND when streak seeded into preequilibrated solutions of this complex. Data were collected from these complex crystals and from each of the four native Fab forms to at least 2.8 A resolution. The genes for the variable domain of the Fab were cloned and sequenced and the primary amino acid sequence was deduced from this information. Knowledge of the three-dimensional structure of this Fab-peptide complex will be important in the understanding of the PND of HIV-1 and its recognition by neutralizing monoclonal antibodies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1469730,

title = {Crystallization of murine major histocompatibility complex class I H-2Kb with single peptides},

author = {E A Stura and M Matsumura and D H Fremont and Y Saito and P A Peterson and I A Wilson},

doi = {10.1016/0022-2836(92)90881-j},

issn = {0022-2836},

year  = {1992},

date = {1992-12-01},

journal = {J Mol Biol},

volume = {228},

number = {3},

pages = {975--982},

abstract = {X-ray quality crystals of a soluble murine class I H-2Kb molecule complexed with three different peptide antigens were grown in several forms by streak seeding and macroseeding methods. Co-crystals with VSV-8 (RGYVYGQL), OVA-8 (SIINFEKL) and SEV-9 (FAPGNYPAL) peptides were grown either from NaH2PO4/HPO4 or from polyethylene glycol 4000 within the pH range 5.0 to 7.5, with the use of 4-methyl-2-pentane diol (MPD) as an additive. The VSV-8 crystals grew in space groups P1, with cell dimensions a = 63.1 A, b = 69.1 A, c = 72.0 A, alpha = 89.9 degrees, beta = 77.1 degrees, gamma = 123.3 degrees and P2(1)2(1)2, with a = 138.1 A, b = 88.6 A, c = 45.7 A, and diffract to 2.9 and 2.3 A, respectively. Crystals of the SEV-9 complex grew from similar crystallization conditions to those of the orthorhombic VSV-8 complex with similar cell parameters and diffract to at least 2.5 A resolution. Crystals of the OVA-8 complex were obtained from either phosphate (space group C2, a = 118.7 A, b = 61.6 A, c = 85.3 A, beta = 108.4 degrees) or polyethylene glycol (space group P1, a = 64.5 A, b = 71.0 A, c = 66.3 A, alpha = 89.7 degrees, beta = 95.7 degrees, gamma = 123.3 degrees) and diffract to 3 A resolution. The crystallization procedures used here significantly increased the rate and production of X-ray quality crystals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1522592,

title = {Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 A resolution. A target enzyme for chemotherapy},

author = {P Chen and U Schulze-Gahmen and E A Stura and J Inglese and D L Johnson and A Marolewski and S J Benkovic and I A Wilson},

doi = {10.1016/0022-2836(92)90698-j},

issn = {0022-2836},

year  = {1992},

date = {1992-09-01},

journal = {J Mol Biol},

volume = {227},

number = {1},

pages = {283--292},

abstract = {The atomic structure of glycinamide ribonucleotide transformylase, an essential enzyme in purine biosynthesis, has been determined at 3.0 A resolution. The last three C-terminal residues and a sequence stretch of 18 residues (residues 113 to 130) are not visible in the electron density map. The enzyme forms a dimer in the crystal structure. Each monomer is divided into two domains, which are connected by a central mainly parallel seven-stranded beta-sheet. The N-terminal domain contains a Rossmann type mononucleotide fold with a phosphate ion bound to the C-terminal end of the first beta-strand. A long narrow cleft stretches from the phosphate to a conserved aspartic acid, Asp144, which has been suggested as an active-site residue. The cleft is lined by a cluster of residues, which are conserved between bacterial, yeast, avian and human enzymes, and likely represents the binding pocket and active site of the enzyme. GAR Tfase binds a reduced folate cofactor and glycinamide ribonucleotide for the catalysis of one of the initial steps in purine biosynthesis. Folate analogs and multi-substrate inhibitors of the enzyme have antineoplastic effects and the structure determination of the unliganded enzyme and enzyme-inhibitor complexes will aid the development of anti-cancer drugs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1323878,

title = {Emerging principles for the recognition of peptide antigens by MHC class I molecules},

author = {M Matsumura and D H Fremont and P A Peterson and I A Wilson},

doi = {10.1126/science.1323878},

issn = {0036-8075},

year  = {1992},

date = {1992-08-01},

journal = {Science},

volume = {257},

number = {5072},

pages = {927--934},

abstract = {Class I major histocompatibility complex (MHC) molecules interact with self and foreign peptides of diverse amino acid sequences yet exhibit distinct allele-specific selectivity for peptide binding. The structures of the peptide-binding specificity pockets (subsites) in the groove of murine H-2Kb as well as human histocompatibility antigen class I molecules have been analyzed. Deep but highly conserved pockets at each end of the groove bind the amino and carboxyl termini of peptide through extensive hydrogen bonding and, hence, dictate the orientation of peptide binding. A deep polymorphic pocket in the middle of the groove provides the chemical and structural complementarity for one of the peptide's anchor residues, thereby playing a major role in allele-specific peptide binding. Although one or two shallow pockets in the groove may also interact with specific peptide side chains, their role in the selection of peptide is minor. Thus, usage of a limited number of both deep and shallow pockets in multiple combinations appears to allow the binding of a broad range of peptides. This binding occurs with high affinity, primarily because of extensive interactions with the peptide backbone and the conserved hydrogen bonding network at both termini of the peptide. Interactions between the anchor residue (or residues) and the corresponding allele-specific pocket provide sufficient extra binding affinity not only to enhance specificity but also to endure the presentation of the peptide at the cell surface for recognition by T cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1323877,

title = {Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb},

author = {D H Fremont and M Matsumura and E A Stura and P A Peterson and I A Wilson},

doi = {10.1126/science.1323877},

issn = {0036-8075},

year  = {1992},

date = {1992-08-01},

journal = {Science},

volume = {257},

number = {5072},

pages = {919--927},

abstract = {The x-ray structures of a murine MHC class I molecule (H-2Kb) were determined in complex with two different viral peptides, derived from the vesicular stomatitis virus nucleoprotein (52-59), VSV-8, and the Sendai virus nucleoprotein (324-332), SEV-9. The H-2Kb complexes were refined at 2.3 A for VSV-8 and 2.5 A for SEV-9. The structure of H-2Kb exhibits a high degree of similarity with human HLA class I, although the individual domains can have slightly altered dispositions. Both peptides bind in extended conformations with most of their surfaces buried in the H-2Kb binding groove. The nonamer peptide maintains the same amino- and carboxyl-terminal interactions as the octamer primarily by the insertion of a bulge in the center of an otherwise beta conformation. Most of the specific interactions are between side-chain atoms of H-2Kb and main-chain atoms of peptide. This binding scheme accounts in large part for the enormous diversity of peptide sequences that bind with high affinity to class I molecules. Small but significant conformational changes in H-2Kb are associated with peptide binding, and these synergistic movements may be an integral part of the T cell receptor recognition process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1629960,

title = {Intermonomer disulfide bonds impair the fusion activity of influenza virus hemagglutinin},

author = {G W Kemble and D L Bodian and J Rosé and I A Wilson and J M White},

doi = {10.1128/JVI.66.8.4940-4950.1992},

issn = {0022-538X},

year  = {1992},

date = {1992-08-01},

journal = {J Virol},

volume = {66},

number = {8},

pages = {4940--4950},

abstract = {At a low pH, the influenza virus hemagglutinin (HA) undergoes conformational changes that promote membrane fusion. While the critical role of fusion peptide release from the trimer interface has been demonstrated previously, the role of globular head dissociation in the overall fusion mechanism remains unclear. To investigate this question, we have analyzed in detail the fusion activity and low pH-induced conformational changes of a mutant, Cys-HA, in which the globular head domains are locked together by engineered intermonomer disulfide bonds (L. Godley, J. Pfeifer, D. Steinhauer, B. Ely, G. Shaw, R. Kaufmann, E. Suchanek, C. Pabo, J. J. Skehel, D. C. Wiley, and S. Wharton, Cell 68:635-645, 1992). In this paper, we show that Cys-HA expressed on the cell surface is predominantly a disulfide-bonded trimer. Cell surface Cys-HA is impaired in its membrane fusion activity, as demonstrated by both content-mixing and lipid-mixing fusion assays. It is also impaired in its ability to change conformation at a low pH, as assessed by proteinase K sensitivity. The fusion activity and low pH-induced conformational changes of cell surface Cys-HA are, however, restored to nearly wild-type levels upon reduction of the intermonomer disulfide bonds. By using a set of conformation-specific monoclonal and anti-peptide antibodies, we found that purified Cys-HA trimers are impaired in changes that occur in the globular head domain interface. In addition, changes that occur at a great distance from the engineered intermonomer disulfide bonds, notably release of the fusion peptides, are also impaired. Our results are discussed with respect to current views of the fusion-active conformation of the HA trimer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1546293,

title = {Structural evidence for induced fit as a mechanism for antibody-antigen recognition},

author = {J M Rini and U Schulze-Gahmen and I A Wilson},

doi = {10.1126/science.1546293},

issn = {0036-8075},

year  = {1992},

date = {1992-02-01},

journal = {Science},

volume = {255},

number = {5047},

pages = {959--965},

abstract = {The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined by x-ray crystallographic techniques at 2.0 A, 2.9 A, and 3.1 A resolution, respectively. The nonapeptide antigen assumes a type I beta turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the beta turn of the peptide, allowing TyrP105 to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1553380,

title = {Crystallization studies of glycosylated and unglycosylated human recombinant interleukin-2},

author = {E A Stura and P Chen and C M Wilmot and J H Arevalo and I A Wilson},

doi = {10.1002/prot.340120104},

issn = {0887-3585},

year  = {1992},

date = {1992-01-01},

journal = {Proteins},

volume = {12},

number = {1},

pages = {24--30},

abstract = {Glycosylated interleukin-2 (glyIL-2) has been crystallized in two crystal forms, and unglycosylated interleukin-2 (uIL-2) has been crystallized in three forms. The glycosylated form of the human recombinant IL-2 has been crystallized from 1.9 M ammonium sulfate, pH 6.5 to 7.0 in the hexagonal space group P6(2)22 or its enantiomorph. The crystals diffract to 2.8 A and contain two or three molecules per asymmetric unit. A second crystal form grows from 1.4 to 1.5 M ammonium sulfate in 0.2 M ammonium acetate, pH 5.0-5.5, as polycrystalline rosettes which are not suitable for even a preliminary crystallographic analysis. The uIL-2 crystallizes from 1.0 to 1.7 M ammonium sulfate, 0.2 M ammonium acetate, pH 4.5-5.6 in the monoclinic space group P2(1), and less frequently in the orthorhombic space group P2(1)2(1)2(1) from 2.5 M ammonium sulfate, pH 4.5 to 5.7. Cross-seeding uIL-2 with seeds from hexagonal crystals of glyIL-2 promotes nucleation of trigonal crystals of unglycosylated IL-2. These trigonal crystals belong to the space group P3(1)21 or its enantiomorph, with similar cell dimensions to the glyIL-2 hexagonal crystals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1959445,

title = {Structural aspects of antibodies and antibody-antigen complexes},

author = {I A Wilson and R L Stanfield and J M Rini and J H Arevalo and U Schulze-Gahmen and D H Fremont and E A Stura},

doi = {10.1002/9780470514108.ch3},

issn = {0300-5208},

year  = {1991},

date = {1991-01-01},

journal = {Ciba Found Symp},

volume = {159},

pages = {13--28; discussion 28--39},

abstract = {The structures of several Fab fragments and Fab-antigen complexes have now been solved at high resolution. These structures of antibodies in complex with proteins, peptides and various other haptens have enabled us to gain insights into the structural basis of immune recognition. Early structures of Fab fragments with and without bound haptens showed the antibody combining sites to be pockets or grooves. More recent Fab-protein complex structures have shown the antibody-antigen interactions to be more extensive with flatter, more undulating binding surfaces. We have solved the structures of three Fab fragments in their native form and as complexes with their respective antigens. Two of these are anti-peptide Fab fragments, the other an anti-progesterone Fab. Comparison of the free and bound structures indicates small but significant changes in the antibody on ligand binding. An analysis of the Fab complexes solved so far indicates that the antibodies can have very differently shaped binding sites, depending on the antigen.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid1762555,

title = {X-ray crystallographic analysis of free and antigen-complexed Fab fragments to investigate structural basis of immune recognition},

author = {I A Wilson and J M Rini and D H Fremont and G G Fieser and E A Stura},

doi = {10.1016/0076-6879(91)03009-6},

issn = {0076-6879},

year  = {1991},

date = {1991-01-01},

journal = {Methods Enzymol},

volume = {203},

pages = {153--176},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2333521,

title = {Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A},

author = {R L Stanfield and T M Fieser and R A Lerner and I A Wilson},

doi = {10.1126/science.2333521},

issn = {0036-8075},

year  = {1990},

date = {1990-05-01},

journal = {Science},

volume = {248},

number = {4956},

pages = {712--719},

abstract = {The three-dimensional structures of an antibody to a peptide and its complex with the peptide antigen have been determined at 2.8 A resolution. The antigen is a synthetic 19-amino acid peptide homolog of the C helix of myohemerythrin (Mhr). The unliganded Fab' crystals are orthorhombic with two molecules per asymmetric unit, whereas the complex crystals are hexagonal with one molecule per asymmetric unit. The Fab' and the Fab'-peptide complex structures have been solved independently by molecular replacement methods and have crystallographic R factors of 0.197 and 0.215, respectively, with no water molecules included. The amino-terminal portion of the peptide sequence (NH2-Glu-Val-Val-Pro-His-Lys-Lys) is clearly interpretable in the electron density map of the Fab'-peptide complex and adopts a well-defined type II beta-turn in the concave antigen binding pocket. This same peptide amino acid sequence in native Mhr is alpha-helical. The peptide conformation when bound to the Fab' is inconsistent with binding of the Fab' to native Mhr, and suggests that binding of the Fab' to conformationally altered forms of the native Mhr or to apo-Mhr. Immunological mapping previously identified this sequence as the peptide epitope, and its fine specificity correlates well with the structural analysis. The binding pocket includes a large percentage of hydrophobic residues. The buried surfaces of the peptide and the antibody are complementary in shape and cover 460 A2 and 540 A2, respectively. These two structures now enable a comparison of a specific monoclonal Fab' both in its free and antigen complexed state. While no major changes in the antibody were observed when peptide was bound, there were some small but significant side chain and main chain rearrangements.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2188678,

title = {Structural basis of immune recognition of influenza virus hemagglutinin},

author = {I A Wilson and N J Cox},

doi = {10.1146/annurev.iy.08.040190.003513},

issn = {0732-0582},

year  = {1990},

date = {1990-01-01},

journal = {Annu Rev Immunol},

volume = {8},

pages = {737--771},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2504725,

title = {Preliminary crystallographic data and primary sequence for anti-peptide Fab' B13I2 and its complex with the C-helix peptide from myohemerythrin},

author = {E A Stura and R L Stanfield and T M Fieser and R S Balderas and L R Smith and R A Lerner and I A Wilson},

issn = {0021-9258},

year  = {1989},

date = {1989-09-01},

journal = {J Biol Chem},

volume = {264},

number = {26},

pages = {15721--15725},

abstract = {Crystals of the Fab' fragment from the monoclonal anti-peptide antibody B1312 and of the Fab'-peptide antigen complex have been characterized. The monoclonal antibodies were raised against a synthetic homologue of the C-helix of myohemerythrin (residues 69-87 in myohemerythrin). The Fab'-peptide complex crystallizes in space group P6322 with unit cell dimensions a = b = 142.5 A, c = 101.5 A, alpha = beta = 90 degrees, gamma = 120 degrees, and Z = 1. The native Fab' crystallizes in space group P212121 with unit cell dimensions a = 98.0 A, b = 151.7 A, c = 80.8 A, alpha = beta = gamma = 90 degrees, and Z = 2. Both crystal forms diffract to beyond 2.6 A resolution. We also report the cDNA and predicted amino acid sequences for the variable regions of both the light and heavy chains of this anti-peptide antibody.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2787321,

title = {Crystallization and preliminary X-ray diffraction studies of a complex between interleukin-2 and a soluble form of the p55 component of the high affinity interleukin-2 receptor},

author = {G Lambert and E A Stura and I A Wilson},

issn = {0021-9258},

year  = {1989},

date = {1989-07-01},

journal = {J Biol Chem},

volume = {264},

number = {21},

pages = {12730--12736},

abstract = {Human recombinant interleukin-2 (IL-2) and a soluble recombinant form of the human p55 (Tac antigen) component of the IL-2 receptor (IL-2R) have been cocrystallized in 1.7-1.8 M ammonium sulfate, in the pH range 7.0-8.2. Variously glycosylated forms of both receptor and ligand can be cocrystallized under those conditions. The best crystals of the putative receptor-ligand complex involve the enzymatically desialylated receptor and unglycosylated IL-2. These crystals belong to the trigonal space group P3(1)2(1) or its enantiomorph, with unit cell dimensions a = b = 91 A and c = 119 A, and diffract to 3.5 A resolution. There is one receptor-ligand complex asymmetric unit, with a Matthews coefficient of 2.7, assuming the presence of one IL-2 molecule-receptor molecule. Interestingly, in addition to IL-2 (Mr = 14,000), the p55 IL-2 receptor (Mr = 44,000) and two fragments of the receptor, of apparent Mr = 35,000 and 25,000, respectively, in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the crystals are enriched in a reducible dimeric form of the desialylated receptor (apparent Mr = 90,000), as compared with protein solution from which the crystals grow. The overall amino acid content in the crystals is consistent with a 1:1 ratio of receptor to ligand. A native data set has been collected on a multiwire area detector and the search for suitable heavy atom derivatives is in progress.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2656702,

title = {Preliminary crystallographic investigations of glycinamide ribonucleotide transformylase},

author = {E A Stura and D L Johnson and J Inglese and J M Smith and S J Benkovic and I A Wilson},

issn = {0021-9258},

year  = {1989},

date = {1989-06-01},

journal = {J Biol Chem},

volume = {264},

number = {16},

pages = {9703--9706},

abstract = {Crystals of glycinamide ribonucleotide transformylase have been grown from 0.4 to 1 M ammonium sulfate, 0.6 to 1 M sodium-potassium phosphate, or 0.65 to 1 M citrate in the pH range 4.5-7.0. The single crystals display variable morphology with varying pH. The crystals belong to the orthorhombic space group C222 with cell dimensions a = 141.4 A, b = 98.2 A, c = 103.5 A. Co-crystals have also been obtained in the presence of the inhibitor 5,8-dideazafolate (KI = 18 microM) under similar crystallization conditions. Crystals of a chemically modified enzyme, iodinated at Cys-21, were grown under similar conditions within the pH range 6.5-7.0. These crystals are isomorphous with the unmodified enzyme. Crystals suitable for high resolution (less than 2.5 A) x-ray diffraction studies have been obtained for each of the above.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2485209,

title = {Monoclonal antibodies against an identical short peptide sequence shared by two unrelated proteins},

author = {U Schulze-Gahmen and I A Wilson},

issn = {1040-5704},

year  = {1989},

date = {1989-01-01},

journal = {Pept Res},

volume = {2},

number = {5},

pages = {322--331},

abstract = {Antipeptide antibodies provide the opportunity to explore the molecular basis for antigen-antibody recognition and to test theories of immune recognition. We investigated the possibility of raising monoclonal antipeptide antibodies against a specific epitope consisting of six amino acid residues, which is common to two unrelated proteins. The goal of this investigation was to analyze the reactivity of these epitope specific antibodies towards the same sequence in these two different proteins. A correlation between antibody reactivity and secondary structures of the same peptide sequence in different proteins could help to understand the ability of antipeptide antibodies to react with their cognate sequence in intact folded proteins. Monoclonal antibodies were raised against one hexamer sequence, PGTAPK, that is present in both thioredoxin and Fab New lambda-light chain. The antipeptide antibodies reacted only with thioredoxin but not with Fab New in ELISA's, immune precipitation and Western blots. Determination of the antibody specificity through binding tests with peptide analogs revealed the influence of the residue N-terminal from the hexamer epitope on antibody binding. Because of the observed influence of the N-1 adjacent residue in peptide analogs, the discrimination between the protein antigens could not be interpreted clearly as the result of the different hexamer conformations present in the native structures of the two proteins. However, analysis of the antibody reactivity with peptide analogs with varying "frame residues" surrounding the hexamer epitope indicates the possible discrimination of different peptide conformations by the antibody.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2461945,

title = {Addition of carbohydrate side chains at novel sites on influenza virus hemagglutinin can modulate the folding, transport, and activity of the molecule},

author = {P Gallagher and J Henneberry and I Wilson and J Sambrook and M J Gething},

doi = {10.1083/jcb.107.6.2059},

issn = {0021-9525},

year  = {1988},

date = {1988-12-01},

journal = {J Cell Biol},

volume = {107},

number = {6 Pt 1},

pages = {2059--2073},

abstract = {We have constructed and expressed a series of mutant influenza virus hemagglutinins, each containing a new consensus site for glycosylation in addition to the seven sites found on the wild-type protein. Oligosaccharide side chains were added with high efficiency at four of the five novel sites, located on areas of the protein's surface that are not normally shielded by carbohydrate. Investigations of the structure, intracellular transport, and biological activities of the mutant hemagglutinin molecules indicated that (a) supernumerary carbohydrate side chains can be used to shield or disrupt functional epitopes on the surface of hemagglutinin, and (b) the presence of an additional oligosaccharide may cause temperature-dependent defects in the transport of the glycoprotein. We discuss the addition of supernumerary oligosaccharides as a general tool for shielding chosen areas of the surface of proteins that enter or traverse the secretory pathway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid3182835,

title = {Preliminary crystallographic data, primary sequence, and binding data for an anti-peptide Fab and its complex with a synthetic peptide from influenza virus hemagglutinin},

author = {U Schulze-Gahmen and J M Rini and J Arevalo and E A Stura and J H Kenten and I A Wilson},

issn = {0021-9258},

year  = {1988},

date = {1988-11-01},

journal = {J Biol Chem},

volume = {263},

number = {32},

pages = {17100--17105},

abstract = {X-ray quality crystals which diffract to high resolution (less than or equal to 1.9-2.1 A) have been grown of an anti-peptide Fab and its complex with a 9-residue peptide antigen. Both crystals are monoclinic P2(1), with unit cell dimensions a = 90.3 A, b = 82.9 A, c = 73.4 A, beta = 122.5 degrees for the native Fab and a = 63.9 A, b = 73.0 A, c = 49.1 A, beta = 120.6 degrees for the complex. The peptide sequence corresponds to residues 100-108 of all influenza virus hemagglutinins (HA1) of the H3 subtype (1968-1987). The peptide antigen has been well characterized immunologically (Wilson, I.A., Niman, H.L., Houghton, R.A., Cherenson, A.R., Connolly, M.L., and Lerner, R.A. (1984) Cell 37, 767-778; Wilson, I.A., Bergmann, K.F., and Stura, E.A. (1986) in Vaccines '86 (Channock, R.M., Lerner, R.A., and Brown, F., eds) pp. 33-37, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY), structurally, as a free peptide by NMR (Dyson, J.H., Cross, K.J., Houghton, R.A., Wilson, I.A., Wright, P.E., and Lerner, R.A. (1985) Nature 318, 480-483; Dyson, J.H., Lerner, R.A., and Wright, P.E., (1988) Annu. Rev. Biophys. Chem. 17, 305-324), as part of the intact antigen by x-ray crystallography (Wilson, I.A., Skehel, J.J., and Wiley, D. C. (1981) Nature 289, 366-373) and by binding studies to the HA molecule (White, J.M., and Wilson, I.A. (1987) J. Cell Biol. 105, 2887-2896). Knowledge of the three-dimensional structure of the complex will elucidate the details of how anti-peptide antibodies recognize a small peptide antigen and provide insights into the recognition of the same sequence in the intact protein antigen. As both native Fab and the peptide-Fab complex have been crystallized, we can also determine in addition whether changes in the structure of the antibody accompany antigen binding. The nucleotide sequence of the mRNA coding region of the anti-peptide Fab has been determined to provide the amino acid sequence ultimately required for the high resolution three-dimensional structure determination.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2455217,

title = {Purification of a RAS-responsive adenylyl cyclase complex from Saccharomyces cerevisiae by use of an epitope addition method},

author = {J Field and J Nikawa and D Broek and B MacDonald and L Rodgers and I A Wilson and R A Lerner and M Wigler},

doi = {10.1128/mcb.8.5.2159-2165.1988},

issn = {0270-7306},

year  = {1988},

date = {1988-05-01},

journal = {Mol Cell Biol},

volume = {8},

number = {5},

pages = {2159--2165},

abstract = {We developed a method for immunoaffinity purification of Saccharomyces cerevisiae adenylyl cyclase based on creating a fusion with a small peptide epitope. Using oligonucleotide technology to encode the peptide epitope we constructed a plasmid that expressed the fusion protein from the S. cerevisiae alcohol dehydrogenase promoter ADH1. A monoclonal antibody previously raised against the peptide was used to purify adenylyl cyclase by affinity chromatography. The purified enzyme appeared to be a multisubunit complex consisting of the 200-kilodalton adenylyl cyclase fusion protein and an unidentified 70-kilodalton protein. The purified protein could be activated by RAS proteins. Activation had an absolute requirement for a guanine nucleoside triphosphate.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid3123368,

title = {Analysis of an anti-progesterone antibody: variable crystal morphology of the Fab' and steroid-Fab' complexes},

author = {E A Stura and J H Arevalo and A Feinstein and R B Heap and M J Taussig and I A Wilson},

issn = {0019-2805},

year  = {1987},

date = {1987-12-01},

journal = {Immunology},

volume = {62},

number = {4},

pages = {511--521},

abstract = {Anti-progesterone monoclonal antibodies are being used for structural studies of antibody-antigen interaction, for their ability to block pregnancy shortly after fertilization, and for hormone immunoassay. A mouse anti-progesterone monoclonal Fab' fragment has been crystallized in its native form and co-crystallized with seven different, but structurally related, steroids. The crystals show interesting preferences in their crystal morphology, depending on the bound steroid ligand. The X-ray crystallographic analysis of this Fab', complexed with a series of related steroid ligands, should reveal details of the chemistry of antibody-antigen union and provide insights into how steroids interact with proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2447101,

title = {Anti-peptide antibodies detect steps in a protein conformational change: low-pH activation of the influenza virus hemagglutinin},

author = {J M White and I A Wilson},

doi = {10.1083/jcb.105.6.2887},

issn = {0021-9525},

year  = {1987},

date = {1987-12-01},

journal = {J Cell Biol},

volume = {105},

number = {6 Pt 2},

pages = {2887--2896},

abstract = {At low pH, the hemagglutinin (HA) of influenza virus undergoes an irreversible conformational change that potentiates its essential membrane fusion function. We have probed the details of this conformational change using a panel of 14 anti-HA-peptide antibodies. Whereas some antibodies reacted equally well with both the neutral and low-pH HA conformations, others reacted to a significantly greater extent with the low-pH form. The locations of the peptides recognized by the latter antibodies in the three-dimensional HA structure indicated regions of the protein that change in response to low pH. Moreover, kinetic experiments suggested steps in the conformational change. In addition to their relevance to membrane fusion, our results show that anti-peptide antibodies can be used to study some types of biologically important protein conformational changes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid3315651,

title = {The influenza hemagglutinin precursor as an acid-sensitive probe of the biosynthetic pathway},

author = {F Boulay and R W Doms and I Wilson and A Helenius},

doi = {10.1002/j.1460-2075.1987.tb02555.x},

issn = {0261-4189},

year  = {1987},

date = {1987-09-01},

journal = {EMBO J},

volume = {6},

number = {9},

pages = {2643--2650},

abstract = {The hemagglutinin of influenza virus (HA), an acid-activated membrane fusion protein, is synthesized in the endoplasmic reticulum and transported through the Golgi complex to the cell surface of infected cells as an uncleaved, fusion-incompetent precursor, HA0. The mature, proteolytically activated HA is known to undergo a rapid, irreversible, acid-induced conformational change which mediates membrane fusion and virus penetration. On the basis of antigenic modifications and the acquisition of trypsin susceptibility, we demonstrate here that HA0, while unable to cause fusion, is acid sensitive. It undergoes irreversible conformational changes quite similar to those of HA at mildly acidic pH (pH less than 6.0). The ectodomain of HA0 does not, however, acquire hydrophobic properties and the changes occur in a less concerted manner (the pH dependence is much broader and the rate of conversion slower). These differences are likely to account for the inability of acid-treated HA0 to trigger membrane fusion. It was shown, moreover, that HA0 acquired its acid-sensitive properties immediately following trimerization in the endoplasmic reticulum. Since HA0 did not convert to the acid form at any point during its intracellular transport, we concluded that the trans-Golgi compartment, known to be more acidic than the cytosol and involved in constitutive membrane transport, is not likely to have a pH less than 6.0.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid3593255,

title = {Crystallographic analysis of the three-dimensional structure of baboon alpha-lactalbumin at low resolution. Homology with lysozyme},

author = {S G Smith and M Lewis and R Aschaffenburg and R E Fenna and I A Wilson and M Sundaralingam and D I Stuart and D C Phillips},

doi = {10.1042/bj2420353},

issn = {0264-6021},

year  = {1987},

date = {1987-03-01},

journal = {Biochem J},

volume = {242},

number = {2},

pages = {353--360},

abstract = {The crystal structure of baboon alpha-lactalbumin has been determined at 6 A and at 4.5 A (0.6 nm and 0.45 nm) resolution by the method of isomorphous replacement. The principal derivative was prepared by reducing a disulphide bridge in the crystals and inserting a mercury atom. Detailed comparison of the electron-density maps with corresponding maps of hen egg-white lysozyme shows that they are closely similar, with correlation coefficients of 0.57 and 0.44 at 6 A and 4.5 A resolution respectively. This result, in accordance with earlier predictions based upon comparisons of amino-acid sequences, provides further evidence that class C lysozymes and alpha-lactalbumins are homologous proteins and it is in keeping with the hypothesis that the alpha-lactalbumins evolved from a lysozyme precursor.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid3586022,

title = {Crystallization and preliminary crystallographic data for an antiprogesterone monoclonal antibody Fab' and steroid-Fab' complexes},

author = {E A Stura and A Feinstein and I A Wilson},

doi = {10.1016/0022-2836(87)90642-5},

issn = {0022-2836},

year  = {1987},

date = {1987-01-01},

journal = {J Mol Biol},

volume = {193},

number = {1},

pages = {229--231},

abstract = {Crystals of an Fab' from an antiprogesterone monoclonal antibody (IgG1) have been grown from 1.5 M-ammonium sulfate, pH 5.5 to 8.5. The single crystals are hexagonal rods, space group P6222 (or P6422), with cell dimensions a = b = 135.2 A, and c = 124.2 A. Cocrystals of the Fab' with progesterone, pregnanedione and other related steroids have been grown. The complex crystals have different morphology but are isomorphous with the native crystals. A hydroxy-progesterone derivative obtained by substituting an iodo-benzoyl group at the 11 alpha-hydroxyl position looks promising as a suitable heavy-atom candidate in addition to other potential conventional heavy-atom derivatives. All crystals diffract to at least 2.8 A resolution and are suitable for high-resolution X-ray diffraction studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid3525041,

title = {Selection by site-directed antibodies of small regions of peptides which are ordered in water},

author = {H J Dyson and K J Cross and J Ostresh and R A Houghten and I A Wilson and P E Wright and R A Lerner},

doi = {10.1002/9780470513286.ch4},

issn = {0300-5208},

year  = {1986},

date = {1986-01-01},

journal = {Ciba Found Symp},

volume = {119},

pages = {58--75},

abstract = {High resolution nuclear magnetic resonance has been used to study a short peptide which corresponds to the antigenic region of a larger peptide immunogen. This work shows that there is a strong conformational preference for a Type II beta-turn in solution. This observation has implications for the nature of the immunogenicity and antigenicity of peptide antigens as well as for the more general question of protein-folding mechanisms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid4069219,

title = {The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn},

author = {H J Dyson and K J Cross and R A Houghten and I A Wilson and P E Wright and R A Lerner},

doi = {10.1038/318480a0},

issn = {0028-0836},

year  = {1985},

date = {1985-12-05},

journal = {Nature},

volume = {318},

number = {6045},

pages = {480--483},

abstract = {Many short synthetic peptides have now been shown to induce antibodies reactive with their cognate sequences in the intact folded protein. Aside from the usefulness of such antibodies as site-specific reagents, the frequency with which this recognition occurs has raised several theoretical issues, the central one being that of how an antibody to a short synthetic peptide, which represents one of the most disordered states of a site in a protein, can react with the more ordered version of the same sequence in the folded protein. This apparent paradox can be resolved if the target site on the protein approaches disorder or if the peptide in solution or on a carrier adopts, with significant frequency, a conformation compatible with that of the cognate site in the protein. Various studies already suggest that antigenic sites in proteins correspond to regions of high atomic mobility. We now show, using high-field nuclear magnetic resonance (NMR) spectroscopy, that a nonapeptide selected by several monoclonal antibodies as the immunodominant site of a 36-amino-acid immunogen (residues 75-110 of influenza virus haemagglutinin) adopts a highly populated type-II reverse-turn conformation in water. This suggests that in this case the antibodies have selected a sequence possessing a conformational preference. Apart from helping us to understand immunological recognition, anti-peptide antibodies may provide reagents of sufficient precision for an immunological approach to the problem of protein folding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2410917,

title = {Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition},

author = {I A Wilson and D H Haft and E D Getzoff and J A Tainer and R A Lerner and S Brenner},

doi = {10.1073/pnas.82.16.5255},

issn = {0027-8424},

year  = {1985},

date = {1985-08-01},

journal = {Proc Natl Acad Sci U S A},

volume = {82},

number = {16},

pages = {5255--5259},

abstract = {The ability of antibodies raised against disordered short peptides to interact frequently with their cognate sequences in intact folded proteins has raised a major theoretical issue in protein chemistry. We propose to address this issue by using antibodies raised against peptides with identical sequences, but different conformations, in pairs of unrelated proteins of known three-dimensional structure. The general search method presented here enabled us to detect candidate sequences for such immunological studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid2581826,

title = {Studies with monoclonal antibodies prepared against X-31 influenza virus haemagglutinin},

author = {J J Skehel and E Brown and R S Daniels and A R Douglas and M Knossow and I A Wilson and N G Wrigley and D C Wiley},

doi = {10.1042/bst0130012},

issn = {0300-5127},

year  = {1985},

date = {1985-02-01},

journal = {Biochem Soc Trans},

volume = {13},

number = {1},

pages = {12--14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid6204768,

title = {The structure of an antigenic determinant in a protein},

author = {I A Wilson and H L Niman and R A Houghten and A R Cherenson and M L Connolly and R A Lerner},

doi = {10.1016/0092-8674(84)90412-4},

issn = {0092-8674},

year  = {1984},

date = {1984-07-01},

journal = {Cell},

volume = {37},

number = {3},

pages = {767--778},

abstract = {The immunogenic and antigenic determinants of a synthetic peptide and the corresponding antigenic determinants in the parent protein have been elucidated. Four determinants have been defined by reactivity of a large panel of antipeptide monoclonal antibodies with short, overlapping peptides (7-28 amino acids), the immunizing peptide (36 amino acids), and the intact parent protein (the influenza virus hemagglutinin, HA). The majority of the antipeptide antibodies that also react strongly with the intact protein recognize one specific nine amino acid sequence. This immunodominant peptide determinant is located in the subunit interface in the HA trimeric structure. The relative inaccessibility of this site implies that antibody binding to the protein is to a more unfolded HA conformation. This antigenic determinant differs from those previously described for the hemagglutinin and clearly demonstrates the ability of synthetic peptides to generate antibodies that interact with regions of the protein not immunogenic or generally accessible when the protein is the immunogen.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid6584912,

title = {A carbohydrate side chain on hemagglutinins of Hong Kong influenza viruses inhibits recognition by a monoclonal antibody},

author = {J J Skehel and D J Stevens and R S Daniels and A R Douglas and M Knossow and I A Wilson and D C Wiley},

doi = {10.1073/pnas.81.6.1779},

issn = {0027-8424},

year  = {1984},

date = {1984-03-01},

journal = {Proc Natl Acad Sci U S A},

volume = {81},

number = {6},

pages = {1779--1783},

abstract = {A single amino acid substitution, Asp-63 to Asn-63, was detected in the hemagglutinin of an antigenic variant of the 1968 Hong Kong (H3) influenza virus that was selected by growth of the wild-type virus in the presence of a monoclonal antibody. The mutation generates an oligosaccharide attachment site, Asn-Cys-Thr at residues 63-65, that is glycosylated. Immunoprecipitation experiments with extracts from variant virus-infected cells prepared in the presence or absence of tunicamycin, which inhibits glycosylation, demonstrate that addition of the new oligosaccharide side chain is required to prevent reaction with the monoclonal antibody. Similar experiments with the virus of the 1969 Hong Kong influenza epidemic, A/England/878/69, which also contains a hemagglutinin glycosylated at residue 63, support this conclusion and provide evidence for the epidemiological significance of carbohydrate-mediated modifications of hemagglutinin antigenicity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid6085884,

title = {Structure of antigenic and immunogenic determinants in proteins and synthetic peptides},

author = {I A Wilson},

issn = {0003-472X},

year  = {1984},

date = {1984-01-01},

journal = {Ann Sclavo Collana Monogr},

volume = {1},

number = {2},

pages = {129--138},

keywords = {},

pubstate = {published},

tppubtype = {article}

}