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* Residue conservation analysis
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DOI no:
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Science
248:712-719
(1990)
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PubMed id:
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Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A.
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R.L.Stanfield,
T.M.Fieser,
R.A.Lerner,
I.A.Wilson.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
|
|
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|
|
|
S.M.Khor,
G.Liu,
C.Fairman,
S.G.Iyengar,
and
J.J.Gooding
(2011).
The importance of interfacial design for the sensitivity of a label-free electrochemical immuno-biosensor for small organic molecules.
|
| |
Biosens Bioelectron,
26,
2038-2044.
|
|
|
|
|
|
|
B.Yan,
Z.Yates,
A.Balland,
and
G.R.Kleemann
(2009).
Human IgG1 hinge fragmentation as the result of H2O2-mediated radical cleavage.
|
| |
J Biol Chem,
284,
35390-35402.
|
|
|
|
|
|
|
D.C.de Geus,
A.M.van Roon,
E.A.Thomassen,
C.H.Hokke,
A.M.Deelder,
and
J.P.Abrahams
(2009).
Characterization of a diagnostic Fab fragment binding trimeric Lewis X.
|
| |
Proteins,
76,
439-447.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.J.Kao,
and
R.S.Hodges
(2009).
Advantages of a synthetic peptide immunogen over a protein immunogen in the development of an anti-pilus vaccine for Pseudomonas aeruginosa.
|
| |
Chem Biol Drug Des,
74,
33-42.
|
|
|
|
|
|
|
C.W.Cobaugh,
J.C.Almagro,
M.Pogson,
B.Iverson,
and
G.Georgiou
(2008).
Synthetic antibody libraries focused towards peptide ligands.
|
| |
J Mol Biol,
378,
622-633.
|
|
|
|
|
|
|
J.Du,
S.Hou,
C.Zhong,
Z.Lai,
H.Yang,
J.Dai,
D.Zhang,
H.Wang,
Y.Guo,
and
J.Ding
(2008).
Molecular basis of recognition of human osteopontin by 23C3, a potential therapeutic antibody for treatment of rheumatoid arthritis.
|
| |
J Mol Biol,
382,
835-842.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Garcia-Boronat,
C.M.Diez-Rivero,
E.L.Reinherz,
and
P.A.Reche
(2008).
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
|
| |
Nucleic Acids Res,
36,
W35-W41.
|
|
|
|
|
|
|
E.O.Saphire,
M.Montero,
A.Menendez,
N.E.van Houten,
M.B.Irving,
R.Pantophlet,
M.B.Zwick,
P.W.Parren,
D.R.Burton,
J.K.Scott,
and
I.A.Wilson
(2007).
Structure of a high-affinity "mimotope" peptide bound to HIV-1-neutralizing antibody b12 explains its inability to elicit gp120 cross-reactive antibodies.
|
| |
J Mol Biol,
369,
696-709.
|
|
|
|
|
|
|
J.N.Arnold,
M.R.Wormald,
R.B.Sim,
P.M.Rudd,
and
R.A.Dwek
(2007).
The impact of glycosylation on the biological function and structure of human immunoglobulins.
|
| |
Annu Rev Immunol,
25,
21-50.
|
|
|
|
|
|
|
L.W.Gapper,
D.E.Copestake,
D.E.Otter,
and
H.E.Indyk
(2007).
Analysis of bovine immunoglobulin G in milk, colostrum and dietary supplements: a review.
|
| |
Anal Bioanal Chem,
389,
93.
|
|
|
|
|
|
|
M.Hata,
and
G.R.Marshall
(2006).
Do benzodiazepines mimic reverse-turn structures?
|
| |
J Comput Aided Mol Des,
20,
321-331.
|
|
|
|
|
|
|
Y.Che,
B.R.Brooks,
and
G.R.Marshall
(2006).
Development of small molecules designed to modulate protein-protein interactions.
|
| |
J Comput Aided Mol Des,
20,
109-130.
|
|
|
|
|
|
|
L.Zheng,
R.Manetsch,
W.D.Woggon,
U.Baumann,
and
J.L.Reymond
(2005).
Mechanistic study of proton transfer and hysteresis in catalytic antibody 16E7 by site-directed mutagenesis and homology modeling.
|
| |
Bioorg Med Chem,
13,
1021-1029.
|
|
|
|
|
|
|
T.Lama,
P.Campiglia,
A.Carotenuto,
L.Auriemma,
I.Gomez-Monterrey,
E.Novellino,
and
P.Grieco
(2005).
A novel route to synthesize Freidinger lactams by micowave irradiation.
|
| |
J Pept Res,
66,
231-235.
|
|
|
|
|
|
|
T.T.Tran,
J.McKie,
W.D.Meutermans,
G.T.Bourne,
P.R.Andrews,
and
M.L.Smythe
(2005).
Topological side-chain classification of beta-turns: ideal motifs for peptidomimetic development.
|
| |
J Comput Aided Mol Des,
19,
551-566.
|
|
|
|
|
|
|
P.J.Cachia,
D.J.Kao,
and
R.S.Hodges
(2004).
Synthetic peptide vaccine development: measurement of polyclonal antibody affinity and cross-reactivity using a new peptide capture and release system for surface plasmon resonance spectroscopy.
|
| |
J Mol Recognit,
17,
540-557.
|
|
|
|
|
|
|
P.J.Cachia,
and
R.S.Hodges
(2003).
Synthetic peptide vaccine and antibody therapeutic development: prevention and treatment of Pseudomonas aeruginosa.
|
| |
Biopolymers,
71,
141-168.
|
|
|
|
|
|
|
R.Pantophlet,
I.A.Wilson,
and
D.R.Burton
(2003).
Hyperglycosylated mutants of human immunodeficiency virus (HIV) type 1 monomeric gp120 as novel antigens for HIV vaccine design.
|
| |
J Virol,
77,
5889-5901.
|
|
|
|
|
|
|
P.A.Ramsland,
and
W.Farrugia
(2002).
Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products.
|
| |
J Mol Recognit,
15,
248-259.
|
|
|
|
|
|
|
P.Rezacova,
J.Brynda,
M.Fabry,
M.Horejsi,
R.Stouracova,
J.Lescar,
V.Chitarra,
M.M.Riottot,
J.Sedlacek,
and
G.A.Bentley
(2002).
Inhibition of HIV protease by monoclonal antibodies.
|
| |
J Mol Recognit,
15,
272-276.
|
|
|
|
|
|
|
B.Piekarska,
L.Konieczny,
J.Rybarska,
B.Stopa,
G.Zemanek,
E.Szneler,
M.Król,
M.Nowak,
and
I.Roterman
(2001).
Heat-induced formation of a specific binding site for self-assembled Congo Red in the V domain of immunoglobulin L chain lambda.
|
| |
Biopolymers,
59,
446-456.
|
|
|
|
|
|
|
E.Yuriev,
P.A.Ramsland,
and
A.B.Edmundson
(2001).
Docking of combinatorial peptide libraries into a broadly cross-reactive human IgM.
|
| |
J Mol Recognit,
14,
172-184.
|
|
|
|
|
|
|
A.P.Campbell,
W.Y.Wong,
R.T.Irvin,
and
B.D.Sykes
(2000).
Interaction of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK with a cross-reactive antibody: conformation of the bound peptide.
|
| |
Biochemistry,
39,
14847-14864.
|
|
|
|
|
|
|
D.J.Suich,
S.A.Mousa,
G.Singh,
G.Liapakis,
T.Reisine,
and
W.F.DeGrado
(2000).
Template-constrained cyclic peptide analogues of somatostatin: subtype-selective binding to somatostatin receptors and antiangiogenic activity.
|
| |
Bioorg Med Chem,
8,
2229-2241.
|
|
|
|
|
|
|
D.W.Ritchie,
and
G.J.Kemp
(2000).
Protein docking using spherical polar Fourier correlations.
|
| |
Proteins,
39,
178-194.
|
|
|
|
|
|
|
E.Cabezas,
M.Wang,
P.W.Parren,
R.L.Stanfield,
and
A.C.Satterthwait
(2000).
A structure-based approach to a synthetic vaccine for HIV-1.
|
| |
Biochemistry,
39,
14377-14391.
|
|
|
|
|
|
|
C.Oefner,
A.Binggeli,
V.Breu,
D.Bur,
J.P.Clozel,
A.D'Arcy,
A.Dorn,
W.Fischli,
F.Grüninger,
R.Güller,
G.Hirth,
H.Märki,
S.Mathews,
M.M ller,
R.G.Ridley,
H.Stadler,
E.Vieira,
M.Wilhelm,
F.Winkler,
and
W.Wostl
(1999).
Renin inhibition by substituted piperidines: a novel paradigm for the inhibition of monomeric aspartic proteinases?
|
| |
Chem Biol,
6,
127-131.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.K.Dziadulewicz,
M.C.Brown,
A.R.Dunstan,
W.Lee,
N.B.Said,
and
P.J.Garratt
(1999).
The design of non-peptide human bradykinin B2 receptor antagonists employing the benzodiazepine peptidomimetic scaffold.
|
| |
Bioorg Med Chem Lett,
9,
463-468.
|
|
|
|
|
|
|
E.S.Calderon-Aranda,
B.Selisko,
E.J.York,
G.B.Gurrola,
J.M.Stewart,
and
L.D.Possani
(1999).
Mapping of an epitope recognized by a neutralizing monoclonal antibody specific to toxin Cn2 from the scorpion Centruroides noxius, using discontinuous synthetic peptides.
|
| |
Eur J Biochem,
264,
746-755.
|
|
|
|
|
|
|
J.L.Pellequer,
S.Chen,
V.A.Roberts,
J.A.Tainer,
and
E.D.Getzoff
(1999).
Unraveling the effect of changes in conformation and compactness at the antibody V(L)-V(H) interface upon antigen binding.
|
| |
J Mol Recognit,
12,
267-275.
|
|
|
|
|
|
|
J.M.van Den Elsen,
D.A.Kuntz,
F.J.Hoedemaeker,
and
D.R.Rose
(1999).
Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein.
|
| |
Proc Natl Acad Sci U S A,
96,
13679-13684.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Gruber,
B.Zhou,
K.N.Houk,
R.A.Lerner,
C.G.Shevlin,
and
I.A.Wilson
(1999).
Structural basis for antibody catalysis of a disfavored ring closure reaction.
|
| |
Biochemistry,
38,
7062-7074.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Choulier,
N.Rauffer-Bruyère,
M.Ben Khalifa,
F.Martin,
T.Vernet,
and
D.Altschuh
(1999).
Kinetic analysis of the effect on Fab binding of identical substitutions in a peptide and its parent protein.
|
| |
Biochemistry,
38,
3530-3537.
|
|
|
|
|
|
|
R.Stanfield,
E.Cabezas,
A.Satterthwait,
E.Stura,
A.Profy,
and
I.Wilson
(1999).
Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.
|
| |
Structure,
7,
131-142.
|
|
|
PDB codes:
|
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|
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C.L.Casipit,
R.Tal,
V.Wittman,
P.A.Chavaillaz,
K.Arbuthnott,
J.A.Weidanz,
J.A.Jiao,
and
H.C.Wong
(1998).
Improving the binding affinity of an antibody using molecular modeling and site-directed mutagenesis.
|
| |
Protein Sci,
7,
1671-1680.
|
|
|
|
|
|
|
J.E.McElveen,
M.R.Clark,
S.J.Smith,
H.F.Sewell,
and
F.Shakib
(1998).
Primary sequence and molecular model of the variable region of a mouse monoclonal anti-Der p 1 antibody showing a similar epitope specificity as human IgE.
|
| |
Clin Exp Allergy,
28,
1427-1434.
|
|
|
|
|
|
|
M.A.Molins,
M.A.Contreras,
I.Fita,
and
M.Pons
(1998).
Solution conformation of an immunogenic peptide from HRV2: comparison with the conformation found in a complex with a Fab fragment of an anti-HRV2 neutralizing antibody.
|
| |
J Pept Sci,
4,
101-110.
|
|
|
|
|
|
|
R.Murali,
D.J.Sharkey,
J.L.Daiss,
and
H.M.Murthy
(1998).
Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme.
|
| |
Proc Natl Acad Sci U S A,
95,
12562-12567.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.P.Campbell,
D.L.Bautista,
B.Tripet,
W.Y.Wong,
R.T.Irvin,
R.S.Hodges,
and
B.D.Sykes
(1997).
Solution secondary structure of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK: A heteronuclear multidimensional NMR study.
|
| |
Biochemistry,
36,
12791-12801.
|
|
|
|
|
|
|
C.H.Trinh,
S.D.Hemmington,
M.E.Verhoeyen,
and
S.E.Phillips
(1997).
Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity.
|
| |
Structure,
5,
937-948.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.A.Hubbard,
D.P.Raleigh,
J.R.Bonnerjea,
and
C.M.Dobson
(1997).
Identification of the epitopes of calcitonin gene-related peptide (CGRP) for two anti-CGRP monoclonal antibodies by 2D NMR.
|
| |
Protein Sci,
6,
1945-1952.
|
|
|
|
|
|
|
J.C.Morris,
E.R.Bergert,
and
W.P.Bryant
(1997).
Binding of immunoglobulin G from patients with autoimmune thyroid disease to rat sodium-iodide symporter peptides: evidence for the iodide transporter as an autoantigen.
|
| |
Thyroid,
7,
527-534.
|
|
|
|
|
|
|
J.L.Pellequer,
and
S.W.Chen
(1997).
Does conformational free energy distinguish loop conformations in proteins?
|
| |
Biophys J,
73,
2359-2375.
|
|
|
|
|
|
|
M.R.Wormald,
P.M.Rudd,
D.J.Harvey,
S.C.Chang,
I.G.Scragg,
and
R.A.Dwek
(1997).
Variations in oligosaccharide-protein interactions in immunoglobulin G determine the site-specific glycosylation profiles and modulate the dynamic motion of the Fc oligosaccharides.
|
| |
Biochemistry,
36,
1370-1380.
|
|
|
|
|
|
|
T.Schneider,
T.Dudler,
R.R.Annand,
M.H.Gelb,
T.P.King,
and
M.Suter
(1997).
Comparison of the antibody response to bee venom phospholipase A2 induced by natural exposure in humans or by immunization in mice.
|
| |
J Mol Recognit,
10,
93.
|
|
|
|
|
|
|
C.A.Sotriffer,
R.H.Winger,
K.R.Liedl,
B.M.Rode,
and
J.M.Varga
(1996).
Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4.
|
| |
J Comput Aided Mol Des,
10,
305-320.
|
|
|
|
|
|
|
C.Tenette,
F.Ducancel,
and
J.C.Smith
(1996).
Structural model of the anti-snake-toxin antibody, M alpha 2,3.
|
| |
Proteins,
26,
9.
|
|
|
|
|
|
|
L.C.Hsieh-Wilson,
P.G.Schultz,
and
R.C.Stevens
(1996).
Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.
|
| |
Proc Natl Acad Sci U S A,
93,
5363-5367.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.A.Rejto,
and
G.M.Verkhivker
(1996).
Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.
|
| |
Proc Natl Acad Sci U S A,
93,
8945-8950.
|
|
|
|
|
|
|
P.Orlewski,
M.Marraud,
M.T.Cung,
V.Tsikaris,
M.Sakarellos-Daitsiotis,
C.Sakarellos,
E.Vatzaki,
and
S.J.Tzartos
(1996).
Compared structures of the free nicotinic acetylcholine receptor main immunogenic region (MIR) decapeptide and the antibody-bound [A76]MIR analogue: a molecular dynamics simulation from two-dimensional NMR data.
|
| |
Biopolymers,
40,
419-432.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
W.Xu,
and
A.D.Ellington
(1996).
Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope.
|
| |
Proc Natl Acad Sci U S A,
93,
7475-7480.
|
|
|
|
|
|
|
Y.H.Chien,
R.Jores,
and
M.P.Crowley
(1996).
Recognition by gamma/delta T cells.
|
| |
Annu Rev Immunol,
14,
511-532.
|
|
|
|
|
|
|
A.R.Neurath,
N.Strick,
and
A.K.Debnath
(1995).
Structural requirements for and consequences of an antiviral porphyrin binding to the V3 loop of the human immunodeficiency virus (HIV-1) envelope glycoprotein gp120.
|
| |
J Mol Recognit,
8,
345-357.
|
|
|
|
|
|
|
A.Zvi,
I.Kustanovich,
D.Feigelson,
R.Levy,
M.Eisenstein,
S.Matsushita,
P.Richalet-Sécordel,
M.H.Regenmortel,
and
J.Anglister
(1995).
NMR mapping of the antigenic determinant recognized by an anti-gp120, human immunodeficiency virus neutralizing antibody.
|
| |
Eur J Biochem,
229,
178-187.
|
|
|
|
|
|
|
G.Siligardi,
and
A.F.Drake
(1995).
The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides.
|
| |
Biopolymers,
37,
281-292.
|
|
|
|
|
|
|
J.C.Almagro,
E.Vargas-Madrazo,
F.Lara-Ochoa,
and
E.Horjales
(1995).
Molecular modeling of a T-cell receptor bound to a major histocompatibility complex molecule: implications for T-cell recognition.
|
| |
Protein Sci,
4,
1708-1717.
|
|
|
|
|
|
|
M.W.Wien,
D.J.Filman,
E.A.Stura,
S.Guillot,
F.Delpeyroux,
R.Crainic,
and
J.M.Hogle
(1995).
Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope.
|
| |
Nat Struct Biol,
2,
232-243.
|
|
|
PDB code:
|
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|
|
P.D.Jeffrey,
J.Bajorath,
C.Y.Chang,
D.Yelton,
I.Hellström,
K.E.Hellström,
and
S.Sheriff
(1995).
The x-ray structure of an anti-tumour antibody in complex with antigen.
|
| |
Nat Struct Biol,
2,
466-471.
|
|
|
PDB codes:
|
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|
|
|
|
|
R.L.Stanfield,
and
I.A.Wilson
(1995).
Protein-peptide interactions.
|
| |
Curr Opin Struct Biol,
5,
103-113.
|
|
|
|
|
|
|
A.R.Friedman,
V.A.Roberts,
and
J.A.Tainer
(1994).
Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.
|
| |
Proteins,
20,
15-24.
|
|
|
|
|
|
|
C.McInnes,
C.M.Kay,
R.S.Hodges,
and
B.D.Sykes
(1994).
Conformational differences between cis and trans proline isomers of a peptide antigen representing the receptor binding domain of Pseudomonas aeruginosa as studied by 1H-NMR.
|
| |
Biopolymers,
34,
1221-1230.
|
|
|
|
|
|
|
D.I.Papac,
J.Hoyes,
and
K.B.Tomer
(1994).
Epitope mapping of the gastrin-releasing peptide/anti-bombesin monoclonal antibody complex by proteolysis followed by matrix-assisted laser desorption ionization mass spectrometry.
|
| |
Protein Sci,
3,
1485-1492.
|
|
|
|
|
|
|
G.Zhong,
J.Berry,
and
R.C.Brunham
(1994).
Antibody recognition of a neutralization epitope on the major outer membrane protein of Chlamydia trachomatis.
|
| |
Infect Immun,
62,
1576-1583.
|
|
|
|
|
|
|
I.A.Wilson,
and
R.L.Stanfield
(1994).
Antibody-antigen interactions: new structures and new conformational changes.
|
| |
Curr Opin Struct Biol,
4,
857-867.
|
|
|
|
|
|
|
J.F.Schildbach,
S.Y.Shaw,
R.E.Bruccoleri,
E.Haber,
L.A.Herzenberg,
G.C.Jager,
P.D.Jeffrey,
D.J.Panka,
D.R.Parks,
and
R.I.Near
(1994).
Contribution of a single heavy chain residue to specificity of an anti-digoxin monoclonal antibody.
|
| |
Protein Sci,
3,
737-749.
|
|
|
|
|
|
|
J.N.Herron,
A.H.Terry,
S.Johnston,
X.M.He,
L.W.Guddat,
E.W.Voss,
and
A.B.Edmundson
(1994).
High resolution structures of the 4-4-20 Fab-fluorescein complex in two solvent systems: effects of solvent on structure and antigen-binding affinity.
|
| |
Biophys J,
67,
2167-2183.
|
|
|
|
|
|
|
J.Tormo,
D.Blaas,
N.R.Parry,
D.Rowlands,
D.Stuart,
and
I.Fita
(1994).
Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2.
|
| |
EMBO J,
13,
2247-2256.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.L.France,
P.G.Piatti,
J.F.Newman,
I.Toth,
W.A.Gibbons,
and
F.Brown
(1994).
Circular dichroism, molecular modeling, and serology indicate that the structural basis of antigenic variation in foot-and-mouth disease virus is alpha-helix formation.
|
| |
Proc Natl Acad Sci U S A,
91,
8442-8446.
|
|
|
|
|
|
|
R.L.Stanfield,
and
I.A.Wilson
(1994).
Antigen-induced conformational changes in antibodies: a problem for structural prediction and design.
|
| |
Trends Biotechnol,
12,
275-279.
|
|
|
|
|
|
|
T.Nakatani,
R.Umeshita,
J.Hiratake,
A.Shinzaki,
T.Suzuki,
H.Nakajima,
and
J.Oda
(1994).
Characterization of a catalytic antibody for stereoselective ester hydrolysis--a catalytic residue and mode of product inhibition.
|
| |
Bioorg Med Chem,
2,
457-468.
|
|
|
|
|
|
|
Y.Ichiyoshi,
and
P.Casali
(1994).
Analysis of the structural correlates for antibody polyreactivity by multiple reassortments of chimeric human immunoglobulin heavy and light chain V segments.
|
| |
J Exp Med,
180,
885-895.
|
|
|
|
|
|
|
A.B.Edmundson,
D.L.Harris,
Z.C.Fan,
L.W.Guddat,
B.T.Schley,
B.L.Hanson,
G.Tribbick,
and
H.M.Geysen
(1993).
Principles and pitfalls in designing site-directed peptide ligands.
|
| |
Proteins,
16,
246-267.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.D.Sykes
(1993).
Determination of the conformations of bound peptides using NMR-transferred nOe techniques.
|
| |
Curr Opin Biotechnol,
4,
392-396.
|
|
|
|
|
|
|
G.Zeder-Lutz,
D.Altschuh,
S.Denery-Papini,
J.P.Briand,
G.Tribbick,
and
M.H.Van Regenmortel
(1993).
Epitope analysis using kinetic measurements of antibody binding to synthetic peptides presenting single amino acid substitutions.
|
| |
J Mol Recognit,
6,
71-79.
|
|
|
|
|
|
|
J.M.Rini,
R.L.Stanfield,
E.A.Stura,
P.A.Salinas,
A.T.Profy,
and
I.A.Wilson
(1993).
Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen.
|
| |
Proc Natl Acad Sci U S A,
90,
6325-6329.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.J.Zvelebil,
and
J.M.Thornton
(1993).
Peptide-protein interactions: an overview.
|
| |
Q Rev Biophys,
26,
333-363.
|
|
|
|
|
|
|
M.T.Kasaian,
and
P.Casali
(1993).
Autoimmunity-prone B-1 (CD5 B) cells, natural antibodies and self recognition.
|
| |
Autoimmunity,
15,
315-329.
|
|
|
|
|
|
|
O.Vix,
B.Rees,
J.C.Thierry,
and
D.Altschuh
(1993).
Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody.
|
| |
Proteins,
15,
339-348.
|
|
|
|
|
|
|
R.L.Stanfield,
M.Takimoto-Kamimura,
J.M.Rini,
A.T.Profy,
and
I.A.Wilson
(1993).
Major antigen-induced domain rearrangements in an antibody.
|
| |
Structure,
1,
83-93.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.Veerapandian,
G.L.Gilliland,
R.Raag,
A.L.Svensson,
Y.Masui,
Y.Hirai,
and
T.L.Poulos
(1992).
Functional implications of interleukin-1 beta based on the three-dimensional structure.
|
| |
Proteins,
12,
10-23.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Witkop
(1992).
Peptides in health and disease: retrospection and outlook.
|
| |
Med Res Rev,
12,
275-296.
|
|
|
|
|
|
|
D.R.Davies,
and
E.A.Padlan
(1992).
Twisting into shape.
|
| |
Curr Biol,
2,
254-256.
|
|
|
|
|
|
|
E.A.Stura,
R.L.Stanfield,
G.G.Fieser,
S.Silver,
M.Roguska,
L.M.Hincapie,
H.K.Simmerman,
A.T.Profy,
and
I.A.Wilson
(1992).
Crystallization, sequence, and preliminary crystallographic data for an antipeptide Fab 50.1 and peptide complexes with the principal neutralizing determinant of HIV-1 gp120.
|
| |
Proteins,
14,
499-508.
|
|
|
|
|
|
|
J.P.Langedijk,
N.K.Back,
E.Kinney-Thomas,
C.Bruck,
M.Francotte,
J.Goudsmit,
and
R.H.Meloen
(1992).
Comparison and fine mapping of both high and low neutralizing monoclonal antibodies against the principal neutralization domain of HIV-1.
|
| |
Arch Virol,
126,
129-146.
|
|
|
|
|
|
|
M.B.Lascombe,
P.M.Alzari,
R.J.Poljak,
and
A.Nisonoff
(1992).
Three-dimensional structure of two crystal forms of FabR19.9 from a monoclonal anti-arsonate antibody.
|
| |
Proc Natl Acad Sci U S A,
89,
9429-9433.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.D.Walkinshaw
(1992).
Protein targets for structure-based drug design.
|
| |
Med Res Rev,
12,
317-372.
|
|
|
|
|
|
|
N.Tuaillon,
T.Martin,
A.M.Knapp,
J.L.Pasquali,
and
S.Muller
(1992).
Double reactivity of monoclonal and polyclonal rheumatoid factors for IgG and histones: mapping of binding sites by means of histone synthetic peptides and anti-Id antibodies.
|
| |
J Autoimmun,
5,
1.
|
|
|
|
|
|
|
P.Poumbourios,
D.A.McPhee,
and
B.E.Kemp
(1992).
Antibody epitopes sensitive to the state of human immunodeficiency virus type 1 gp41 oligomerization map to a putative alpha-helical region.
|
| |
AIDS Res Hum Retroviruses,
8,
2055-2062.
|
|
|
|
|
|
|
X.M.He,
F.Rüker,
E.Casale,
and
D.C.Carter
(1992).
Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1.
|
| |
Proc Natl Acad Sci U S A,
89,
7154-7158.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Plückthun
(1991).
Antibody engineering.
|
| |
Curr Opin Biotechnol,
2,
238-246.
|
|
|
|
|
|
|
G.M.Zhong,
and
R.C.Brunham
(1991).
Antigenic determinants of the chlamydial major outer membrane protein resolved at a single amino acid level.
|
| |
Infect Immun,
59,
1141-1147.
|
|
|
|
|
|
|
J.A.Tainer,
C.D.Deal,
H.M.Geysen,
V.A.Roberts,
and
E.D.Getzoff
(1991).
Defining antibody-antigen recognition: towards engineered antibodies and epitopes.
|
| |
Int Rev Immunol,
7,
165-188.
|
|
|
|
|
|
|
J.C.Cheetham,
D.P.Raleigh,
R.E.Griest,
C.Redfield,
C.M.Dobson,
and
A.R.Rees
(1991).
Antigen mobility in the combining site of an anti-peptide antibody.
|
| |
Proc Natl Acad Sci U S A,
88,
7968-7972.
|
|
|
|
|
|
|
J.F.Wedgwood,
L.Hatam,
and
V.R.Bonagura
(1991).
Expression of large quantities of rheumatoid factor major cross-reactive idiotype in the serum of adults with seropositive rheumatoid arthritis.
|
| |
Arthritis Rheum,
34,
840-845.
|
|
|
|
|
|
|
J.N.Herron,
X.M.He,
D.W.Ballard,
P.R.Blier,
P.E.Pace,
A.L.Bothwell,
E.W.Voss,
and
A.B.Edmundson
(1991).
An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.
|
| |
Proteins,
11,
159-175.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.H.Holley,
J.Goudsmit,
and
M.Karplus
(1991).
Prediction of optimal peptide mixtures to induce broadly neutralizing antibodies to human immunodeficiency virus type 1.
|
| |
Proc Natl Acad Sci U S A,
88,
6800-6804.
|
|
|
|
|
|
|
M.Shoham,
P.Proctor,
D.Hughes,
and
E.T.Baldwin
(1991).
Crystal parameters and molecular replacement of an anticholera toxin peptide complex.
|
| |
Proteins,
11,
218-222.
|
|
|
|
|
|
|
S.J.Smith-Gill
(1991).
Protein-protein interactions: structural motifs and molecular recognition.
|
| |
Curr Opin Biotechnol,
2,
568-575.
|
|
|
|
|
|
|
T.J.Harris
(1991).
Catalytic antibodies--something for everyone.
|
| |
Trends Biotechnol,
9,
39-41.
|
|
|
|
|
|
|
D.L.Rimm,
D.A.Kaiser,
D.Bhandari,
P.Maupin,
D.P.Kiehart,
and
T.D.Pollard
(1990).
Identification of functional regions on the tail of Acanthamoeba myosin-II using recombinant fusion proteins. I. High resolution epitope mapping and characterization of monoclonal antibody binding sites.
|
| |
J Cell Biol,
111,
2405-2416.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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 |
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