|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Proc Natl Acad Sci U S A
91:1089-1093
(1994)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Bound water molecules and conformational stabilization help mediate an antigen-antibody association.
|
|
T.N.Bhat,
G.A.Bentley,
G.Boulot,
M.I.Greene,
D.Tello,
W.Dall'Acqua,
H.Souchon,
F.P.Schwarz,
R.A.Mariuzza,
R.J.Poljak.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
We report the three-dimensional structures, at 1.8-A resolution, of the Fv
fragment of the anti-hen egg white lysozyme antibody D1.3 in its free and
antigen-bound forms. These structures reveal a role for solvent molecules in
stabilizing the complex and provide a molecular basis for understanding the
thermodynamic forces which drive the association reaction. Four water molecules
are buried and others form a hydrogen-bonded network around the interface,
bridging antigen and antibody. Comparison of the structures of free and bound Fv
fragment of D1.3 reveals that several of the ordered water molecules in the free
antibody combining site are retained and that additional water molecules link
antigen and antibody upon complex formation. This solvation of the complex
should weaken the hydrophobic effect, and the resulting large number of
solvent-mediated hydrogen bonds, in conjunction with direct protein-protein
interactions, should generate a significant enthalpic component. Furthermore, a
stabilization of the relative mobilities of the antibody heavy- and light-chain
variable domains and of that of the third complementarity-determining loop of
the heavy chain seen in the complex should generate a negative entropic
contribution opposing the enthalpic and the hydrophobic (solvent entropy)
effects. This structural analysis is consistent with measurements of enthalpy
and entropy changes by titration calorimetry, which show that enthalpy drives
the antigen-antibody reaction. Thus, the main forces stabilizing the complex
arise from antigen-antibody hydrogen bonding, van der Waals interactions,
enthalpy of hydration, and conformational stabilization rather than solvent
entropy (hydrophobic) effects.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
J.A.Rakestraw,
D.Aird,
P.M.Aha,
B.M.Baynes,
and
D.Lipovsek
(2011).
Secretion-and-capture cell-surface display for selection of target-binding proteins.
|
| |
Protein Eng Des Sel,
24,
525-530.
|
|
|
|
|
|
|
M.Ui,
Y.Tanaka,
T.Tsumuraya,
I.Fujii,
M.Inoue,
M.Hirama,
and
K.Tsumoto
(2011).
Structural and energetic hot-spots for the interaction between a ladder-like polycyclic ether and the anti-ciguatoxin antibody 10C9Fab.
|
| |
Mol Biosyst,
7,
793-798.
|
|
|
|
|
|
|
S.Y.Lu,
Y.J.Jiang,
J.Lv,
J.W.Zou,
and
T.X.Wu
(2011).
Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
|
| |
J Comput Chem,
32,
1907-1918.
|
|
|
|
|
|
|
A.Yokota,
K.Tsumoto,
M.Shiroishi,
T.Nakanishi,
H.Kondo,
and
I.Kumagai
(2010).
Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme.
|
| |
J Biol Chem,
285,
7686-7696.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.J.Diller,
C.Humblet,
X.Zhang,
and
L.M.Westerhoff
(2010).
Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.
|
| |
Proteins,
78,
2329-2337.
|
|
|
|
|
|
|
Z.Cai,
H.Zhang,
J.Liu,
A.Berezov,
R.Murali,
Q.Wang,
and
M.I.Greene
(2010).
Targeting erbB receptors.
|
| |
Semin Cell Dev Biol,
21,
961-966.
|
|
|
|
|
|
|
A.Szumna
(2009).
Water co-encapsulation in an inverted molecular capsule.
|
| |
Chem Commun (Camb),
(),
4191-4193.
|
|
|
|
|
|
|
E.J.Hong,
S.M.Lippow,
B.Tidor,
and
T.Lozano-Pérez
(2009).
Rotamer optimization for protein design through MAP estimation and problem-size reduction.
|
| |
J Comput Chem,
30,
1923-1945.
|
|
|
|
|
|
|
M.A.Argiriadi,
T.Xiang,
C.Wu,
T.Ghayur,
and
D.W.Borhani
(2009).
Unusual water-mediated antigenic recognition of the proinflammatory cytokine interleukin-18.
|
| |
J Biol Chem,
284,
24478-24489.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.L.Harris,
and
P.Fernsten
(2009).
Thermodynamics and density of binding of a panel of antibodies to high-molecular-weight capsular polysaccharides.
|
| |
Clin Vaccine Immunol,
16,
37-42.
|
|
|
|
|
|
|
S.Szep,
S.Park,
E.T.Boder,
G.D.Van Duyne,
and
J.G.Saven
(2009).
Structural coupling between FKBP12 and buried water.
|
| |
Proteins,
74,
603-611.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
V.Král,
P.Mader,
R.Collard,
M.Fábry,
M.Horejsí,
P.Rezácová,
M.Kozísek,
J.Závada,
J.Sedlácek,
L.Rulísek,
and
J.Brynda
(2008).
Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations.
|
| |
Proteins,
71,
1275-1287.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Arouri,
P.Garidel,
W.Kliche,
and
A.Blume
(2007).
Hydrophobic interactions are the driving force for the binding of peptide mimotopes and Staphylococcal protein A to recombinant human IgG1.
|
| |
Eur Biophys J,
36,
647-660.
|
|
|
|
|
|
|
A.J.Wilson,
J.Hong,
S.Fletcher,
and
A.D.Hamilton
(2007).
Recognition of solvent exposed protein surfaces using anthracene derived receptors.
|
| |
Org Biomol Chem,
5,
276-285.
|
|
|
|
|
|
|
D.Reichmann,
O.Rahat,
M.Cohen,
H.Neuvirth,
and
G.Schreiber
(2007).
The molecular architecture of protein-protein binding sites.
|
| |
Curr Opin Struct Biol,
17,
67-76.
|
|
|
|
|
|
|
I.S.Moreira,
P.A.Fernandes,
and
M.J.Ramos
(2007).
Computational alanine scanning mutagenesis--an improved methodological approach.
|
| |
J Comput Chem,
28,
644-654.
|
|
|
|
|
|
|
S.Casares,
E.Ab,
H.Eshuis,
O.Lopez-Mayorga,
N.A.van Nuland,
and
F.Conejero-Lara
(2007).
The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3.
|
| |
BMC Struct Biol,
7,
22.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Z.Li,
and
T.Lazaridis
(2007).
Water at biomolecular binding interfaces.
|
| |
Phys Chem Chem Phys,
9,
573-581.
|
|
|
|
|
|
|
C.Schröder,
T.Rudas,
S.Boresch,
and
O.Steinhauser
(2006).
Simulation studies of the protein-water interface. I. Properties at the molecular resolution.
|
| |
J Chem Phys,
124,
234907.
|
|
|
|
|
|
|
G.E.Gómez,
A.Cauerhff,
P.O.Craig,
F.A.Goldbaum,
and
J.M.Delfino
(2006).
Exploring protein interfaces with a general photochemical reagent.
|
| |
Protein Sci,
15,
744-752.
|
|
|
|
|
|
|
H.Younus,
S.Jamal,
B.Ahmad,
and
M.Saleemuddin
(2006).
Investigation of conformational changes induced by binding of pancreatic RNase to anti-RNase IgG derived Fab monomer using optical procedures.
|
| |
Biochemistry (Mosc),
71,
218-221.
|
|
|
|
|
|
|
J.C.Almagro,
V.Quintero-Hernández,
M.Ortiz-León,
A.Velandia,
S.L.Smith,
and
B.Becerril
(2006).
Design and validation of a synthetic VH repertoire with tailored diversity for protein recognition.
|
| |
J Mol Recognit,
19,
413-422.
|
|
|
|
|
|
|
M.G.Rudolph,
R.L.Stanfield,
and
I.A.Wilson
(2006).
How TCRs bind MHCs, peptides, and coreceptors.
|
| |
Annu Rev Immunol,
24,
419-466.
|
|
|
|
|
|
|
N.S.Longo,
and
P.E.Lipsky
(2006).
Why do B cells mutate their immunoglobulin receptors?
|
| |
Trends Immunol,
27,
374-380.
|
|
|
|
|
|
|
P.Gupta,
M.Saleemuddin,
and
R.H.Khan
(2006).
Hydrophobic interactions are the prevalent force in bromelain:Fab' complex.
|
| |
Biochemistry (Mosc),
71,
S31-S37.
|
|
|
|
|
|
|
P.Monecke,
T.Borosch,
J.Brickmann,
and
S.M.Kast
(2006).
Determination of the interfacial water content in protein-protein complexes from free energy simulations.
|
| |
Biophys J,
90,
841-850.
|
|
|
|
|
|
|
R.J.Duquesnoy
(2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
|
| |
Hum Immunol,
67,
847-862.
|
|
|
|
|
|
|
Y.Levy,
and
J.N.Onuchic
(2006).
Water mediation in protein folding and molecular recognition.
|
| |
Annu Rev Biophys Biomol Struct,
35,
389-415.
|
|
|
|
|
|
|
D.Segal,
and
M.Eisenstein
(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
|
| |
Proteins,
59,
580-591.
|
|
|
|
|
|
|
F.Rodier,
R.P.Bahadur,
P.Chakrabarti,
and
J.Janin
(2005).
Hydration of protein-protein interfaces.
|
| |
Proteins,
60,
36-45.
|
|
|
|
|
|
|
G.H.Cohen,
E.W.Silverton,
E.A.Padlan,
F.Dyda,
J.A.Wibbenmeyer,
R.C.Willson,
and
D.R.Davies
(2005).
Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
628-633.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Yin,
and
A.D.Hamilton
(2005).
Strategies for targeting protein-protein interactions with synthetic agents.
|
| |
Angew Chem Int Ed Engl,
44,
4130-4163.
|
|
|
|
|
|
|
S.D.Sharrow,
K.A.Edmonds,
M.A.Goodman,
M.V.Novotny,
and
M.J.Stone
(2005).
Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex.
|
| |
Protein Sci,
14,
249-256.
|
|
|
|
|
|
|
A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
|
| |
Proteins,
56,
130-142.
|
|
|
|
|
|
|
A.Cauerhff,
F.A.Goldbaum,
and
B.C.Braden
(2004).
Structural mechanism for affinity maturation of an anti-lysozyme antibody.
|
| |
Proc Natl Acad Sci U S A,
101,
3539-3544.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Jayaram,
and
T.Jain
(2004).
The role of water in protein-DNA recognition.
|
| |
Annu Rev Biophys Biomol Struct,
33,
343-361.
|
|
|
|
|
|
|
M.Nakasako
(2004).
Water-protein interactions from high-resolution protein crystallography.
|
| |
Philos Trans R Soc Lond B Biol Sci,
359,
1191.
|
|
|
|
|
|
|
W.D.Crill,
and
G.J.Chang
(2004).
Localization and characterization of flavivirus envelope glycoprotein cross-reactive epitopes.
|
| |
J Virol,
78,
13975-13986.
|
|
|
|
|
|
|
Y.Levy,
and
J.N.Onuchic
(2004).
Water and proteins: a love-hate relationship.
|
| |
Proc Natl Acad Sci U S A,
101,
3325-3326.
|
|
|
|
|
|
|
A.T.García-Sosa,
R.L.Mancera,
and
P.M.Dean
(2003).
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.
|
| |
J Mol Model,
9,
172-182.
|
|
|
|
|
|
|
E.Ben-Zeev,
and
M.Eisenstein
(2003).
Weighted geometric docking: incorporating external information in the rotation-translation scan.
|
| |
Proteins,
52,
24-27.
|
|
|
|
|
|
|
H.O.Andersson,
K.Fridborg,
S.Löwgren,
M.Alterman,
A.Mühlman,
M.Björsne,
N.Garg,
I.Kvarnström,
W.Schaal,
B.Classon,
A.Karlén,
U.H.Danielsson,
G.Ahlsén,
U.Nillroth,
L.Vrang,
B.Oberg,
B.Samuelsson,
A.Hallberg,
and
T.Unge
(2003).
Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors.
|
| |
Eur J Biochem,
270,
1746-1758.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Sanz,
L.García-Bermejo,
F.J.Blanco,
P.Kristensen,
M.Feijóo,
E.Suárez,
B.Blanco,
and
L.Alvarez-Vallina
(2003).
A novel cell binding site in the coiled-coil domain of laminin involved in capillary morphogenesis.
|
| |
EMBO J,
22,
1508-1517.
|
|
|
|
|
|
|
M.Adachi,
Y.Kurihara,
H.Nojima,
M.Takeda-Shitaka,
K.Kamiya,
and
H.Umeyama
(2003).
Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex.
|
| |
Protein Sci,
12,
2125-2131.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
T.Wang,
and
R.C.Wade
(2003).
Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.
|
| |
Proteins,
50,
158-169.
|
|
|
|
|
|
|
A.Heifetz,
E.Katchalski-Katzir,
and
M.Eisenstein
(2002).
Electrostatics in protein-protein docking.
|
| |
Protein Sci,
11,
571-587.
|
|
|
|
|
|
|
H.I.Jung,
S.J.Bowden,
A.Cooper,
and
R.N.Perham
(2002).
Thermodynamic analysis of the binding of component enzymes in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
|
| |
Protein Sci,
11,
1091-1100.
|
|
|
|
|
|
|
J.G.Luz,
M.Huang,
K.C.Garcia,
M.G.Rudolph,
V.Apostolopoulos,
L.Teyton,
and
I.A.Wilson
(2002).
Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
|
| |
J Exp Med,
195,
1175-1186.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Higo,
and
M.Nakasako
(2002).
Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole.
|
| |
J Comput Chem,
23,
1323-1336.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.G.Rudolph,
and
I.A.Wilson
(2002).
The specificity of TCR/pMHC interaction.
|
| |
Curr Opin Immunol,
14,
52-65.
|
|
|
|
|
|
|
N.Sinha,
S.Mohan,
C.A.Lipschultz,
and
S.J.Smith-Gill
(2002).
Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity.
|
| |
Biophys J,
83,
2946-2968.
|
|
|
|
|
|
|
J.C.Burnett,
P.Botti,
D.J.Abraham,
and
G.E.Kellogg
(2001).
Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins.
|
| |
Proteins,
42,
355-377.
|
|
|
|
|
|
|
K.M.Peterson,
K.V.Gopalan,
A.Nandy,
and
D.K.Srivastava
(2001).
Influence of Glu-376 --> Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase.
|
| |
Protein Sci,
10,
1822-1834.
|
|
|
|
|
|
|
K.Welfle,
R.Misselwitz,
R.Sabat,
H.D.Volk,
J.Schneider-Mergener,
U.Reineke,
and
H.Welfle
(2001).
Interaction of a designed interleukin-10 epitope mimic with an antibody studied by isothermal titration microcalorimetry.
|
| |
J Mol Recognit,
14,
89-98.
|
|
|
|
|
|
|
S.Y.Noskov,
and
C.Lim
(2001).
Free energy decomposition of protein-protein interactions.
|
| |
Biophys J,
81,
737-750.
|
|
|
|
|
|
|
D.W.Ritchie,
and
G.J.Kemp
(2000).
Protein docking using spherical polar Fourier correlations.
|
| |
Proteins,
39,
178-194.
|
|
|
|
|
|
|
E.J.Sundberg,
M.Urrutia,
B.C.Braden,
J.Isern,
D.Tsuchiya,
B.A.Fields,
E.L.Malchiodi,
J.Tormo,
F.P.Schwarz,
and
R.A.Mariuzza
(2000).
Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.
|
| |
Biochemistry,
39,
15375-15387.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.C.Burnett,
G.E.Kellogg,
and
D.J.Abraham
(2000).
Computational methodology for estimating changes in free energies of biomolecular association upon mutation. The importance of bound water in dimer-tetramer assembly for beta 37 mutant hemoglobins.
|
| |
Biochemistry,
39,
1622-1633.
|
|
|
|
|
|
|
J.Maynard,
and
G.Georgiou
(2000).
Antibody engineering.
|
| |
Annu Rev Biomed Eng,
2,
339-376.
|
|
|
|
|
|
|
K.W.Rodenburg,
F.Vallée,
N.Juge,
N.Aghajari,
X.Guo,
R.Haser,
and
B.Svensson
(2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
|
| |
Eur J Biochem,
267,
1019-1029.
|
|
|
|
|
|
|
L.Choulier,
V.Lafont,
N.Hugo,
and
D.Altschuh
(2000).
Covariance analysis of protein families: the case of the variable domains of antibodies.
|
| |
Proteins,
41,
475-484.
|
|
|
|
|
|
|
M.A.Olson,
and
L.T.Reinke
(2000).
Modeling implicit reorganization in continuum descriptions of protein-protein interactions.
|
| |
Proteins,
38,
115-119.
|
|
|
|
|
|
|
M.Kontou,
D.D.Leonidas,
E.H.Vatzaki,
P.Tsantili,
A.Mamalaki,
N.G.Oikonomakos,
K.R.Acharya,
and
S.J.Tzartos
(2000).
The crystal structure of the Fab fragment of a rat monoclonal antibody against the main immunogenic region of the human muscle acetylcholine receptor.
|
| |
Eur J Biochem,
267,
2389-2397.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Li,
H.Li,
S.J.Smith-Gill,
and
R.A.Mariuzza
(2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
|
| |
Biochemistry,
39,
6296-6309.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.Selisko,
A.F.Licea,
B.Becerril,
F.Zamudio,
L.D.Possani,
and
E.Horjales
(1999).
Antibody BCF2 against scorpion toxin Cn2 from Centuroides noxius Hoffmann: primary structure and three-dimensional model as free Fv fragment and complexed with its antigen.
|
| |
Proteins,
37,
130-143.
|
|
|
|
|
|
|
E.Freire
(1999).
The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme.
|
| |
Proc Natl Acad Sci U S A,
96,
10118-10122.
|
|
|
|
|
|
|
H.Li,
A.Llera,
E.L.Malchiodi,
and
R.A.Mariuzza
(1999).
The structural basis of T cell activation by superantigens.
|
| |
Annu Rev Immunol,
17,
435-466.
|
|
|
|
|
|
|
I.Jelesarov,
and
H.R.Bosshard
(1999).
Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition.
|
| |
J Mol Recognit,
12,
3.
|
|
|
|
|
|
|
J.J.Boniface,
Z.Reich,
D.S.Lyons,
and
M.M.Davis
(1999).
Thermodynamics of T cell receptor binding to peptide-MHC: evidence for a general mechanism of molecular scanning.
|
| |
Proc Natl Acad Sci U S A,
96,
11446-11451.
|
|
|
|
|
|
|
J.Janin
(1999).
Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
|
| |
Structure,
7,
R277-R279.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
N.Fuller,
and
R.P.Rand
(1999).
Water in actin polymerization.
|
| |
Biophys J,
76,
3261-3266.
|
|
|
|
|
|
|
N.Kessler,
D.Perl-Treves,
L.Addadi,
and
M.Eisenstein
(1999).
Structural and chemical complementarity between antibodies and the crystal surfaces they recognize.
|
| |
Proteins,
34,
383-394.
|
|
|
|
|
|
|
B.C.Braden,
E.R.Goldman,
R.A.Mariuzza,
and
R.J.Poljak
(1998).
Anatomy of an antibody molecule: structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1.3.
|
| |
Immunol Rev,
163,
45-57.
|
|
|
|
|
|
|
B.L.Neal,
D.Asthagiri,
and
A.M.Lenhoff
(1998).
Molecular origins of osmotic second virial coefficients of proteins.
|
| |
Biophys J,
75,
2469-2477.
|
|
|
|
|
|
|
F.Vallée,
A.Kadziola,
Y.Bourne,
M.Juy,
K.W.Rodenburg,
B.Svensson,
and
R.Haser
(1998).
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
|
| |
Structure,
6,
649-659.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Li,
A.Llera,
D.Tsuchiya,
L.Leder,
X.Ysern,
P.M.Schlievert,
K.Karjalainen,
and
R.A.Mariuzza
(1998).
Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B.
|
| |
Immunity,
9,
807-816.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.A.Kornblatt,
M.J.Kornblatt,
I.Rajotte,
G.H.Hoa,
and
P.C.Kahn
(1998).
Thermodynamic volume cycles for electron transfer in the cytochrome c oxidase and for the binding of cytochrome c to cytochrome c oxidase.
|
| |
Biophys J,
75,
435-444.
|
|
|
|
|
|
|
J.C.Eads,
N.M.Mahoney,
S.Vorobiev,
A.R.Bresnick,
K.K.Wen,
P.A.Rubenstein,
B.K.Haarer,
and
S.C.Almo
(1998).
Structure determination and characterization of Saccharomyces cerevisiae profilin.
|
| |
Biochemistry,
37,
11171-11181.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.H.Lakey,
and
E.M.Raggett
(1998).
Measuring protein-protein interactions.
|
| |
Curr Opin Struct Biol,
8,
119-123.
|
|
|
|
|
|
|
J.J.VanAntwerp,
and
K.D.Wittrup
(1998).
Thermodynamic characterization of affinity maturation: the D1.3 antibody and a higher-affinity mutant.
|
| |
J Mol Recognit,
11,
10-13.
|
|
|
|
|
|
|
K.Andersson,
J.Wrammert,
and
T.Leanderson
(1998).
Affinity selection and repertoire shift: paradoxes as a consequence of somatic mutation?
|
| |
Immunol Rev,
162,
173-182.
|
|
|
|
|
|
|
M.A.Holmes,
T.N.Buss,
and
J.Foote
(1998).
Conformational correction mechanisms aiding antigen recognition by a humanized antibody.
|
| |
J Exp Med,
187,
479-485.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.G.Taylor,
A.Rajpal,
and
J.F.Kirsch
(1998).
Kinetic epitope mapping of the chicken lysozyme.HyHEL-10 Fab complex: delineation of docking trajectories.
|
| |
Protein Sci,
7,
1857-1867.
|
|
|
|
|
|
|
M.H.Van Regenmortel,
D.Altschuh,
J.Chatellier,
L.Christensen,
N.Rauffer-Bruyère,
P.Richalet-Secordel,
J.Witz,
and
G.Zeder-Lutz
(1998).
Measurement of antigen-antibody interactions with biosensors.
|
| |
J Mol Recognit,
11,
163-167.
|
|
|
|
|
|
|
M.H.Van Regenmortel
(1998).
Thermodynamic parameters in immunoassay.
|
| |
Clin Chem Lab Med,
36,
353-354.
|
|
|
|
|
|
|
M.Lauwereys,
M.Arbabi Ghahroudi,
A.Desmyter,
J.Kinne,
W.Hölzer,
E.De Genst,
L.Wyns,
and
S.Muyldermans
(1998).
Potent enzyme inhibitors derived from dromedary heavy-chain antibodies.
|
| |
EMBO J,
17,
3512-3520.
|
|
|
|
|
|
|
R.Murali,
and
M.I.Greene
(1998).
Structure-based design of immunologically active therapeutic peptides.
|
| |
Immunol Res,
17,
163-169.
|
|
|
|
|
|
|
T.R.Transue,
E.De Genst,
M.A.Ghahroudi,
L.Wyns,
and
S.Muyldermans
(1998).
Camel single-domain antibody inhibits enzyme by mimicking carbohydrate substrate.
|
| |
Proteins,
32,
515-522.
|
|
|
|
|
|
|
W.Dall'Acqua,
A.L.Simon,
M.G.Mulkerrin,
and
P.Carter
(1998).
Contribution of domain interface residues to the stability of antibody CH3 domain homodimers.
|
| |
Biochemistry,
37,
9266-9273.
|
|
|
|
|
|
|
W.Dall'Acqua,
E.R.Goldman,
W.Lin,
C.Teng,
D.Tsuchiya,
H.Li,
X.Ysern,
B.C.Braden,
Y.Li,
S.J.Smith-Gill,
and
R.A.Mariuzza
(1998).
A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.
|
| |
Biochemistry,
37,
7981-7991.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
X.Ysern,
H.Li,
and
R.A.Mariuzza
(1998).
Imperfect interfaces.
|
| |
Nat Struct Biol,
5,
412-414.
|
|
|
|
|
|
|
D.Housset,
G.Mazza,
C.Grégoire,
C.Piras,
B.Malissen,
and
J.C.Fontecilla-Camps
(1997).
The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.
|
| |
EMBO J,
16,
4205-4216.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Szwajkajzer,
and
J.Carey
(1997).
Molecular and biological constraints on ligand-binding affinity and specificity.
|
| |
Biopolymers,
44,
181-198.
|
|
|
|
|
|
|
F.A.Goldbaum,
C.A.Velikovsky,
W.Dall'Acqua,
C.A.Fossati,
B.A.Fields,
B.C.Braden,
R.J.Poljak,
and
R.A.Mariuzza
(1997).
Characterization of anti-anti-idiotypic antibodies that bind antigen and an anti-idiotype.
|
| |
Proc Natl Acad Sci U S A,
94,
8697-8701.
|
|
|
|
|
|
|
K.A.Xavier,
K.A.Shick,
S.J.Smith-Gil,
and
R.C.Willson
(1997).
Involvement of water molecules in the association of monoclonal antibody HyHEL-5 with bobwhite quail lysozyme.
|
| |
Biophys J,
73,
2116-2125.
|
|
|
|
|
|
|
P.D.Hodgkin
(1997).
An antigen valence theory to explain the evolution and organization of the humoral immune response.
|
| |
Immunol Cell Biol,
75,
604-618.
|
|
|
|
|
|
|
P.England,
F.Brégégère,
and
H.Bedouelle
(1997).
Energetic and kinetic contributions of contact residues of antibody D1.3 in the interaction with lysozyme.
|
| |
Biochemistry,
36,
164-172.
|
|
|
|
|
|
|
T.Keitel,
A.Kramer,
H.Wessner,
C.Scholz,
J.Schneider-Mergener,
and
W.Höhne
(1997).
Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity.
|
| |
Cell,
91,
811-820.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
X.Zhang,
M.Gaubin,
L.Briant,
V.Srikantan,
R.Murali,
U.Saragovi,
D.Weiner,
C.Devaux,
M.Autiero,
D.Piatier-Tonneau,
and
M.I.Greene
(1997).
Synthetic CD4 exocyclics inhibit binding of human immunodeficiency virus type 1 envelope to CD4 and virus replication in T lymphocytes.
|
| |
Nat Biotechnol,
15,
150-154.
|
|
|
|
|
|
|
A.Desmyter,
T.R.Transue,
M.A.Ghahroudi,
M.H.Thi,
F.Poortmans,
R.Hamers,
S.Muyldermans,
and
L.Wyns
(1996).
Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme.
|
| |
Nat Struct Biol,
3,
803-811.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.A.Fields,
F.A.Goldbaum,
W.Dall'Acqua,
E.L.Malchiodi,
A.Cauerhff,
F.P.Schwarz,
X.Ysern,
R.J.Poljak,
and
R.A.Mariuzza
(1996).
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
|
| |
Biochemistry,
35,
15494-15503.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.M.Baker,
and
K.P.Murphy
(1996).
Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry.
|
| |
Biophys J,
71,
2049-2055.
|
|
|
|
|
|
|
D.R.Davies,
and
G.H.Cohen
(1996).
Interactions of protein antigens with antibodies.
|
| |
Proc Natl Acad Sci U S A,
93,
7.
|
|
|
|
|
|
|
F.A.Goldbaum,
F.P.Schwarz,
E.Eisenstein,
A.Cauerhff,
R.A.Mariuzza,
and
R.J.Poljak
(1996).
The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1.
|
| |
J Mol Recognit,
9,
6.
|
|
|
|
|
|
|
H.Resat,
and
M.Mezei
(1996).
Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.
|
| |
Biophys J,
71,
1179-1190.
|
|
|
|
|
|
|
H.Wu,
D.G.Myszka,
S.W.Tendian,
C.G.Brouillette,
R.W.Sweet,
I.M.Chaiken,
and
W.A.Hendrickson
(1996).
Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding.
|
| |
Proc Natl Acad Sci U S A,
93,
15030-15035.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Cacia,
R.Keck,
L.G.Presta,
and
J.Frenz
(1996).
Isomerization of an aspartic acid residue in the complementarity-determining regions of a recombinant antibody to human IgE: identification and effect on binding affinity.
|
| |
Biochemistry,
35,
1897-1903.
|
|
|
|
|
|
|
J.K.Myers,
and
C.N.Pace
(1996).
Hydrogen bonding stabilizes globular proteins.
|
| |
Biophys J,
71,
2033-2039.
|
|
|
|
|
|
|
J.R.Tame,
S.H.Sleigh,
A.J.Wilkinson,
and
J.E.Ladbury
(1996).
The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.
|
| |
Nat Struct Biol,
3,
998.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.J.Castro,
and
S.Anderson
(1996).
Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitor: effects on the kinetics and thermodynamics of binding to beta-trypsin and alpha-chymotrypsin.
|
| |
Biochemistry,
35,
11435-11446.
|
|
|
|
|
|
|
W.Dall'Acqua,
E.R.Goldman,
E.Eisenstein,
and
R.A.Mariuzza
(1996).
A mutational analysis of the binding of two different proteins to the same antibody.
|
| |
Biochemistry,
35,
9667-9676.
|
|
|
|
|
|
|
W.E.Royer,
A.Pardanani,
Q.H.Gibson,
E.S.Peterson,
and
J.M.Friedman
(1996).
Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin.
|
| |
Proc Natl Acad Sci U S A,
93,
14526-14531.
|
|
|
|
|
|
|
B.C.Braden,
B.A.Fields,
and
R.J.Poljak
(1995).
Conservation of water molecules in an antibody-antigen interaction.
|
| |
J Mol Recognit,
8,
317-325.
|
|
|
|
|
|
|
F.P.Schwarz,
D.Tello,
F.A.Goldbaum,
R.A.Mariuzza,
and
R.J.Poljak
(1995).
Thermodynamics of antigen-antibody binding using specific anti-lysozyme antibodies.
|
| |
Eur J Biochem,
228,
388-394.
|
|
|
|
|
|
|
J.Janin
(1995).
Elusive affinities.
|
| |
Proteins,
21,
30-39.
|
|
|
|
|
|
|
K.P.Murphy,
E.Freire,
and
Y.Paterson
(1995).
Configurational effects in antibody-antigen interactions studied by microcalorimetry.
|
| |
Proteins,
21,
83-90.
|
|
|
|
|
|
|
V.Helms,
and
R.C.Wade
(1995).
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.
|
| |
Biophys J,
69,
810-824.
|
|
|
|
|
|
|
D.Tello,
E.Eisenstein,
F.P.Schwarz,
F.A.Goldbaum,
B.A.Fields,
R.A.Mariuzza,
and
R.J.Poljak
(1994).
Structural and physicochemical analysis of the reaction between the anti-lysozyme antibody D1.3 and the anti-idiotopic antibodies E225 and E5.2.
|
| |
J Mol Recognit,
7,
57-62.
|
|
|
|
|
|
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
codes are
shown on the right.
|
 |
Links
