-
1
-
-
0036890316
-
Electrostatics in protein binding and function
-
Sinha, N. and Smith-Gill, S. J. (2002) Electrostatics in protein binding and function. Curr. Prot. Pept. Sci. 3, 601-614.
-
(2002)
Curr. Prot. Pept. Sci.
, vol.3
, pp. 601-614
-
-
Sinha, N.1
Smith-Gill, S.J.2
-
2
-
-
0017747498
-
Unusual distributions of amino acids in complementarity-determining (hyper-variable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites
-
Kabat, E. A., Wu, T. T., and Bilofsky, H. (1977) Unusual distributions of amino acids in complementarity-determining (hyper-variable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites. J. Biol. Chem. 252, 6609-6616.
-
(1977)
J. Biol. Chem.
, vol.252
, pp. 6609-6616
-
-
Kabat, E.A.1
Wu, T.T.2
Bilofsky, H.3
-
3
-
-
0032474463
-
A mutational analysis of binding interactions in an antigen-antibody protein-protein complex
-
Dall'Acqua, W., Goldman, E. R., Lin, W., Teng, C., Tsuchiya, D., Li, H., et al. (1998) A mutational analysis of binding interactions in an antigen-antibody protein-protein complex. Biochemistry 37, 7981-7991.
-
(1998)
Biochemistry
, vol.37
, pp. 7981-7991
-
-
Dall'Acqua, W.1
Goldman, E.R.2
Lin, W.3
Teng, C.4
Tsuchiya, D.5
Li, H.6
-
5
-
-
0028877602
-
Structural features of the reactions between antibodies and protein antigens
-
Braden, B. C. and Poljak, R. J. (1995) Structural features of the reactions between antibodies and protein antigens. FASEB J. 9, 9-16.
-
(1995)
FASEB J.
, vol.9
, pp. 9-16
-
-
Braden, B.C.1
Poljak, R.J.2
-
6
-
-
0026209439
-
Protein-protein interactions: Structural motifs and molecular recognition
-
Smith-Gill, S. J. (1991) Protein-protein interactions: structural motifs and molecular recognition. Curr. Opin. Biotech. 2, 568-575.
-
(1991)
Curr. Opin. Biotech.
, vol.2
, pp. 568-575
-
-
Smith-Gill, S.J.1
-
7
-
-
0028052272
-
Contribution to antibody-antigen interaction of structurally perturbed antigenic residues upon antibody binding
-
Tsumoto, K., Ueda, Y., Maenaka, K., Watanabe, K., Ogasahara, K., Yutani, K., et al. (1994) Contribution to antibody-antigen interaction of structurally perturbed antigenic residues upon antibody binding. J. Biol. Chem. 269, 28777-28782.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 28777-28782
-
-
Tsumoto, K.1
Ueda, Y.2
Maenaka, K.3
Watanabe, K.4
Ogasahara, K.5
Yutani, K.6
-
8
-
-
0033405041
-
Molecular dynamics and free energy calculations applied to affinity maturation in antibody 48G7
-
Chong, L. T., Duan, Y., Wang, L., Massova, I., and Kollman, P. A. (1999) Molecular dynamics and free energy calculations applied to affinity maturation in antibody 48G7. Proc. Natl. Acad. Sci. USA 96, 14330-14335.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 14330-14335
-
-
Chong, L.T.1
Duan, Y.2
Wang, L.3
Massova, I.4
Kollman, P.A.5
-
9
-
-
0024362070
-
On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL5
-
Novotny, J., Bruccoleri, R. E., and Saul, F. A. (1989) On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL5. Biochemistry 28, 4735-4749.
-
(1989)
Biochemistry
, vol.28
, pp. 4735-4749
-
-
Novotny, J.1
Bruccoleri, R.E.2
Saul, F.A.3
-
10
-
-
0033621118
-
The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme
-
Freire, E. (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. USA 96, 10118-10122.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 10118-10122
-
-
Freire, E.1
-
11
-
-
0034687780
-
Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface
-
Sundberg, E. J., Urrutia, M., Braden, B. C., Isern, J., Tsuchiya, D., Fields, B. A., et al. (2000) Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. Biochemistry 39, 15375-15387.
-
(2000)
Biochemistry
, vol.39
, pp. 15375-15387
-
-
Sundberg, E.J.1
Urrutia, M.2
Braden, B.C.3
Isern, J.4
Tsuchiya, D.5
Fields, B.A.6
-
12
-
-
0033578783
-
Salt-links dominate affinity of antibody HyHEL-5 for lysozyme through enthalpic contributions
-
Wibbenmeyer, J. A., Schuck, P., Smith-Gill, S. J., and Willson, R. C. (1999) Salt-links dominate affinity of antibody HyHEL-5 for lysozyme through enthalpic contributions. J. Biol. Chem. 274, 26838-26842.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 26838-26842
-
-
Wibbenmeyer, J.A.1
Schuck, P.2
Smith-Gill, S.J.3
Willson, R.C.4
-
13
-
-
0034732988
-
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63
-
Li, Y., Li, H., Smith-Gill, S. J., and Mariuzza, R. A. (2000) Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63. Biochemistry 39, 6296-6309.
-
(2000)
Biochemistry
, vol.39
, pp. 6296-6309
-
-
Li, Y.1
Li, H.2
Smith-Gill, S.J.3
Mariuzza, R.A.4
-
14
-
-
0035916256
-
Mutations of an epitope hot-spot residue alter rate limiting steps of antigen-antibody protein-protein associations
-
Li, Y., Lipschultz, C. A., Mohan, S., and Smith-Gill, S. J. (2001) Mutations of an epitope hot-spot residue alter rate limiting steps of antigen-antibody protein-protein associations. Biochemistry 40, 2011-2022.
-
(2001)
Biochemistry
, vol.40
, pp. 2011-2022
-
-
Li, Y.1
Lipschultz, C.A.2
Mohan, S.3
Smith-Gill, S.J.4
-
15
-
-
0034660904
-
Luxury accommodations: The expanding role of structural plasticity in protein-protein interactions
-
Sundberg, E. J. and Mariuzza, R. A. (2000) Luxury accommodations: the expanding role of structural plasticity in protein-protein interactions. Structure Fold Des. 8, R137-R142.
-
(2000)
Structure Fold Des.
, vol.8
-
-
Sundberg, E.J.1
Mariuzza, R.A.2
-
16
-
-
0035853126
-
Point mutations and sequence variability in proteins: Redistributions of preexisting populations
-
Sinha, N. and Nussinov, R. (2001) Point mutations and sequence variability in proteins: redistributions of preexisting populations. Proc. Natl. Acad. Sci. U. S. A. 98, 3139-3144.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 3139-3144
-
-
Sinha, N.1
Nussinov, R.2
-
17
-
-
0035659482
-
Interdomain interactions in hinge-bending transitions
-
Sinha, N., Kumar, S., and Nussinov, R. (2001) Interdomain interactions in hinge-bending transitions. Structure Fold Des. 9, 1165-1181.
-
(2001)
Structure Fold Des.
, vol.9
, pp. 1165-1181
-
-
Sinha, N.1
Kumar, S.2
Nussinov, R.3
-
18
-
-
0035702099
-
Building blocks, hinge-bending motions and protein topology
-
Sinha, N., Tsai, C. J., and Nussinov, R. (2001) Building blocks, hinge-bending motions and protein topology. J. Biomolec. Struct. Dyn. 19, 369-380.
-
(2001)
J. Biomolec. Struct. Dyn.
, vol.19
, pp. 369-380
-
-
Sinha, N.1
Tsai, C.J.2
Nussinov, R.3
-
19
-
-
0036377264
-
Protein structure to function via dynamics
-
Sinha, N. and Smith-Gill, S. J. (2002) Protein structure to function via dynamics. Protein Pept. Lett. 9, 367-377.
-
(2002)
Protein Pept. Lett.
, vol.9
, pp. 367-377
-
-
Sinha, N.1
Smith-Gill, S.J.2
-
20
-
-
0036680063
-
Protein flexibility and drug design: How to hit a moving target
-
Carlson, H. A. (2002) Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 6, 447-452.
-
(2002)
Curr. Opin. Chem. Biol.
, vol.6
, pp. 447-452
-
-
Carlson, H.A.1
-
21
-
-
0036019065
-
Protein flexibility is an important component of structure-based drug discovery
-
Carlson, H. A. (2002) Protein flexibility is an important component of structure-based drug discovery. Curr. Pharm. Des. 8, 1571-1578.
-
(2002)
Curr. Pharm. Des.
, vol.8
, pp. 1571-1578
-
-
Carlson, H.A.1
-
22
-
-
0036298514
-
Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
-
Zoete, V., Michielin, O., and Karplus, M. (2002) Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J. Mol. Biol. 315, 21-52.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 21-52
-
-
Zoete, V.1
Michielin, O.2
Karplus, M.3
-
23
-
-
0029067489
-
Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity
-
Morton, A. and Matthews, B. W. (1995) Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity. Biochemistry 34, 8576-8588.
-
(1995)
Biochemistry
, vol.34
, pp. 8576-8588
-
-
Morton, A.1
Matthews, B.W.2
-
24
-
-
0033604853
-
The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: Flexibility and rigidity
-
Okamoto, A., Ishii, S., Hirotsu, K., and Kagamiyama, H. (1999) The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity. Biochemistry 38, 1176-1184.
-
(1999)
Biochemistry
, vol.38
, pp. 1176-1184
-
-
Okamoto, A.1
Ishii, S.2
Hirotsu, K.3
Kagamiyama, H.4
-
25
-
-
0037422580
-
Flexibility and molecular recognition in the immune system
-
Jimenez, R., Salazar, G., Baldridge, K. K., and Romesberg, F. E. (2003) Flexibility and molecular recognition in the immune system. Proc. Natl. Acad. Sci. USA 100, 92-97.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 92-97
-
-
Jimenez, R.1
Salazar, G.2
Baldridge, K.K.3
Romesberg, F.E.4
-
26
-
-
0036923836
-
Differences in electrostatic properties at antibody-antigen binding sites: Implications for specificity and cross-reactivity
-
Sinha, N., Mohan, S., Lipschultz, C. A., and Smith-Gill, S. J. (2002) Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys. J. 83, 2946-2968.
-
(2002)
Biophys. J.
, vol.83
, pp. 2946-2968
-
-
Sinha, N.1
Mohan, S.2
Lipschultz, C.A.3
Smith-Gill, S.J.4
-
27
-
-
0242385341
-
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: An insight into the molecular basis of antibody cross-reactivity and specificity
-
Mohan, S., Sinha, N., and Smith-Gill, S. J. (2003) Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity. Biophys. J. 85, 3221-3236.
-
(2003)
Biophys. J.
, vol.85
, pp. 3221-3236
-
-
Mohan, S.1
Sinha, N.2
Smith-Gill, S.J.3
-
28
-
-
0030821164
-
Structural insights into the evolution of an antibody combining site
-
Wedemayer, G. J., Patten, P. A., Wang, L. H., Schultz, P. G., and Stevens, R. C. (1997) Structural insights into the evolution of an antibody combining site. Science 276, 1665-1669.
-
(1997)
Science
, vol.276
, pp. 1665-1669
-
-
Wedemayer, G.J.1
Patten, P.A.2
Wang, L.H.3
Schultz, P.G.4
Stevens, R.C.5
-
29
-
-
0032897494
-
An analysis of conformational changes on protein-protein association: Implications for predictive docking
-
Betts, M. J. and Sternberg, M. J. (1999) An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng. 12, 271-283.
-
(1999)
Protein Eng.
, vol.12
, pp. 271-283
-
-
Betts, M.J.1
Sternberg, M.J.2
-
30
-
-
0037435599
-
Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen
-
Li, Y., Urrutia, M., Smith-Gill, S. J., and Mariuzza, R. A. (2003) Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen. Biochemistry 42, 11-22.
-
(2003)
Biochemistry
, vol.42
, pp. 11-22
-
-
Li, Y.1
Urrutia, M.2
Smith-Gill, S.J.3
Mariuzza, R.A.4
-
31
-
-
0034026757
-
Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. substrate-enzyme interactions and dynamics
-
Peters, G. H., Frimurer, T. M., Andersen, J. N., and Olsen, O. H. (2000) Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. substrate-enzyme interactions and dynamics. Biophys J. 78, 2191-2200.
-
(2000)
Biophys J.
, vol.78
, pp. 2191-2200
-
-
Peters, G.H.1
Frimurer, T.M.2
Andersen, J.N.3
Olsen, O.H.4
-
32
-
-
0000051486
-
Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces
-
Maple, J. R., Dinur, U., and Hagler, A. T. (1988) Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces. Proc. Natl. Acad. Sci. USA 85, 5350-5354.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 5350-5354
-
-
Maple, J.R.1
Dinur, U.2
Hagler, A.T.3
-
33
-
-
0017411710
-
The protein data bank: A computer based archival file for macromolecular structures
-
Bernstein, F., Koetzle, T., Williams, G., Meyer, E. J., Brice, M., Rodgers, J., et al. (1997) The protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
-
(1997)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.1
Koetzle, T.2
Williams, G.3
Meyer, E.J.4
Brice, M.5
Rodgers, J.6
-
34
-
-
0030238916
-
Determination of the solution structure of the SH3 domain of human p56 Lck tyrosine kinase
-
Hiroaki, H., Klaus, W., and Senn, H. (1996) Determination of the solution structure of the SH3 domain of human p56 Lck tyrosine kinase J. Biomolec. N. M. R. 8, 105-122.
-
(1996)
J. Biomolec. N. M. R.
, vol.8
, pp. 105-122
-
-
Hiroaki, H.1
Klaus, W.2
Senn, H.3
-
35
-
-
0032958585
-
Energetic analysis of an antigen/antibody interface: Alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/ lysozyme interaction
-
Pons, J., Rajpal, A., and Kirsch, J. F. (1999) Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/ lysozyme interaction. Protein Sci. 8, 958-968.
-
(1999)
Protein Sci.
, vol.8
, pp. 958-968
-
-
Pons, J.1
Rajpal, A.2
Kirsch, J.F.3
-
36
-
-
0029016268
-
Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
-
Morton, A., Baase, W. A., and Matthews, B. W. (1995) Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34, 8564-8575.
-
(1995)
Biochemistry
, vol.34
, pp. 8564-8575
-
-
Morton, A.1
Baase, W.A.2
Matthews, B.W.3
-
37
-
-
0038386270
-
The structure of the membrane distal phosphatase domain of RPTPa reveals interdomain flexibility and an SH2 domain interaction region
-
Sonnenburg, E. D., Bilwes, A., Hunter, T., and Noel, J. P. (2003) The structure of the membrane distal phosphatase domain of RPTPa reveals interdomain flexibility and an SH2 domain interaction region. Biochemistry 42, 7904-7914.
-
(2003)
Biochemistry
, vol.42
, pp. 7904-7914
-
-
Sonnenburg, E.D.1
Bilwes, A.2
Hunter, T.3
Noel, J.P.4
-
38
-
-
0032530836
-
A database of macromolecular motions
-
Gerstein, M. and Krebs, W. (1998) A database of macromolecular motions. Nucleic Acids Res. 26, 4280-4290.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
39
-
-
0033642945
-
Structural stability of binding sites: Consequences for binding affinity and allosteric effects
-
Luque, I. and Freire, E. (2000) Structural stability of binding sites: consequences for binding affinity and allosteric effects. Proteins Struct. Func. Genet. 4, 63-71.
-
(2000)
Proteins Struct. Func. Genet.
, vol.4
, pp. 63-71
-
-
Luque, I.1
Freire, E.2
-
40
-
-
0027496217
-
Conformational flexibility of enzyme active sites
-
Tsou, C. L. (1993) Conformational flexibility of enzyme active sites. Science 262, 380-381.
-
(1993)
Science
, vol.262
, pp. 380-381
-
-
Tsou, C.L.1
-
41
-
-
0034257929
-
The 1.0 a crystal structure of Ca(2+)-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
-
Wilson, M. A. and Brunger, A. T. (2000) The 1.0 A crystal structure of Ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. J. Mol. Biol. 301, 1237-1256.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 1237-1256
-
-
Wilson, M.A.1
Brunger, A.T.2
-
42
-
-
0029040871
-
High resolution crystal structures of amphibian red-cell L ferritin: Potential roles for structural plasticity and solvation in function
-
Trikha, J., Theil, E. C., and Allewell, N. M. (1995) High resolution crystal structures of amphibian red-cell L ferritin: potential roles for structural plasticity and solvation in function. J. Mol. Biol. 248, 949-967.
-
(1995)
J. Mol. Biol.
, vol.248
, pp. 949-967
-
-
Trikha, J.1
Theil, E.C.2
Allewell, N.M.3
-
43
-
-
0027528934
-
Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers
-
Gerstein, M., Schulz, G., and Chothia, C. (1993) Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J. Mol. Biol. 229, 494-501.
-
(1993)
J. Mol. Biol.
, vol.229
, pp. 494-501
-
-
Gerstein, M.1
Schulz, G.2
Chothia, C.3
-
44
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M. and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9, 646-652.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
46
-
-
0003525155
-
-
John Wiley and Sons, New York
-
Brooks, C. L. III., Karplus, M., and Pettitt, B. M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. John Wiley and Sons, New York.
-
(1988)
Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics
-
-
Brooks III, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
47
-
-
0034665864
-
A dynamic model for the allosteric mechanism of GroEL
-
J. Ma, P. B. Sigler, Z. Xu and M. Karplus, A dynamic model for the allosteric mechanism of GroEL. J. Mol. Biol. 302, 303-313 (2000).
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 303-313
-
-
Ma, J.1
Sigler, P.B.2
Xu, Z.3
Karplus, M.4
-
48
-
-
0035815288
-
Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
-
Young, M. A., Gonfloni, S., Superti-Furga, G., Roux, B., and Kuriyan, J. (2001) Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105, 115-126.
-
(2001)
Cell
, vol.105
, pp. 115-126
-
-
Young, M.A.1
Gonfloni, S.2
Superti-Furga, G.3
Roux, B.4
Kuriyan, J.5
-
49
-
-
1542358827
-
Structure, dynamics and interaction with kinase targets: Computer simulations of calmodulin
-
Yang, C., Jas, G. S., and Kuczera, K. (2004) Structure, dynamics and interaction with kinase targets: computer simulations of calmodulin. Biochim. Biophys. Acta 1697, 289-300.
-
(2004)
Biochim. Biophys. Acta
, vol.1697
, pp. 289-300
-
-
Yang, C.1
Jas, G.S.2
Kuczera, K.3
-
50
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
Kumar, S., Ma, B., Tsai, C. J., Sinha, N., and Nussinov, R. (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9, 10-9.
-
(2000)
Protein Sci.
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
51
-
-
0033621104
-
Folding and binding cascades: Shifts in energy landscapes
-
Tsai, C. J., Ma, B., and Nussinov, R. (1999) Folding and binding cascades: shifts in energy landscapes. Proc. Natl. Acad. Sci. USA 96, 9970-9972.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9970-9972
-
-
Tsai, C.J.1
Ma, B.2
Nussinov, R.3
|