-
1
-
-
0036424666
-
Structural basis of macromolecular recognition
-
DOI 10.1016/S0065-3233(02)61001-0
-
Wodak, S.J. & Janin, J. Structural basis of macromolecular recognition. Adv. Protein Chem. 61, 9-73 (2002). (Pubitemid 35303453)
-
(2002)
Advances in Protein Chemistry
, vol.61
, pp. 9-73
-
-
Wodak, S.J.1
Janin, J.2
-
2
-
-
0031058541
-
The statisticalthermodynamic basis for computation of binding affinities: A critical review
-
Gilson, M.K., Given, J.A., Bush, B.L. & McCammon, J.A. The statisticalthermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72, 1047-1069 (1997).
-
(1997)
Biophys. J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
3
-
-
34447108978
-
Water, water everywhere-except where it matters?
-
Homans, S.W. Water, water everywhere-except where it matters? Drug Discov. Today 12, 534-539 (2007).
-
(2007)
Drug Discov. Today
, vol.12
, pp. 534-539
-
-
Homans, S.W.1
-
4
-
-
0017884417
-
The hydrophobic effect and the organization of living matter
-
Tanford, C. The hydrophobic effect and the organization of living matter. Science 200, 1012-1018 (1978). (Pubitemid 8346922)
-
(1978)
Science
, vol.200
, Issue.4345
, pp. 1012-1018
-
-
Tanford, C.1
-
5
-
-
0026416668
-
Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
-
Sharp, K.A., Nicholls, A., Fine, R.F. & Honig, B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252, 106-109 (1991). (Pubitemid 21916946)
-
(1991)
Science
, vol.252
, Issue.5002
, pp. 106-109
-
-
Sharp, K.A.1
Nicholls, A.2
Fine, R.F.3
Honig, B.4
-
6
-
-
26944481188
-
Interfaces and the driving force of hydrophobic assembly
-
DOI 10.1038/nature04162, PII N04162
-
Chandler, D. Interfaces and the driving force of hydrophobic assembly. Nature 437, 640-647 (2005). (Pubitemid 41486526)
-
(2005)
Nature
, vol.437
, Issue.7059
, pp. 640-647
-
-
Chandler, D.1
-
7
-
-
0001666112
-
Entropy changes accompanying association reactions of proteins
-
Steinberg, I.Z. & Scheraga, H.A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238, 172-181 (1963).
-
(1963)
J. Biol. Chem.
, vol.238
, pp. 172-181
-
-
Steinberg, I.Z.1
Scheraga, H.A.2
-
8
-
-
0023475026
-
Configurational entropy of native proteins
-
Karplus, M., Ichiye, T. & Pettitt, B.M. Configurational entropy of native proteins. Biophys. J. 52, 1083-1085 (1987).
-
(1987)
Biophys. J.
, vol.52
, pp. 1083-1085
-
-
Karplus, M.1
Ichiye, T.2
Pettitt, B.M.3
-
9
-
-
0023643422
-
Genetic and structural analysis of the proteins stability problem
-
Matthews, B.W. Genetic and structural analysis of the proteins stability problem. Biochemistry 26, 6885-6888 (1987).
-
(1987)
Biochemistry
, vol.26
, pp. 6885-6888
-
-
Matthews, B.W.1
-
10
-
-
0033988897
-
Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex
-
Lee, A.L., Kinnear, S.A. & Wand, A.J. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat. Struct. Biol. 7, 72-77 (2000).
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 72-77
-
-
Lee, A.L.1
Kinnear, S.A.2
Wand, A.J.3
-
11
-
-
34447503697
-
Conformational entropy in molecular recognition by proteins
-
Frederick, K.K., Marlow, M.S., Valentine, K.G. & Wand, A.J. Conformational entropy in molecular recognition by proteins. Nature 448, 325-329 (2007).
-
(2007)
Nature
, vol.448
, pp. 325-329
-
-
Frederick, K.K.1
Marlow, M.S.2
Valentine, K.G.3
Wand, A.J.4
-
12
-
-
33646945580
-
Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
-
Igumenova, T.I., Frederick, K.K. & Wand, A.J. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem. Rev. 106, 1672-1699 (2006).
-
(2006)
Chem. Rev.
, vol.106
, pp. 1672-1699
-
-
Igumenova, T.I.1
Frederick, K.K.2
Wand, A.J.3
-
13
-
-
0030473440
-
Insights into the local residual entropy of proteins provided by NMR relaxation
-
Li, Z., Raychaudhuri, S. & Wand, A.J. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci. 5, 2647-2650 (1996). (Pubitemid 26424878)
-
(1996)
Protein Science
, vol.5
, Issue.12
, pp. 2647-2650
-
-
Li, Z.1
Raychaudhuri, S.2
Wand, A.J.3
-
14
-
-
0347949547
-
Regulation of cell cycle progression by calcium/calmodulin-dependent pathways
-
DOI 10.1210/er.2003-0008
-
Kahl, C.R. & Means, A.R. Regulation of cell cycle progression by calcium/ calmodulin-dependent pathways. Endocr. Rev. 24, 719-736 (2003). (Pubitemid 38067696)
-
(2003)
Endocrine Reviews
, vol.24
, Issue.6
, pp. 719-736
-
-
Kahl, C.R.1
Means, A.R.2
-
15
-
-
0003161862
-
Calmodulin target database
-
Yap, K.L. et al. Calmodulin target database. J. Struct. Funct. Genomics 1, 8-14 (2000).
-
(2000)
J. Struct. Funct. Genomics
, vol.1
, pp. 8-14
-
-
Yap, K.L.1
-
16
-
-
0029176895
-
Measurement of 2H T1 and T1gamma,pi relaxation times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution
-
Muhandiram, D.R., Yamazaki, T., Sykes, B.D. & Kay, L.E. Measurement of 2H T1 and T1-relaxation-times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution. J. Am. Chem. Soc. 117, 11536-11544 (1995). (Pubitemid 3006291)
-
(1995)
Journal of the American Chemical Society
, vol.117
, Issue.46
, pp. 11536-11544
-
-
Muhandiram, D.R.1
Yamazaki, T.2
Sykes, B.D.3
Kay, L.E.4
-
17
-
-
33746224059
-
Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulinbinding domain
-
Marlow, M.S. & Wand, A.J. Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulinbinding domain. Biochemistry 45, 8732-8741 (2006).
-
(2006)
Biochemistry
, vol.45
, pp. 8732-8741
-
-
Marlow, M.S.1
Wand, A.J.2
-
18
-
-
33747508183
-
Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy
-
Frederick, K.K., Kranz, J.K. & Wand, A.J. Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy. Biochemistry 45, 9841-9848 (2006).
-
(2006)
Biochemistry
, vol.45
, pp. 9841-9848
-
-
Frederick, K.K.1
Kranz, J.K.2
Wand, A.J.3
-
19
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
-
Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559 (1982).
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
20
-
-
53849092076
-
Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation
-
Frederick, K.K., Sharp, K.A., Warischalk, N. & Wand, A.J. Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation. J. Phys. Chem. B 112, 12095-12103 (2008).
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 12095-12103
-
-
Frederick, K.K.1
Sharp, K.A.2
Warischalk, N.3
Wand, A.J.4
-
21
-
-
0029149085
-
Molecular and structural basis of target recognition by calmodulin
-
Crivici, A. & Ikura, M. Molecular and structural basis of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 24, 85-116 (1995).
-
(1995)
Annu. Rev. Biophys. Biomol. Struct.
, vol.24
, pp. 85-116
-
-
Crivici, A.1
Ikura, M.2
-
22
-
-
0028916599
-
A hot spot of binding energy in a hormonereceptor interface
-
Clackson, T. & Wells, J.A. A hot spot of binding energy in a hormonereceptor interface. Science 267, 383-386 (1995).
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
23
-
-
0037137214
-
Temperature dependence of the internal dynamics of a calmodulin-peptide complex
-
DOI 10.1021/bi026380d
-
Lee, A.L., Sharp, K.A., Kranz, J.K., Song, X.J. & Wand, A.J. Temperature dependence of the internal dynamics of a calmodulin-peptide complex. Biochemistry 41, 13814-13825 (2002). (Pubitemid 35332720)
-
(2002)
Biochemistry
, vol.41
, Issue.46
, pp. 13814-13825
-
-
Lee, A.L.1
Sharp, K.A.2
Kranz, J.K.3
Song, X.-J.4
Wand, A.J.5
-
24
-
-
33744908076
-
Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy
-
DOI 10.1021/cr0404287
-
Palmer, A.G.I. & Massi, F. Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700-1719 (2006). (Pubitemid 43840531)
-
(2006)
Chemical Reviews
, vol.106
, Issue.5
, pp. 1700-1719
-
-
Palmer III, A.G.1
Massi, F.2
-
25
-
-
33644774471
-
Optimal isotope labelling for NMR protein structure determinations
-
DOI 10.1038/nature04525, PII N04525
-
Kainosho, M. et al. Optimal isotope labelling for NMR protein structure determinations. Nature 440, 52-57 (2006). (Pubitemid 43336263)
-
(2006)
Nature
, vol.440
, Issue.7080
, pp. 52-57
-
-
Kainosho, M.1
Torizawa, T.2
Iwashita, Y.3
Terauchi, T.4
Mei Ono, A.5
Guntert, P.6
-
26
-
-
0037450635
-
Structural basis for endothelial nitric oxide synthase binding to calmodulin
-
DOI 10.1093/emboj/cdg078
-
Aoyagi, M., Arvai, A.S., Tainer, J.A. & Getzoff, E.D. Structural basis for endothelial nitric oxide synthase binding to calmodulin. EMBO J. 22, 766-775 (2003). (Pubitemid 36227779)
-
(2003)
EMBO Journal
, vol.22
, Issue.4
, pp. 766-775
-
-
Aoyagi, M.1
Arvai, A.S.2
Tainer, J.A.3
Getzoff, E.D.4
-
27
-
-
0026794065
-
Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex
-
Meador, W.E., Means, A.R. & Quiocho, F.A. Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. Science 257, 1251-1255 (1992).
-
(1992)
Science
, vol.257
, pp. 1251-1255
-
-
Meador, W.E.1
Means, A.R.2
Quiocho, F.A.3
-
28
-
-
2242474818
-
Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: Studies of the kinase activation mechanism
-
Clapperton, J.A., Martin, S.R., Smerdon, S.J., Gamblin, S.J. & Bayley, P.M. Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism. Biochemistry 41, 14669-14679 (2002).
-
(2002)
Biochemistry
, vol.41
, pp. 14669-14679
-
-
Clapperton, J.A.1
Martin, S.R.2
Smerdon, S.J.3
Gamblin, S.J.4
Bayley, P.M.5
-
29
-
-
0032834002
-
2+-calmodulin-dependent kinase kinase
-
DOI 10.1038/12271
-
Osawa, M. et al. A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase. Nat. Struct. Biol. 6, 819-824 (1999). (Pubitemid 29415172)
-
(1999)
Nature Structural Biology
, vol.6
, Issue.9
, pp. 819-824
-
-
Osawa, M.1
Tokumitsu, H.2
Swindells, M.B.3
Kurihara, H.4
Orita, M.5
Shibanuma, T.6
Furuya, T.7
Ikura, M.8
-
30
-
-
0029900846
-
The magnitude of the backbone conformational entropy change in protein folding
-
D'Aquino, J.A. et al. The magnitude of the backbone conformational entropy change in protein folding. Proteins 25, 143-156 (1996).
-
(1996)
Proteins
, vol.25
, pp. 143-156
-
-
D'Aquino, J.A.1
-
31
-
-
25444519195
-
Backbone and side chain dynamics of mutant calmodulin-peptide complexes
-
Igumenova, T.I., Lee, A.L. & Wand, A.J. Backbone and side chain dynamics of mutant calmodulin-peptide complexes. Biochemistry 44, 12627-12639 (2005).
-
(2005)
Biochemistry
, vol.44
, pp. 12627-12639
-
-
Igumenova, T.I.1
Lee, A.L.2
Wand, A.J.3
-
32
-
-
0023657949
-
Hydrophobic cluster analysis: An efficient new way to compare and analyse amino acid sequences
-
Gaboriaud, C., Bissery, V., Benchetrit, T. & Mornon, J.P. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Lett. 224, 149-155 (1987).
-
(1987)
FEBS Lett.
, vol.224
, pp. 149-155
-
-
Gaboriaud, C.1
Bissery, V.2
Benchetrit, T.3
Mornon, J.P.4
-
33
-
-
33750624445
-
Ionic volumes in solution
-
DOI 10.1016/j.bpc.2006.04.013, PII S030146220600127X
-
Marcus, Y. Ionic volumes in solution. Biophys. Chem. 124, 200-207 (2006). (Pubitemid 44692361)
-
(2006)
Biophysical Chemistry
, vol.124
, Issue.3
, pp. 200-207
-
-
Marcus, Y.1
-
34
-
-
0037176906
-
Dissection of the pathway of molecular recognition by calmodulin
-
Kranz, J.K., Flynn, P.F., Fuentes, E.J. & Wand, A.J. Dissection of the pathway of molecular recognition by calmodulin. Biochemistry 41, 2599-2608 (2002).
-
(2002)
Biochemistry
, vol.41
, pp. 2599-2608
-
-
Kranz, J.K.1
Flynn, P.F.2
Fuentes, E.J.3
Wand, A.J.4
-
35
-
-
4043156208
-
Direct determination of vibrational density of states change on ligand binding to a protein
-
Balog, E. et al. Direct determination of vibrational density of states change on ligand binding to a protein. Phys. Rev. Lett. 93, 028103 (2004).
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 028103
-
-
Balog, E.1
-
36
-
-
0028247281
-
Side-chain entropy and packing in proteins
-
Bromberg, S. & Dill, K.A. Side-chain entropy and packing in proteins. Protein Sci. 3, 997-1009 (1994). (Pubitemid 24209892)
-
(1994)
Protein Science
, vol.3
, Issue.7
, pp. 997-1009
-
-
Bromberg, S.1
Dill, K.A.2
-
37
-
-
0028956081
-
The energetics and dynamics of molecular recognition by calmodulin
-
Ehrhardt, M.R., Urbauer, J.L. & Wand, A.J. The energetics and dynamics of molecular recognition by calmodulin. Biochemistry 34, 2731-2738 (1995).
-
(1995)
Biochemistry
, vol.34
, pp. 2731-2738
-
-
Ehrhardt, M.R.1
Urbauer, J.L.2
Wand, A.J.3
-
38
-
-
0036468397
-
Coupling of folding and binding for unstructured proteins
-
Dyson, H.J. & Wright, P.E. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12, 54-60 (2002).
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 54-60
-
-
Dyson, H.J.1
Wright, P.E.2
-
39
-
-
0032479048
-
13C NMR relaxation data
-
DOI 10.1021/ja972215n
-
Chatfield, D.C., Szabo, A. & Brooks, B.R. Molecular dynamics of staphylococcal nuclease: comparison of simulation with 15N and 13C NMR relaxation data. J. Am. Chem. Soc. 120, 5301-5311 (1998). (Pubitemid 28328893)
-
(1998)
Journal of the American Chemical Society
, vol.120
, Issue.21
, pp. 5301-5311
-
-
Chatfield, D.C.1
Szabo, A.2
Brooks, B.R.3
-
40
-
-
0037457815
-
Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics
-
Prabhu, N.V., Lee, A.L., Wand, A.J. & Sharp, K.A. Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics. Biochemistry 42, 562-570 (2003).
-
(2003)
Biochemistry
, vol.42
, pp. 562-570
-
-
Prabhu, N.V.1
Lee, A.L.2
Wand, A.J.3
Sharp, K.A.4
-
41
-
-
35948943745
-
Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: Application to the AMBER99SB force field
-
Showalter, S.A. & Brüschweiler, R. Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: application to the AMBER99SB force field. J. Chem. Theory Comput. 3, 961-975 (2007).
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 961-975
-
-
Showalter, S.A.1
Brüschweiler, R.2
-
42
-
-
67650529401
-
A dictionary for protein side-chain entropies from NMR order parameters
-
Li, D.W. & Brüschweiler, R. A dictionary for protein side-chain entropies from NMR order parameters. J. Am. Chem. Soc. 131, 7226-7227 (2009).
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 7226-7227
-
-
Li, D.W.1
Brüschweiler, R.2
-
43
-
-
0037202183
-
Contact model for the prediction of NMR N-H order parameters in globular proteins
-
DOI 10.1021/ja027847a
-
Zhang, F. & Brüschweiler, R. Contact model for the prediction of NMR N-H order parameters in globular proteins. J. Am. Chem. Soc. 124, 12654-12655 (2002). (Pubitemid 35215977)
-
(2002)
Journal of the American Chemical Society
, vol.124
, Issue.43
, pp. 12654-12655
-
-
Zhang, F.1
Bruschweiler, R.2
-
44
-
-
63749108613
-
In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides
-
Li, D.W. & Brüschweiler, R. In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides. Phys. Rev. Lett. 102, 118108 (2009).
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 118108
-
-
Li, D.W.1
Brüschweiler, R.2
-
45
-
-
64049102289
-
Binding of small-molecular ligands to proteins: "What you see" is not always "what you get"
-
Mobley, D.L. & Dill, K.A. Binding of small-molecular ligands to proteins: "What you see" is not always "What you get". Structure 17, 489-498 (2009).
-
(2009)
Structure
, vol.17
, pp. 489-498
-
-
Mobley, D.L.1
Dill, K.A.2
-
46
-
-
0037053380
-
A direct test of the reductionist approach to structural studies of calmodulin activity: Relevance of peptide models of target proteins
-
Kranz, J.K., Lee, E.K., Nairn, A.C. & Wand, A.J. A direct test of the reductionist approach to structural studies of calmodulin activity: relevance of peptide models of target proteins. J. Biol. Chem. 277, 16351-16354 (2002).
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 16351-16354
-
-
Kranz, J.K.1
Lee, E.K.2
Nairn, A.C.3
Wand, A.J.4
-
47
-
-
0024402002
-
Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporine A
-
Dellwo, M.J. & Wand, A.J. Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporine A. J. Am. Chem. Soc. 111, 4571-4578 (1989).
-
(1989)
J. Am. Chem. Soc.
, vol.111
, pp. 4571-4578
-
-
Dellwo, M.J.1
Wand, A.J.2
-
48
-
-
0034809982
-
Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: Application to methionine residues in a cavity mutant of T4 lysozyme
-
DOI 10.1021/ja004179p
-
Skrynnikov, N.R., Mulder, F.A.A., Hon, B., Dahlquist, F.W. & Kay, L.E. Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 123, 4556-4566 (2001). (Pubitemid 32923384)
-
(2001)
Journal of the American Chemical Society
, vol.123
, Issue.19
, pp. 4556-4566
-
-
Skrynnikov, N.R.1
Mulder, F.A.A.2
Hon, B.3
Dahlquist, F.W.4
Kay, L.E.5
-
49
-
-
0028103275
-
The CCP4 suite: Programs for protein crystallography
-
Collaborative Computational Project Number 4
-
Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
-
(1994)
Acta Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
|