-
1
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
DOI 10.1038/nature04105, PII N04105
-
Eisenmesser, E. Z., Millet, O., Labeikovsky, W., Korzhnev, D. M., Wolf-Watz, M., Bosco, D. A., Skalicky, J. J., Kay, L. E., and Kern, D. (2005) Intrinsic dynamics of an enzyme underlies catalysis Nature 438, 117-121 (Pubitemid 41599831)
-
(2005)
Nature
, vol.438
, Issue.7064
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
2
-
-
33748781457
-
The dynamic energy landscape of dihydrofolate reductase catalysis
-
Boehr, D. D., McElheny, D., Dyson, H. J., and Wright, P. E. (2006) The dynamic energy landscape of dihydrofolate reductase catalysis Science 313, 1638-1642
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
3
-
-
0242268469
-
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
-
Miyashita, O., Onuchic, J. N., and Wolynes, P. G. (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc. Natl. Acad. Sci. U.S.A. 100, 12570-12575
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
4
-
-
64849111005
-
Sending signals dynamically
-
Smock, R. G. and Gierasch, L. M. (2009) Sending signals dynamically Science 324, 198-203
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
5
-
-
18144418170
-
Protein structural change upon ligand binding: Linear response theory
-
Ikeguchi, M., Ueno, J., Sato, M., and Kidera, A. (2005) Protein structural change upon ligand binding: Linear response theory Phys. Rev. Lett. 94, 078102
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 078102
-
-
Ikeguchi, M.1
Ueno, J.2
Sato, M.3
Kidera, A.4
-
6
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague, S. J. (2003) Implications of protein flexibility for drug discovery Nat. Rev. Drug Discovery 2, 527-541
-
(2003)
Nat. Rev. Drug Discovery
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
7
-
-
64849101493
-
Protein dynamism and evolvability
-
Tokuriki, N. and Tawfik, D. S. (2009) Protein dynamism and evolvability Science 324, 203-207
-
(2009)
Science
, vol.324
, pp. 203-207
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
8
-
-
0037414270
-
Effect of mutation on enzyme motion in dihydrofolate reductase
-
Watney, J. B., Agarwal, P. K., and Hammes-Schiffer, S. (2003) Effect of mutation on enzyme motion in dihydrofolate reductase J. Am. Chem. Soc. 125, 3745-3750
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 3745-3750
-
-
Watney, J.B.1
Agarwal, P.K.2
Hammes-Schiffer, S.3
-
9
-
-
38049123828
-
Long range communication in the envelope protein domain III and its effect on the resistance of West Nile virus to antibody-mediated neutralization
-
Maillard, R. A., Jordan, M., Beasley, D. W., Barrett, A. D., and Lee, J. C. (2008) Long range communication in the envelope protein domain III and its effect on the resistance of West Nile virus to antibody-mediated neutralization J. Biol. Chem. 283, 613-622
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 613-622
-
-
Maillard, R.A.1
Jordan, M.2
Beasley, D.W.3
Barrett, A.D.4
Lee, J.C.5
-
10
-
-
4744347909
-
Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c
-
Clarkson, M. W. and Lee, A. L. (2004) Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c Biochemistry 43, 12448-12458
-
(2004)
Biochemistry
, vol.43
, pp. 12448-12458
-
-
Clarkson, M.W.1
Lee, A.L.2
-
11
-
-
31144470854
-
The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment
-
Pizzitutti, F., Giansanti, A., Ballario, P., Ornaghi, P., Torreri, P., Ciccotti, G., and Filetici, P. (2006) The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment J. Mol. Recognit. 19, 1-9
-
(2006)
J. Mol. Recognit.
, vol.19
, pp. 1-9
-
-
Pizzitutti, F.1
Giansanti, A.2
Ballario, P.3
Ornaghi, P.4
Torreri, P.5
Ciccotti, G.6
Filetici, P.7
-
12
-
-
0034710950
-
Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
-
Pan, H., Lee, J. C., and Hilser, V. J. (2000) Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble Proc. Natl. Acad. Sci. U.S.A. 97, 12020-12025
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 12020-12025
-
-
Pan, H.1
Lee, J.C.2
Hilser, V.J.3
-
13
-
-
0033618337
-
Matrix metalloproteinases
-
Nagase, H. and Woessner, J. F., Jr. (1999) Matrix metalloproteinases J. Biol. Chem. 274, 21491-21494
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 21491-21494
-
-
Nagase, H.1
Woessner, Jr.J.F.2
-
14
-
-
0035188727
-
How matrix metalloproteinases regulate cell behavior
-
Sternlicht, M. D. and Werb, Z. (2001) How matrix metalloproteinases regulate cell behavior Annu. Rev. Cell. Dev Biol. 17, 463-516
-
(2001)
Annu. Rev. Cell. Dev Biol.
, vol.17
, pp. 463-516
-
-
Sternlicht, M.D.1
Werb, Z.2
-
15
-
-
34648815810
-
Emerging roles of proteases in tumour suppression
-
Lopez-Otin, C. and Matrisian, L. M. (2007) Emerging roles of proteases in tumour suppression Nat. Rev. Cancer 7, 800-808
-
(2007)
Nat. Rev. Cancer
, vol.7
, pp. 800-808
-
-
Lopez-Otin, C.1
Matrisian, L.M.2
-
16
-
-
33847195428
-
Matrix metalloproteinases and the regulation of tissue remodelling
-
Page-McCaw, A., Ewald, A. J., and Werb, Z. (2007) Matrix metalloproteinases and the regulation of tissue remodelling Nat. Rev. Mol. Cell Biol. 8, 221-233
-
(2007)
Nat. Rev. Mol. Cell Biol.
, vol.8
, pp. 221-233
-
-
Page-Mccaw, A.1
Ewald, A.J.2
Werb, Z.3
-
17
-
-
0029150795
-
Proteolytic remodeling of extracellular matrix
-
Birkedal-Hansen, H. (1995) Proteolytic remodeling of extracellular matrix Curr. Opin. Cell Biol. 7, 728-735
-
(1995)
Curr. Opin. Cell Biol.
, vol.7
, pp. 728-735
-
-
Birkedal-Hansen, H.1
-
18
-
-
1842377505
-
Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1
-
Gomis-Ruth, F. X., Maskos, K., Betz, M., Bergner, A., Huber, R., Suzuki, K., Yoshida, N., Nagase, H., Brew, K., Bourenkov, G. P., Bartunik, H., and Bode, W. (1997) Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1 Nature 389, 77-81
-
(1997)
Nature
, vol.389
, pp. 77-81
-
-
Gomis-Ruth, F.X.1
Maskos, K.2
Betz, M.3
Bergner, A.4
Huber, R.5
Suzuki, K.6
Yoshida, N.7
Nagase, H.8
Brew, K.9
Bourenkov, G.P.10
Bartunik, H.11
Bode, W.12
-
19
-
-
0032509104
-
Three-dimensional structure of human tissue inhibitor of metalloproteinases-2 at 2.1 resolution
-
Tuuttila, A., Morgunova, E., Bergmann, U., Lindqvist, Y., Maskos, K., Fernandez-Catalan, C., Bode, W., Tryggvason, K., and Schneider, G. (1998) Three-dimensional structure of human tissue inhibitor of metalloproteinases-2 at 2.1 resolution J. Mol. Biol. 284, 1133-1140
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1133-1140
-
-
Tuuttila, A.1
Morgunova, E.2
Bergmann, U.3
Lindqvist, Y.4
Maskos, K.5
Fernandez-Catalan, C.6
Bode, W.7
Tryggvason, K.8
Schneider, G.9
-
20
-
-
0027973352
-
Solution structure of the active domain of tissue inhibitor of metalloproteinases-2. A new member of the OB fold protein family
-
Williamson, R. A., Martorell, G., Carr, M. D., Murphy, G., Docherty, A. J., Freedman, R. B., and Feeney, J. (1994) Solution structure of the active domain of tissue inhibitor of metalloproteinases-2. A new member of the OB fold protein family Biochemistry 33, 11745-11759
-
(1994)
Biochemistry
, vol.33
, pp. 11745-11759
-
-
Williamson, R.A.1
Martorell, G.2
Carr, M.D.3
Murphy, G.4
Docherty, A.J.5
Freedman, R.B.6
Feeney, J.7
-
21
-
-
0032167522
-
Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor
-
Fernandez-Catalan, C., Bode, W., Huber, R., Turk, D., Calvete, J. J., Lichte, A., Tschesche, H., and Maskos, K. (1998) Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor EMBO J. 17, 5238-5248
-
(1998)
EMBO J.
, vol.17
, pp. 5238-5248
-
-
Fernandez-Catalan, C.1
Bode, W.2
Huber, R.3
Turk, D.4
Calvete, J.J.5
Lichte, A.6
Tschesche, H.7
Maskos, K.8
-
22
-
-
33846675236
-
Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2
-
Maskos, K., Lang, R., Tschesche, H., and Bode, W. (2007) Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2 J. Mol. Biol. 366, 1222-1231
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1222-1231
-
-
Maskos, K.1
Lang, R.2
Tschesche, H.3
Bode, W.4
-
23
-
-
0029876136
-
Folding and characterization of the amino-terminal domain of human tissue inhibitor of metalloproteinases-1 (TIMP-1) expressed at high yield in E. coli
-
Huang, W., Suzuki, K., Nagase, H., Arumugam, S., Van Doren, S. R., and Brew, K. (1996) Folding and characterization of the amino-terminal domain of human tissue inhibitor of metalloproteinases-1 (TIMP-1) expressed at high yield in E. coli FEBS Lett. 384, 155-161
-
(1996)
FEBS Lett.
, vol.384
, pp. 155-161
-
-
Huang, W.1
Suzuki, K.2
Nagase, H.3
Arumugam, S.4
Van Doren, S.R.5
Brew, K.6
-
24
-
-
0025944065
-
The N-terminal domain of tissue inhibitor of metalloproteinases retains metalloproteinase inhibitory activity
-
Murphy, G., Houbrechts, A., Cockett, M. I., Williamson, R. A., OShea, M., and Docherty, A. J. (1991) The N-terminal domain of tissue inhibitor of metalloproteinases retains metalloproteinase inhibitory activity Biochemistry 30, 8097-8102
-
(1991)
Biochemistry
, vol.30
, pp. 8097-8102
-
-
Murphy, G.1
Houbrechts, A.2
Cockett, M.I.3
Williamson, R.A.4
Oshea, M.5
Docherty, A.J.6
-
25
-
-
0028279004
-
Different domain interactions are involved in the binding of tissue inhibitors of metalloproteinases to stromelysin-1 and gelatinase A
-
Nguyen, Q., Willenbrock, F., Cockett, M. I., OShea, M., Docherty, A. J., and Murphy, G. (1994) Different domain interactions are involved in the binding of tissue inhibitors of metalloproteinases to stromelysin-1 and gelatinase A Biochemistry 33, 2089-2095
-
(1994)
Biochemistry
, vol.33
, pp. 2089-2095
-
-
Nguyen, Q.1
Willenbrock, F.2
Cockett, M.I.3
Oshea, M.4
Docherty, A.J.5
Murphy, G.6
-
26
-
-
0034805593
-
Full-length and N-TIMP-3 display equal inhibitory activities toward TNF-α convertase
-
Lee, M. H., Knauper, V., Becherer, J. D., and Murphy, G. (2001) Full-length and N-TIMP-3 display equal inhibitory activities toward TNF-α convertase Biochem. Biophys. Res. Commun. 280, 945-950
-
(2001)
Biochem. Biophys. Res. Commun.
, vol.280
, pp. 945-950
-
-
Lee, M.H.1
Knauper, V.2
Becherer, J.D.3
Murphy, G.4
-
27
-
-
0030577022
-
Activation of a recombinant membrane type 1-matrix metalloproteinase (MT1-MMP) by furin and its interaction with tissue inhibitor of metalloproteinases (TIMP)-2
-
Sato, H., Kinoshita, T., Takino, T., Nakayama, K., and Seiki, M. (1996) Activation of a recombinant membrane type 1-matrix metalloproteinase (MT1-MMP) by furin and its interaction with tissue inhibitor of metalloproteinases (TIMP)-2 FEBS Lett. 393, 101-104
-
(1996)
FEBS Lett.
, vol.393
, pp. 101-104
-
-
Sato, H.1
Kinoshita, T.2
Takino, T.3
Nakayama, K.4
Seiki, M.5
-
28
-
-
0030016342
-
The soluble catalytic domain of membrane type 1 matrix metalloproteinase cleaves the propeptide of progelatinase A and initiates autoproteolytic activation. Regulation by TIMP-2 and TIMP-3
-
Will, H., Atkinson, S. J., Butler, G. S., Smith, B., and Murphy, G. (1996) The soluble catalytic domain of membrane type 1 matrix metalloproteinase cleaves the propeptide of progelatinase A and initiates autoproteolytic activation. Regulation by TIMP-2 and TIMP-3 J. Biol. Chem. 271, 17119-17123
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 17119-17123
-
-
Will, H.1
Atkinson, S.J.2
Butler, G.S.3
Smith, B.4
Murphy, G.5
-
29
-
-
0347130906
-
Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP specific features
-
Lang, R., Braun, M., Sounni, N. E., Noel, A., Frankenne, F., Foidart, J. M., Bode, W., and Maskos, K. (2004) Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP specific features J. Mol. Biol. 336, 213-225
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 213-225
-
-
Lang, R.1
Braun, M.2
Sounni, N.E.3
Noel, A.4
Frankenne, F.5
Foidart, J.M.6
Bode, W.7
Maskos, K.8
-
30
-
-
2342427576
-
Threonine 98, the pivotal residue of tissue inhibitor of metalloproteinases (TIMP)-1 in metalloproteinase recognition
-
Lee, M. H., Rapti, M., Knauper, V., and Murphy, G. (2004) Threonine 98, the pivotal residue of tissue inhibitor of metalloproteinases (TIMP)-1 in metalloproteinase recognition J. Biol. Chem. 279, 17562-17569
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 17562-17569
-
-
Lee, M.H.1
Rapti, M.2
Knauper, V.3
Murphy, G.4
-
31
-
-
0036786494
-
Mapping and characterization of the functional epitopes of tissue inhibitor of metalloproteinases (TIMP)-3 using TIMP-1 as the scaffold: A new frontier in TIMP engineering
-
Lee, M. H., Maskos, K., Knauper, V., Dodds, P., and Murphy, G. (2002) Mapping and characterization of the functional epitopes of tissue inhibitor of metalloproteinases (TIMP)-3 using TIMP-1 as the scaffold: A new frontier in TIMP engineering Protein Sci. 11, 2493-2503
-
(2002)
Protein Sci.
, vol.11
, pp. 2493-2503
-
-
Lee, M.H.1
Maskos, K.2
Knauper, V.3
Dodds, P.4
Murphy, G.5
-
32
-
-
0002067212
-
Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions
-
Dudek, M. J., Ramnarayan, K., and Ponder, J. W. (1998) Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions J. Comput. Chem. 19, 548-573
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 548-573
-
-
Dudek, M.J.1
Ramnarayan, K.2
Ponder, J.W.3
-
33
-
-
4444221565
-
UCSF Chimera: A visualization system for exploratory research and analysis
-
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera: A visualization system for exploratory research and analysis J. Comput. Chem. 25, 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
34
-
-
0001486104
-
GROMOS force field
-
In, Vol., John Wiley & Sons, New York
-
Van Gunsteren, W. F., Daura, X., and Mark, A. (1998) GROMOS force field. In Encyclopedia of Computational Chemistry, Vol. 2, John Wiley & Sons, New York.
-
(1998)
Encyclopedia of Computational Chemistry
, vol.2
-
-
Van Gunsteren, W.F.1
Daura, X.2
Mark, A.3
-
35
-
-
0008819754
-
The GROMOS Biomolecular Simulation Program Package
-
Scott, W. R. P., Hnenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krger, P., and Van Gunsteren, W. F. (1999) The GROMOS Biomolecular Simulation Program Package J. Phys. Chem. A 103, 3596-3607
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hnenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Krger, P.9
Van Gunsteren, W.F.10
-
36
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath J. Chem. Phys. 81, 3684
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
37
-
-
0001351515
-
Estimation of Absolute and Relative Entropies of Macromolecules Using the Covariance-Matrix
-
Schlitter, J. (1993) Estimation of Absolute and Relative Entropies of Macromolecules Using the Covariance-Matrix Chem. Phys. Lett. 215, 617-621
-
(1993)
Chem. Phys. Lett.
, vol.215
, pp. 617-621
-
-
Schlitter, J.1
-
38
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276, 307-326
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
39
-
-
0000952473
-
On the treatment of negative intensity observations
-
French, G. S. and Wilson, K. S. (1978) On the treatment of negative intensity observations Acta Crystallogr. A34, 517-525
-
(1978)
Acta Crystallogr.
, vol.34
, pp. 517-525
-
-
French, G.S.1
Wilson, K.S.2
-
40
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. D53, 240-255
-
(1997)
Acta Crystallogr.
, vol.53
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
41
-
-
13244281317
-
Coot: Model-building tools for molecular graphics
-
Emsley, P. and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics Acta Crystallogr. D60, 2126-2132
-
(2004)
Acta Crystallogr.
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
42
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
Chen, V. B., Arendall, W. B., III, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., and Richardson, D. C. (2010) MolProbity: All-atom structure validation for macromolecular crystallography Acta Crystallogr. D66, 12-21
-
(2010)
Acta Crystallogr.
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
Arendall III, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
-
43
-
-
3843091516
-
Anchor residues in protein-protein interactions
-
Rajamani, D., Thiel, S., Vajda, S., and Camacho, C. J. (2004) Anchor residues in protein-protein interactions Proc. Natl. Acad. Sci. U.S.A. 101, 11287-11292
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 11287-11292
-
-
Rajamani, D.1
Thiel, S.2
Vajda, S.3
Camacho, C.J.4
-
44
-
-
0141959313
-
Unveiling the surface epitopes that render tissue inhibitor of metalloproteinase-1 inactive against membrane type 1-matrix metalloproteinase
-
Lee, M. H., Rapti, M., and Murphy, G. (2003) Unveiling the surface epitopes that render tissue inhibitor of metalloproteinase-1 inactive against membrane type 1-matrix metalloproteinase J. Biol. Chem. 278, 40224-40230
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 40224-40230
-
-
Lee, M.H.1
Rapti, M.2
Murphy, G.3
-
45
-
-
33645994825
-
Flexibility and conformational entropy in protein-protein binding
-
Grunberg, R., Nilges, M., and Leckner, J. (2006) Flexibility and conformational entropy in protein-protein binding Structure 14, 683-693
-
(2006)
Structure
, vol.14
, pp. 683-693
-
-
Grunberg, R.1
Nilges, M.2
Leckner, J.3
-
46
-
-
0037470616
-
Increased backbone mobility in β-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3
-
Arumugam, S., Gao, G., Patton, B. L., Semenchenko, V., Brew, K., and Van Doren, S. R. (2003) Increased backbone mobility in β-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3 J. Mol. Biol. 327, 719-734
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 719-734
-
-
Arumugam, S.1
Gao, G.2
Patton, B.L.3
Semenchenko, V.4
Brew, K.5
Van Doren, S.R.6
-
47
-
-
17244369458
-
Conformational variability of matrix metalloproteinases: Beyond a single 3D structure
-
Bertini, I., Calderone, V., Cosenza, M., Fragai, M., Lee, Y. M., Luchinat, C., Mangani, S., Terni, B., and Turano, P. (2005) Conformational variability of matrix metalloproteinases: Beyond a single 3D structure Proc. Natl. Acad. Sci. U.S.A. 102, 5334-5339
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 5334-5339
-
-
Bertini, I.1
Calderone, V.2
Cosenza, M.3
Fragai, M.4
Lee, Y.M.5
Luchinat, C.6
Mangani, S.7
Terni, B.8
Turano, P.9
-
48
-
-
33847007324
-
Crystal structure of the catalytic domain of matrix metalloproteinase-1 in complex with the inhibitory domain of tissue inhibitor of metalloproteinase-1
-
Iyer, S., Wei, S., Brew, K., and Acharya, K. R. (2007) Crystal structure of the catalytic domain of matrix metalloproteinase-1 in complex with the inhibitory domain of tissue inhibitor of metalloproteinase-1 J. Biol. Chem. 282, 364-371
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 364-371
-
-
Iyer, S.1
Wei, S.2
Brew, K.3
Acharya, K.R.4
-
49
-
-
34547460183
-
Molecular evolution of affinity and flexibility in the immune system
-
Thorpe, I. F. and Brooks, C. L., III (2007) Molecular evolution of affinity and flexibility in the immune system Proc. Natl. Acad. Sci. U.S.A. 104, 8821-8826
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 8821-8826
-
-
Thorpe, I.F.1
Brooks III, C.L.2
-
50
-
-
16244382605
-
Modulating the DNA affinity of Elk-1 with computationally selected mutations
-
Park, S., Boder, E. T., and Saven, J. G. (2005) Modulating the DNA affinity of Elk-1 with computationally selected mutations J. Mol. Biol. 348, 75-83
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 75-83
-
-
Park, S.1
Boder, E.T.2
Saven, J.G.3
-
51
-
-
67650561836
-
Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity
-
Manson, A., Whitten, S. T., Ferreon, J. C., Fox, R. O., and Hilser, V. J. (2009) Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity J. Am. Chem. Soc. 131, 6785-6793
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 6785-6793
-
-
Manson, A.1
Whitten, S.T.2
Ferreon, J.C.3
Fox, R.O.4
Hilser, V.J.5
-
52
-
-
70350131719
-
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins
-
Schrank, T. P., Bolen, D. W., and Hilser, V. J. (2009) Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins Proc. Natl. Acad. Sci. U.S.A. 106, 16984-16989
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 16984-16989
-
-
Schrank, T.P.1
Bolen, D.W.2
Hilser, V.J.3
-
53
-
-
34447503697
-
Conformational entropy in molecular recognition by proteins
-
Frederick, K. K., Marlow, M. S., Valentine, K. G., and Wand, A. J. (2007) Conformational entropy in molecular recognition by proteins Nature 448, 325-329
-
(2007)
Nature
, vol.448
, pp. 325-329
-
-
Frederick, K.K.1
Marlow, M.S.2
Valentine, K.G.3
Wand, A.J.4
-
54
-
-
70450191983
-
Dynamic activation of an allosteric regulatory protein
-
Tzeng, S. R. and Kalodimos, C. G. (2009) Dynamic activation of an allosteric regulatory protein Nature 462, 368-372
-
(2009)
Nature
, vol.462
, pp. 368-372
-
-
Tzeng, S.R.1
Kalodimos, C.G.2
-
55
-
-
0001651169
-
Design and therapeutic application of matrix metalloproteinase inhibitors
-
Whittaker, M., Floyd, C. D., Brown, P., and Gearing, A. J. (1999) Design and therapeutic application of matrix metalloproteinase inhibitors Chem. Rev. 99, 2735-2776
-
(1999)
Chem. Rev.
, vol.99
, pp. 2735-2776
-
-
Whittaker, M.1
Floyd, C.D.2
Brown, P.3
Gearing, A.J.4
-
56
-
-
15244350894
-
Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs
-
Cuniasse, P., Devel, L., Makaritis, A., Beau, F., Georgiadis, D., Matziari, A., Yiotakis, A., and Dive, V. (2005) Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs Biochimie 87, 393-402
-
(2005)
Biochimie
, vol.87
, pp. 393-402
-
-
Cuniasse, P.1
Devel, L.2
Makaritis, A.3
Beau, F.4
Georgiadis, D.5
Matziari, A.6
Yiotakis, A.7
Dive, V.8
-
57
-
-
15244350894
-
Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs
-
Cuniasse, P., Devel, L., Makaritis, A., Beau, F., Georgiadis, D., Matziari, M., Yiotakis, A., and Dive, V. (2005) Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs Biochimie 87, 393-402
-
(2005)
Biochimie
, vol.87
, pp. 393-402
-
-
Cuniasse, P.1
Devel, L.2
Makaritis, A.3
Beau, F.4
Georgiadis, D.5
Matziari, M.6
Yiotakis, A.7
Dive, V.8
-
58
-
-
34247593757
-
Key feature of the catalytic cycle of TNF-α converting enzyme involves communication between distal protein sites and the enzyme catalytic core
-
Solomon, A., Akabayov, B., Frenkel, A., Milla, M. E., and Sagi, I. (2007) Key feature of the catalytic cycle of TNF-α converting enzyme involves communication between distal protein sites and the enzyme catalytic core Proc. Natl. Acad. Sci. U.S.A. 104, 4931-4936
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 4931-4936
-
-
Solomon, A.1
Akabayov, B.2
Frenkel, A.3
Milla, M.E.4
Sagi, I.5
-
59
-
-
0033538059
-
Residue 2 of TIMP-1 is a major determinant of affinity and specificity for matrix metalloproteinases but effects of substitutions do not correlate with those of the corresponding P1′ residue of substrate
-
Meng, Q., Malinovskii, V., Huang, W., Hu, Y., Chung, L., Nagase, H., Bode, W., Maskos, K., and Brew, K. (1999) Residue 2 of TIMP-1 is a major determinant of affinity and specificity for matrix metalloproteinases but effects of substitutions do not correlate with those of the corresponding P1′ residue of substrate J. Biol. Chem. 274, 10184-10189
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 10184-10189
-
-
Meng, Q.1
Malinovskii, V.2
Huang, W.3
Hu, Y.4
Chung, L.5
Nagase, H.6
Bode, W.7
Maskos, K.8
Brew, K.9
-
60
-
-
34548436604
-
Constraining specificity in the N-domain of tissue inhibitor of metalloproteinases-1: Gelatinase-selective inhibitors
-
Hamze, A. B., Wei, S., Bahudhanapati, H., Kota, S., Acharya, K. R., and Brew, K. (2007) Constraining specificity in the N-domain of tissue inhibitor of metalloproteinases-1: Gelatinase-selective inhibitors Protein Sci. 16, 1905-1913
-
(2007)
Protein Sci.
, vol.16
, pp. 1905-1913
-
-
Hamze, A.B.1
Wei, S.2
Bahudhanapati, H.3
Kota, S.4
Acharya, K.R.5
Brew, K.6
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