-
1
-
-
0037022683
-
Network of coupled promoting motions in enzyme catalysis
-
P.K. Agarwal, S.R. Billeter, P.T. Rajagopalan, S.J. Benkovic, and S. Hammes-Schiffer Network of coupled promoting motions in enzyme catalysis Proc. Natl. Acad. Sci. USA 99 2002 2794 2799
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 2794-2799
-
-
Agarwal, P.K.1
Billeter, S.R.2
Rajagopalan, P.T.3
Benkovic, S.J.4
Hammes-Schiffer, S.5
-
2
-
-
0029050533
-
Deficiency of retinoblastoma protein leads to inappropriate S-phase entry, activation of E2F-responsive genes, and apoptosis
-
A. Almasan, Y. Yin, R.E. Kelly, E.Y. Lee, A. Bradley, W. Li, J.R. Bertino, and G.M. Wahl Deficiency of retinoblastoma protein leads to inappropriate S-phase entry, activation of E2F-responsive genes, and apoptosis Proc. Natl. Acad. Sci. USA 92 1995 5436 5440
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 5436-5440
-
-
Almasan, A.1
Yin, Y.2
Kelly, R.E.3
Lee, E.Y.4
Bradley, A.5
Li, W.6
Bertino, J.R.7
Wahl, G.M.8
-
3
-
-
0041821836
-
A perspective on enzyme catalysis
-
S.J. Benkovic, and S. Hammes-Schiffer A perspective on enzyme catalysis Science 301 2003 1196 1202
-
(2003)
Science
, vol.301
, pp. 1196-1202
-
-
Benkovic, S.J.1
Hammes-Schiffer, S.2
-
4
-
-
79953823548
-
A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
-
G. Bhabha, J. Lee, D.C. Ekiert, J. Gam, I.A. Wilson, H.J. Dyson, S.J. Benkovic, and P.E. Wright A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis Science 332 2011 234 238
-
(2011)
Science
, vol.332
, pp. 234-238
-
-
Bhabha, G.1
Lee, J.2
Ekiert, D.C.3
Gam, J.4
Wilson, I.A.5
Dyson, H.J.6
Benkovic, S.J.7
Wright, P.E.8
-
5
-
-
33748781457
-
The dynamic energy landscape of dihydrofolate reductase catalysis
-
D.D. Boehr, D. McElheny, H.J. Dyson, and P.E. Wright The dynamic energy landscape of dihydrofolate reductase catalysis Science 313 2006 1638 1642
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
6
-
-
76549109225
-
Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands
-
D.D. Boehr, D. McElheny, H.J. Dyson, and P.E. Wright Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands Proc. Natl. Acad. Sci. USA 107 2010 1373 1378
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 1373-1378
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
7
-
-
48449087454
-
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
-
D.K. Breslow, D.M. Cameron, S.R. Collins, M. Schuldiner, J. Stewart-Ornstein, H.W. Newman, S. Braun, H.D. Madhani, N.J. Krogan, and J.S. Weissman A comprehensive strategy enabling high-resolution functional analysis of the yeast genome Nat. Methods 5 2008 711 718
-
(2008)
Nat. Methods
, vol.5
, pp. 711-718
-
-
Breslow, D.K.1
Cameron, D.M.2
Collins, S.R.3
Schuldiner, M.4
Stewart-Ornstein, J.5
Newman, H.W.6
Braun, S.7
Madhani, H.D.8
Krogan, N.J.9
Weissman, J.S.10
-
8
-
-
35348942279
-
Allosteric communication in dihydrofolate reductase: Signaling network and pathways for closed to occluded transition and back
-
J. Chen, R.I. Dima, and D. Thirumalai Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back J. Mol. Biol. 374 2007 250 266
-
(2007)
J. Mol. Biol.
, vol.374
, pp. 250-266
-
-
Chen, J.1
Dima, R.I.2
Thirumalai, D.3
-
9
-
-
33746911627
-
Dynamic coupling and allosteric behavior in a nonallosteric protein
-
M.W. Clarkson, S.A. Gilmore, M.H. Edgell, and A.L. Lee Dynamic coupling and allosteric behavior in a nonallosteric protein Biochemistry 45 2006 7693 7699
-
(2006)
Biochemistry
, vol.45
, pp. 7693-7699
-
-
Clarkson, M.W.1
Gilmore, S.A.2
Edgell, M.H.3
Lee, A.L.4
-
10
-
-
48249141040
-
Allostery and cooperativity revisited
-
Q. Cui, and M. Karplus Allostery and cooperativity revisited Protein Sci. 17 2008 1295 1307
-
(2008)
Protein Sci.
, vol.17
, pp. 1295-1307
-
-
Cui, Q.1
Karplus, M.2
-
11
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
E.Z. Eisenmesser, O. Millet, W. Labeikovsky, D.M. Korzhnev, M. Wolf-Watz, D.A. Bosco, J.J. Skalicky, L.E. Kay, and D. Kern Intrinsic dynamics of an enzyme underlies catalysis Nature 438 2005 117 121
-
(2005)
Nature
, vol.438
, 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
-
12
-
-
33846300981
-
Signal transduction pathway of TonB-dependent transporters
-
A.D. Ferguson, C.A. Amezcua, N.M. Halabi, Y. Chelliah, M.K. Rosen, R. Ranganathan, and J. Deisenhofer Signal transduction pathway of TonB-dependent transporters Proc. Natl. Acad. Sci. USA 104 2007 513 518
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 513-518
-
-
Ferguson, A.D.1
Amezcua, C.A.2
Halabi, N.M.3
Chelliah, Y.4
Rosen, M.K.5
Ranganathan, R.6
Deisenhofer, J.7
-
13
-
-
0023668190
-
Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
-
C.A. Fierke, K.A. Johnson, and S.J. Benkovic Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli Biochemistry 26 1987 4085 4092
-
(1987)
Biochemistry
, vol.26
, pp. 4085-4092
-
-
Fierke, C.A.1
Johnson, K.A.2
Benkovic, S.J.3
-
14
-
-
71449103005
-
Hidden alternative structures of proline isomerase essential for catalysis
-
J.S. Fraser, M.W. Clarkson, S.C. Degnan, R. Erion, D. Kern, and T. Alber Hidden alternative structures of proline isomerase essential for catalysis Nature 462 2009 669 673
-
(2009)
Nature
, vol.462
, pp. 669-673
-
-
Fraser, J.S.1
Clarkson, M.W.2
Degnan, S.C.3
Erion, R.4
Kern, D.5
Alber, T.6
-
15
-
-
0034464742
-
Uncovering molecular mechanisms involved in activation of G protein-coupled receptors
-
U. Gether Uncovering molecular mechanisms involved in activation of G protein-coupled receptors Endocr. Rev. 21 2000 90 113
-
(2000)
Endocr. Rev.
, vol.21
, pp. 90-113
-
-
Gether, U.1
-
16
-
-
68749107059
-
Protein sectors: Evolutionary units of three-dimensional structure
-
N. Halabi, O. Rivoire, S. Leibler, and R. Ranganathan Protein sectors: evolutionary units of three-dimensional structure Cell 138 2009 774 786
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
17
-
-
37049002915
-
N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa
-
A.S. Halavaty, and K. Moffat N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa Biochemistry 46 2007 14001 14009
-
(2007)
Biochemistry
, vol.46
, pp. 14001-14009
-
-
Halavaty, A.S.1
Moffat, K.2
-
18
-
-
0141707094
-
Structural basis of a phototropin light switch
-
S.M. Harper, L.C. Neil, and K.H. Gardner Structural basis of a phototropin light switch Science 301 2003 1541 1544
-
(2003)
Science
, vol.301
, pp. 1541-1544
-
-
Harper, S.M.1
Neil, L.C.2
Gardner, K.H.3
-
19
-
-
0345492351
-
Allosteric determinants in guanine nucleotide-binding proteins
-
M.E. Hatley, S.W. Lockless, S.K. Gibson, A.G. Gilman, and R. Ranganathan Allosteric determinants in guanine nucleotide-binding proteins Proc. Natl. Acad. Sci. USA 100 2003 14445 14450
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 14445-14450
-
-
Hatley, M.E.1
Lockless, S.W.2
Gibson, S.K.3
Gilman, A.G.4
Ranganathan, R.5
-
20
-
-
37249067732
-
The origin of protein interactions and allostery in colocalization
-
J. Kuriyan, and D. Eisenberg The origin of protein interactions and allostery in colocalization Nature 450 2007 983 990
-
(2007)
Nature
, vol.450
, pp. 983-990
-
-
Kuriyan, J.1
Eisenberg, D.2
-
21
-
-
54249105941
-
Surface sites for engineering allosteric control in proteins
-
J. Lee, M. Natarajan, V.C. Nashine, M. Socolich, T. Vo, W.P. Russ, S.J. Benkovic, and R. Ranganathan Surface sites for engineering allosteric control in proteins Science 322 2008 438 442
-
(2008)
Science
, vol.322
, pp. 438-442
-
-
Lee, J.1
Natarajan, M.2
Nashine, V.C.3
Socolich, M.4
Vo, T.5
Russ, W.P.6
Benkovic, S.J.7
Ranganathan, R.8
-
22
-
-
66149157329
-
Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K(+) channels
-
S.Y. Lee, A. Banerjee, and R. MacKinnon Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K(+) channels PLoS Biol. 7 2009 e47
-
(2009)
PLoS Biol.
, vol.7
, pp. 47
-
-
Lee, S.Y.1
Banerjee, A.2
MacKinnon, R.3
-
23
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
S.W. Lockless, and R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 286 1999 295 299
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
24
-
-
0036088602
-
The linkage between protein folding and functional cooperativity: Two sides of the same coin?
-
I. Luque, S.A. Leavitt, and E. Freire The linkage between protein folding and functional cooperativity: two sides of the same coin? Annu. Rev. Biophys. Biomol. Struct. 31 2002 235 256
-
(2002)
Annu. Rev. Biophys. Biomol. Struct.
, vol.31
, pp. 235-256
-
-
Luque, I.1
Leavitt, S.A.2
Freire, E.3
-
25
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
E.M. Marcotte, M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates, and D. Eisenberg Detecting protein function and protein-protein interactions from genome sequences Science 285 1999 751 753
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
26
-
-
17044401342
-
Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis
-
D. McElheny, J.R. Schnell, J.C. Lansing, H.J. Dyson, and P.E. Wright Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis Proc. Natl. Acad. Sci. USA 102 2005 5032 5037
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 5032-5037
-
-
McElheny, D.1
Schnell, J.R.2
Lansing, J.C.3
Dyson, H.J.4
Wright, P.E.5
-
27
-
-
0034784920
-
Rhodopsin: Structural basis of molecular physiology
-
S.T. Menon, M. Han, and T.P. Sakmar Rhodopsin: structural basis of molecular physiology Physiol. Rev. 81 2001 1659 1688
-
(2001)
Physiol. Rev.
, vol.81
, pp. 1659-1688
-
-
Menon, S.T.1
Han, M.2
Sakmar, T.P.3
-
28
-
-
72849144434
-
Sequencing technologies - The next generation
-
M.L. Metzker Sequencing technologies - the next generation Nat. Rev. Genet. 11 2010 31 46
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
29
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
J. Monod, J. Wyman, and J.P. Changeux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 1965 88 118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
30
-
-
0032055632
-
CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90
-
M. Niethammer, J.G. Valtschanoff, T.M. Kapoor, D.W. Allison, R.J. Weinberg, A.M. Craig, and M. Sheng CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90 Neuron 20 1998 693 707
-
(1998)
Neuron
, vol.20
, pp. 693-707
-
-
Niethammer, M.1
Valtschanoff, J.G.2
Kapoor, T.M.3
Allison, D.W.4
Weinberg, R.J.5
Craig, A.M.6
Sheng, M.7
-
31
-
-
0012927828
-
PDZ domain proteins: Plug and play!
-
C. Nourry, S.G. Grant, and J.P. Borg PDZ domain proteins: plug and play! Sci. STKE 2003 2003 RE7
-
(2003)
Sci. STKE
, vol.2003
, pp. 7
-
-
Nourry, C.1
Grant, S.G.2
Borg, J.P.3
-
32
-
-
1642276423
-
Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition
-
F.C. Peterson, R.R. Penkert, B.F. Volkman, and K.E. Prehoda Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition Mol. Cell 13 2004 665 676
-
(2004)
Mol. Cell
, vol.13
, pp. 665-676
-
-
Peterson, F.C.1
Penkert, R.R.2
Volkman, B.F.3
Prehoda, K.E.4
-
33
-
-
0002902139
-
Preorganization and protein dynamics in enzyme catalysis
-
P.T. Rajagopalan, and S.J. Benkovic Preorganization and protein dynamics in enzyme catalysis Chem. Rec. 2 2002 24 36
-
(2002)
Chem. Rec.
, vol.2
, pp. 24-36
-
-
Rajagopalan, P.T.1
Benkovic, S.J.2
-
34
-
-
0037159205
-
Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates
-
P.T. Rajagopalan, S. Lutz, and S.J. Benkovic Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates Biochemistry 41 2002 12618 12628
-
(2002)
Biochemistry
, vol.41
, pp. 12618-12628
-
-
Rajagopalan, P.T.1
Lutz, S.2
Benkovic, S.J.3
-
35
-
-
25644442464
-
Natural-like function in artificial WW domains
-
W.P. Russ, D.M. Lowery, P. Mishra, M.B. Yaffe, and R. Ranganathan Natural-like function in artificial WW domains Nature 437 2005 579 583
-
(2005)
Nature
, vol.437
, pp. 579-583
-
-
Russ, W.P.1
Lowery, D.M.2
Mishra, P.3
Yaffe, M.B.4
Ranganathan, R.5
-
36
-
-
38049148291
-
Principles underlying energetic coupling along an allosteric communication trajectory of a voltage-activated K+ channel
-
E. Sadovsky, and O. Yifrach Principles underlying energetic coupling along an allosteric communication trajectory of a voltage-activated K+ channel Proc. Natl. Acad. Sci. USA 104 2007 19813 19818
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 19813-19818
-
-
Sadovsky, E.1
Yifrach, O.2
-
37
-
-
0035940398
-
An optomechanical transducer in the blue light receptor phototropin from Avena sativa
-
M. Salomon, W. Eisenreich, H. Dürr, E. Schleicher, E. Knieb, V. Massey, W. Rüdiger, F. Müller, A. Bacher, and G. Richter An optomechanical transducer in the blue light receptor phototropin from Avena sativa Proc. Natl. Acad. Sci. USA 98 2001 12357 12361
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12357-12361
-
-
Salomon, M.1
Eisenreich, W.2
Dürr, H.3
Schleicher, E.4
Knieb, E.5
Massey, V.6
Rüdiger, W.7
Müller, F.8
Bacher, A.9
Richter, G.10
-
39
-
-
3042660150
-
Structure, dynamics, and catalytic function of dihydrofolate reductase
-
J.R. Schnell, H.J. Dyson, and P.E. Wright Structure, dynamics, and catalytic function of dihydrofolate reductase Annu. Rev. Biophys. Biomol. Struct. 33 2004 119 140
-
(2004)
Annu. Rev. Biophys. Biomol. Struct.
, vol.33
, pp. 119-140
-
-
Schnell, J.R.1
Dyson, H.J.2
Wright, P.E.3
-
40
-
-
1642304065
-
Structural determinants of allosteric ligand activation in RXR heterodimers
-
A.I. Shulman, C. Larson, D.J. Mangelsdorf, and R. Ranganathan Structural determinants of allosteric ligand activation in RXR heterodimers Cell 116 2004 417 429
-
(2004)
Cell
, vol.116
, pp. 417-429
-
-
Shulman, A.I.1
Larson, C.2
Mangelsdorf, D.J.3
Ranganathan, R.4
-
41
-
-
64849111005
-
Sending signals dynamically
-
R.G. Smock, and L.M. Gierasch Sending signals dynamically Science 324 2009 198 203
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
42
-
-
77957274298
-
An interdomain sector mediating allostery in Hsp70 molecular chaperones
-
R.G. Smock, O. Rivoire, W.P. Russ, J.F. Swain, S. Leibler, R. Ranganathan, and L.M. Gierasch An interdomain sector mediating allostery in Hsp70 molecular chaperones Mol. Syst. Biol. 6 2010 414
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 414
-
-
Smock, R.G.1
Rivoire, O.2
Russ, W.P.3
Swain, J.F.4
Leibler, S.5
Ranganathan, R.6
Gierasch, L.M.7
-
43
-
-
25644452032
-
Evolutionary information for specifying a protein fold
-
M. Socolich, S.W. Lockless, W.P. Russ, H. Lee, K.H. Gardner, and R. Ranganathan Evolutionary information for specifying a protein fold Nature 437 2005 512 518
-
(2005)
Nature
, vol.437
, pp. 512-518
-
-
Socolich, M.1
Lockless, S.W.2
Russ, W.P.3
Lee, H.4
Gardner, K.H.5
Ranganathan, R.6
-
44
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
G.M. Süel, S.W. Lockless, M.A. Wall, and R. Ranganathan Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nat. Struct. Biol. 10 2003 59 69
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 59-69
-
-
Süel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
45
-
-
33747153121
-
Ploidy controls the success of mutators and nature of mutations during budding yeast evolution
-
D.A. Thompson, M.M. Desai, and A.W. Murray Ploidy controls the success of mutators and nature of mutations during budding yeast evolution Curr. Biol. 16 2006 1581 1590
-
(2006)
Curr. Biol.
, vol.16
, pp. 1581-1590
-
-
Thompson, D.A.1
Desai, M.M.2
Murray, A.W.3
-
46
-
-
0037131520
-
Energetics of pore opening in a voltage-gated K(+) channel
-
O. Yifrach, and R. MacKinnon Energetics of pore opening in a voltage-gated K(+) channel Cell 111 2002 231 239
-
(2002)
Cell
, vol.111
, pp. 231-239
-
-
Yifrach, O.1
MacKinnon, R.2
-
47
-
-
68749107059
-
Protein sectors: Evolutionary units of three-dimensional structure
-
Halabi, N.; Rivoire, O.; Leibler, S.; and Ranganathan, R. (2009). Protein sectors: evolutionary units of three-dimensional structure. Cell 138, 774-786.
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
48
-
-
54249105941
-
Surface sites for engineering allosteric control in proteins
-
Lee, J.; Natarajan, M.; Nashine, V.C.; Socolich, M.; Vo, T.; Russ, W.P.; Benkovic, S.J.; and Ranganathan, R. (2008). Surface sites for engineering allosteric control in proteins. Science 322, 438-442.
-
(2008)
Science
, vol.322
, pp. 438-442
-
-
Lee, J.1
Natarajan, M.2
Nashine, V.C.3
Socolich, M.4
Vo, T.5
Russ, W.P.6
Benkovic, S.J.7
Ranganathan, R.8
-
49
-
-
1642529522
-
FamClash: A method for ranking the activity of engineered enzymes
-
Saraf, M.C.; Horswill, A.R.; Benkovic, S.J.; and Maranas, C.D. (2004). FamClash: a method for ranking the activity of engineered enzymes. Proc. Natl. Acad. Sci. USA 101, 4142-4147.
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(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4142-4147
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Saraf, M.C.1
Horswill, A.R.2
Benkovic, S.J.3
Maranas, C.D.4
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