-
1
-
-
77953607331
-
The mechanical properties of PCNA: Implications for the loading and function of a DNA sliding clamp
-
J.L. Adelman, J.D. Chodera, I.F. Kuo, T.F. Miller 3rd, and D. Barsky The mechanical properties of PCNA: implications for the loading and function of a DNA sliding clamp Biophys. J. 98 2010 3062 3069
-
(2010)
Biophys. J.
, vol.98
, pp. 3062-3069
-
-
Adelman, J.L.1
Chodera, J.D.2
Kuo, I.F.3
Miller III, T.F.4
Barsky, D.5
-
2
-
-
0033564238
-
Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution
-
S.C. Alley, V.K. Shier, E. Abel-Santos, D.J. Sexton, P. Soumillion, and S.J. Benkovic Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution Biochemistry 38 1999 7696 7709
-
(1999)
Biochemistry
, vol.38
, pp. 7696-7709
-
-
Alley, S.C.1
Shier, V.K.2
Abel-Santos, E.3
Sexton, D.J.4
Soumillion, P.5
Benkovic, S.J.6
-
3
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
I. Bahar, T.R. Lezon, L.W. Yang, and E. Eyal Global dynamics of proteins: bridging between structure and function Annu. Rev. Biophys. 39 2010 23 42
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.W.3
Eyal, E.4
-
4
-
-
0027250665
-
Primary structure effects on peptide group hydrogen exchange
-
Y. Bai, J.S. Milne, L. Mayne, and S.W. Englander Primary structure effects on peptide group hydrogen exchange Proteins 17 1993 75 86
-
(1993)
Proteins
, vol.17
, pp. 75-86
-
-
Bai, Y.1
Milne, J.S.2
Mayne, L.3
Englander, S.W.4
-
5
-
-
84863903852
-
How proteins slide on DNA
-
M.C. Williams, I. Maher, L. James, Springer New York
-
D. Barsky, T.A. Laurence, and Č. Venclovas How proteins slide on DNA M.C. Williams, I. Maher, L. James, Biophysics of DNA-Protein Interactions: From Single Molecules to Biological Systems 2011 Springer New York 39 68
-
(2011)
Biophysics of DNA-Protein Interactions: From Single Molecules to Biological Systems
, pp. 39-68
-
-
Barsky, D.1
Laurence, T.A.2
Venclovas, Č.3
-
6
-
-
3042588011
-
Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex
-
G.D. Bowman, M. O'Donnell, and J. Kuriyan Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex Nature 429 2004 724 730
-
(2004)
Nature
, vol.429
, pp. 724-730
-
-
Bowman, G.D.1
O'Donnell, M.2
Kuriyan, J.3
-
8
-
-
33947715332
-
The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding
-
S. Chen, S. Brier, T.E. Smithgall, and J.R. Engen The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding Protein Sci. 16 2007 572 581
-
(2007)
Protein Sci.
, vol.16
, pp. 572-581
-
-
Chen, S.1
Brier, S.2
Smithgall, T.E.3
Engen, J.R.4
-
9
-
-
0035949599
-
A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems
-
B.P. Dalrymple, K. Kongsuwan, G. Wijffels, N.E. Dixon, and P.A. Jennings A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems Proc. Natl. Acad. Sci. USA 98 2001 11627 11632
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 11627-11632
-
-
Dalrymple, B.P.1
Kongsuwan, K.2
Wijffels, G.3
Dixon, N.E.4
Jennings, P.A.5
-
10
-
-
33846823909
-
Particle mesh Ewald - An N.Log(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle mesh Ewald - an N.Log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
11
-
-
79951996226
-
Reduced stability and increased dynamics in the human proliferating cell nuclear antigen (PCNA) relative to the yeast homolog
-
A. De Biasio, R. Sánchez, J. Prieto, M. Villate, R. Campos-Olivas, and F.J. Blanco Reduced stability and increased dynamics in the human proliferating cell nuclear antigen (PCNA) relative to the yeast homolog PLoS ONE 6 2011 e16600
-
(2011)
PLoS ONE
, vol.6
, pp. 16600
-
-
De Biasio, A.1
Sánchez, R.2
Prieto, J.3
Villate, M.4
Campos-Olivas, R.5
Blanco, F.J.6
-
12
-
-
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
-
13
-
-
0020855355
-
Hydrogen exchange and structural dynamics of proteins and nucleic acids
-
S.W. Englander, and N.R. Kallenbach Hydrogen exchange and structural dynamics of proteins and nucleic acids Q. Rev. Biophys. 16 1983 521 655
-
(1983)
Q. Rev. Biophys.
, vol.16
, pp. 521-655
-
-
Englander, S.W.1
Kallenbach, N.R.2
-
15
-
-
79959799630
-
Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution
-
J. Fang, J.R. Engen, and P.J. Beuning Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution Biochemistry 50 2011 5958 5968
-
(2011)
Biochemistry
, vol.50
, pp. 5958-5968
-
-
Fang, J.1
Engen, J.R.2
Beuning, P.J.3
-
16
-
-
0026320866
-
The energy landscapes and motions of proteins
-
H. Frauenfelder, S.G. Sligar, and P.G. Wolynes The energy landscapes and motions of proteins Science 254 1991 1598 1603
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
17
-
-
84886597018
-
Structural and functional importance of local and global conformational fluctuations in the RNase A superfamily
-
D. Gagné, and N. Doucet Structural and functional importance of local and global conformational fluctuations in the RNase A superfamily FEBS J. 280 2013 5596 5607
-
(2013)
FEBS J.
, vol.280
, pp. 5596-5607
-
-
Gagné, D.1
Doucet, N.2
-
18
-
-
84871735453
-
Conservation of flexible residue clusters among structural and functional enzyme homologues
-
D. Gagné, L.A. Charest, S. Morin, E.L. Kovrigin, and N. Doucet Conservation of flexible residue clusters among structural and functional enzyme homologues J. Biol. Chem. 287 2012 44289 44300
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 44289-44300
-
-
Gagné, D.1
Charest, L.A.2
Morin, S.3
Kovrigin, E.L.4
Doucet, N.5
-
19
-
-
0031666414
-
Analogous enzymes: Independent inventions in enzyme evolution
-
M.Y. Galperin, D.R. Walker, and E.V. Koonin Analogous enzymes: independent inventions in enzyme evolution Genome Res. 8 1998 779 790
-
(1998)
Genome Res.
, vol.8
, pp. 779-790
-
-
Galperin, M.Y.1
Walker, D.R.2
Koonin, E.V.3
-
20
-
-
84875686450
-
Structural dynamics flexibility informs function and evolution at a proteome scale
-
Z.N. Gerek, S. Kumar, and S.B. Ozkan Structural dynamics flexibility informs function and evolution at a proteome scale Evol. Appl. 6 2013 423 433
-
(2013)
Evol. Appl.
, vol.6
, pp. 423-433
-
-
Gerek, Z.N.1
Kumar, S.2
Ozkan, S.B.3
-
21
-
-
63049084861
-
The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS
-
S.J. Geromanos, J.P. Vissers, J.C. Silva, C.A. Dorschel, G.Z. Li, M.V. Gorenstein, R.H. Bateman, and J.I. Langridge The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS Proteomics 9 2009 1683 1695
-
(2009)
Proteomics
, vol.9
, pp. 1683-1695
-
-
Geromanos, S.J.1
Vissers, J.P.2
Silva, J.C.3
Dorschel, C.A.4
Li, G.Z.5
Gorenstein, M.V.6
Bateman, R.H.7
Langridge, J.I.8
-
22
-
-
0030592544
-
Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA
-
J.M. Gulbis, Z. Kelman, J. Hurwitz, M. O'Donnell, and J. Kuriyan Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA Cell 87 1996 297 306
-
(1996)
Cell
, vol.87
, pp. 297-306
-
-
Gulbis, J.M.1
Kelman, Z.2
Hurwitz, J.3
O'Donnell, M.4
Kuriyan, J.5
-
23
-
-
36749083505
-
Illuminating the mechanistic roles of enzyme conformational dynamics
-
J.A. Hanson, K. Duderstadt, L.P. Watkins, S. Bhattacharyya, J. Brokaw, J.W. Chu, and H. Yang Illuminating the mechanistic roles of enzyme conformational dynamics Proc. Natl. Acad. Sci. USA 104 2007 18055 18060
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 18055-18060
-
-
Hanson, J.A.1
Duderstadt, K.2
Watkins, L.P.3
Bhattacharyya, S.4
Brokaw, J.5
Chu, J.W.6
Yang, H.7
-
24
-
-
66549119395
-
Advances and pitfalls of protein structural alignment
-
H. Hasegawa, and L. Holm Advances and pitfalls of protein structural alignment Curr. Opin. Struct. Biol. 19 2009 341 348
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 341-348
-
-
Hasegawa, H.1
Holm, L.2
-
26
-
-
84860995211
-
Exploring protein dynamics space: The dynasome as the missing link between protein structure and function
-
U. Hensen, T. Meyer, J. Haas, R. Rex, G. Vriend, and H. Grubmüller Exploring protein dynamics space: the dynasome as the missing link between protein structure and function PLoS ONE 7 2012 e33931
-
(2012)
PLoS ONE
, vol.7
, pp. 33931
-
-
Hensen, U.1
Meyer, T.2
Haas, J.3
Rex, R.4
Vriend, G.5
Grubmüller, H.6
-
27
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
29
-
-
0000277207
-
Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions
-
A. Hvidt, and K. Linderstrøm-Lang Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions Biochim. Biophys. Acta 14 1954 574 575
-
(1954)
Biochim. Biophys. Acta
, vol.14
, pp. 574-575
-
-
Hvidt, A.1
Linderstrøm-Lang, K.2
-
31
-
-
0037195243
-
Monomeric yeast PCNA mutants are defective in interacting with and stimulating the ATPase activity of RFC
-
C.N. Ionescu, K.A. Shea, R. Mehra, L. Prundeanu, and M.A. McAlear Monomeric yeast PCNA mutants are defective in interacting with and stimulating the ATPase activity of RFC Biochemistry 41 2002 12975 12985
-
(2002)
Biochemistry
, vol.41
, pp. 12975-12985
-
-
Ionescu, C.N.1
Shea, K.A.2
Mehra, R.3
Prundeanu, L.4
McAlear, M.A.5
-
32
-
-
33845625617
-
Proliferating cell nuclear antigen loaded onto double-stranded DNA: Dynamics, minor groove interactions and functional implications
-
I. Ivanov, B.R. Chapados, J.A. McCammon, and J.A. Tainer Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications Nucleic Acids Res. 34 2006 6023 6033
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 6023-6033
-
-
Ivanov, I.1
Chapados, B.R.2
McCammon, J.A.3
Tainer, J.A.4
-
33
-
-
0035943342
-
Crystal structure of the processivity clamp loader gamma (gamma) complex of E. Coli DNA polymerase III
-
D. Jeruzalmi, M. O'Donnell, and J. Kuriyan Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III Cell 106 2001 429 441
-
(2001)
Cell
, vol.106
, pp. 429-441
-
-
Jeruzalmi, D.1
O'Donnell, M.2
Kuriyan, J.3
-
34
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
35
-
-
25444469141
-
Out-of-plane motions in open sliding clamps: Molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen
-
S.L. Kazmirski, Y. Zhao, G.D. Bowman, M. O'donnell, and J. Kuriyan Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen Proc. Natl. Acad. Sci. USA 102 2005 13801 13806
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13801-13806
-
-
Kazmirski, S.L.1
Zhao, Y.2
Bowman, G.D.3
O'Donnell, M.4
Kuriyan, J.5
-
36
-
-
84455163347
-
How a DNA polymerase clamp loader opens a sliding clamp
-
B.A. Kelch, D.L. Makino, M. O'Donnell, and J. Kuriyan How a DNA polymerase clamp loader opens a sliding clamp Science 334 2011 1675 1680
-
(2011)
Science
, vol.334
, pp. 1675-1680
-
-
Kelch, B.A.1
Makino, D.L.2
O'Donnell, M.3
Kuriyan, J.4
-
37
-
-
0029163487
-
Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps
-
Z. Kelman, and M. O'Donnell Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps Nucleic Acids Res. 23 1995 3613 3620
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 3613-3620
-
-
Kelman, Z.1
O'Donnell, M.2
-
38
-
-
67650531111
-
Proliferating cell nuclear antigen uses two distinct modes to move along DNA
-
A.B. Kochaniak, S. Habuchi, J.J. Loparo, D.J. Chang, K.A. Cimprich, J.C. Walter, and A.M. van Oijen Proliferating cell nuclear antigen uses two distinct modes to move along DNA J. Biol. Chem. 284 2009 17700 17710
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 17700-17710
-
-
Kochaniak, A.B.1
Habuchi, S.2
Loparo, J.J.3
Chang, D.J.4
Cimprich, K.A.5
Walter, J.C.6
Van Oijen, A.M.7
-
39
-
-
13844316580
-
Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design
-
G. Kontopidis, S.Y. Wu, D.I. Zheleva, P. Taylor, C. McInnes, D.P. Lane, P.M. Fischer, and M.D. Walkinshaw Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design Proc. Natl. Acad. Sci. USA 102 2005 1871 1876
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 1871-1876
-
-
Kontopidis, G.1
Wu, S.Y.2
Zheleva, D.I.3
Taylor, P.4
McInnes, C.5
Lane, D.P.6
Fischer, P.M.7
Walkinshaw, M.D.8
-
40
-
-
0028618183
-
Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA
-
T.S. Krishna, X.P. Kong, S. Gary, P.M. Burgers, and J. Kuriyan Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA Cell 79 1994 1233 1243
-
(1994)
Cell
, vol.79
, pp. 1233-1243
-
-
Krishna, T.S.1
Kong, X.P.2
Gary, S.3
Burgers, P.M.4
Kuriyan, J.5
-
41
-
-
0031614960
-
Proteins from hyperthermophiles: Stability and enzymatic catalysis close to the boiling point of water
-
R. Ladenstein, and G. Antranikian Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water Adv. Biochem. Eng. Biotechnol. 61 1998 37 85
-
(1998)
Adv. Biochem. Eng. Biotechnol.
, vol.61
, pp. 37-85
-
-
Ladenstein, R.1
Antranikian, G.2
-
42
-
-
79952610080
-
Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis
-
J.E. Ladner, M. Pan, J. Hurwitz, and Z. Kelman Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis Proc. Natl. Acad. Sci. USA 108 2011 2711 2716
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 2711-2716
-
-
Ladner, J.E.1
Pan, M.2
Hurwitz, J.3
Kelman, Z.4
-
43
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, and S. Ha et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
44
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
A.D. Mackerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
46
-
-
4944231970
-
On the solution structure of the T4 sliding clamp (gp45)
-
D. Millar, M.A. Trakselis, and S.J. Benkovic On the solution structure of the T4 sliding clamp (gp45) Biochemistry 43 2004 12723 12727
-
(2004)
Biochemistry
, vol.43
, pp. 12723-12727
-
-
Millar, D.1
Trakselis, M.A.2
Benkovic, S.J.3
-
47
-
-
25444480278
-
Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis
-
T. Miyata, H. Suzuki, T. Oyama, K. Mayanagi, Y. Ishino, and K. Morikawa Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis Proc. Natl. Acad. Sci. USA 102 2005 13795 13800
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 13795-13800
-
-
Miyata, T.1
Suzuki, H.2
Oyama, T.3
Mayanagi, K.4
Ishino, Y.5
Morikawa, K.6
-
48
-
-
0034628915
-
Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage
-
I. Moarefi, D. Jeruzalmi, J. Turner, M. O'Donnell, and J. Kuriyan Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage J. Mol. Biol. 296 2000 1215 1223
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1215-1223
-
-
Moarefi, I.1
Jeruzalmi, D.2
Turner, J.3
O'Donnell, M.4
Kuriyan, J.5
-
49
-
-
0027671977
-
Overproduction and purification of sigma 32, the Escherichia coli heat shock transcription factor
-
L.H. Nguyen, D.B. Jensen, and R.R. Burgess Overproduction and purification of sigma 32, the Escherichia coli heat shock transcription factor Protein Expr. Purif. 4 1993 425 433
-
(1993)
Protein Expr. Purif.
, vol.4
, pp. 425-433
-
-
Nguyen, L.H.1
Jensen, D.B.2
Burgess, R.R.3
-
50
-
-
84926811618
-
Constant pressure molecular dynamics for molecular systems
-
S. Nose, and M.L. Klein Constant pressure molecular dynamics for molecular systems Mol. Phys. 50 1983 1055 1076
-
(1983)
Mol. Phys.
, vol.50
, pp. 1055-1076
-
-
Nose, S.1
Klein, M.L.2
-
51
-
-
0038455931
-
Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III
-
A.J. Oakley, P. Prosselkov, G. Wijffels, J.L. Beck, M.C. Wilce, and N.E. Dixon Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III Acta Crystallogr. D Biol. Crystallogr. 59 2003 1192 1199
-
(2003)
Acta Crystallogr. D Biol. Crystallogr.
, vol.59
, pp. 1192-1199
-
-
Oakley, A.J.1
Prosselkov, P.2
Wijffels, G.3
Beck, J.L.4
Wilce, M.C.5
Dixon, N.E.6
-
52
-
-
28644451763
-
Comparative molecular dynamics - Similar folds and similar motions?
-
A. Pang, Y. Arinaminpathy, M.S. Sansom, and P.C. Biggin Comparative molecular dynamics - similar folds and similar motions? Proteins 61 2005 809 822
-
(2005)
Proteins
, vol.61
, pp. 809-822
-
-
Pang, A.1
Arinaminpathy, Y.2
Sansom, M.S.3
Biggin, P.C.4
-
53
-
-
18244380348
-
High-density miniaturized thermal shift assays as a general strategy for drug discovery
-
M.W. Pantoliano, E.C. Petrella, J.D. Kwasnoski, V.S. Lobanov, J. Myslik, E. Graf, T. Carver, E. Asel, B.A. Springer, P. Lane, and F.R. Salemme High-density miniaturized thermal shift assays as a general strategy for drug discovery J. Biomol. Screen. 6 2001 429 440
-
(2001)
J. Biomol. Screen.
, vol.6
, pp. 429-440
-
-
Pantoliano, M.W.1
Petrella, E.C.2
Kwasnoski, J.D.3
Lobanov, V.S.4
Myslik, J.5
Graf, E.6
Carver, T.7
Asel, E.8
Springer, B.A.9
Lane, P.10
Salemme, F.R.11
-
54
-
-
0019707626
-
Polymorphic transitions in single crystals - A new molecular dynamics method
-
M. Parrinello, and A. Rahman Polymorphic transitions in single crystals - a new molecular dynamics method J. Appl. Phys. 52 1981 7182 7190
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
55
-
-
42449090264
-
PROMALS3D: A tool for multiple protein sequence and structure alignments
-
J. Pei, B.-H. Kim, and N.V. Grishin PROMALS3D: a tool for multiple protein sequence and structure alignments Nucleic Acids Res. 36 2008 2295 2300
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2295-2300
-
-
Pei, J.1
Kim, B.-H.2
Grishin, N.V.3
-
56
-
-
84877707944
-
DNTP-dependent conformational transitions in the fingers subdomain of Klentaq1 DNA polymerase: Insights into the role of the "nucleotide- binding" state
-
P.J. Rothwell, W.J. Allen, E. Sisamakis, S. Kalinin, S. Felekyan, J. Widengren, G. Waksman, and C.A. Seidel dNTP-dependent conformational transitions in the fingers subdomain of Klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state J. Biol. Chem. 288 2013 13575 13591
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 13575-13591
-
-
Rothwell, P.J.1
Allen, W.J.2
Sisamakis, E.3
Kalinin, S.4
Felekyan, S.5
Widengren, J.6
Waksman, G.7
Seidel, C.A.8
-
57
-
-
0024348537
-
The 44P subunit of the T4 DNA polymerase accessory protein complex catalyzes ATP hydrolysis
-
J. Rush, T.C. Lin, M. Quinones, E.K. Spicer, I. Douglas, K.R. Williams, and W.H. Konigsberg The 44P subunit of the T4 DNA polymerase accessory protein complex catalyzes ATP hydrolysis J. Biol. Chem. 264 1989 10943 10953
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 10943-10953
-
-
Rush, J.1
Lin, T.C.2
Quinones, M.3
Spicer, E.K.4
Douglas, I.5
Williams, K.R.6
Konigsberg, W.H.7
-
58
-
-
20144367589
-
Structural basis for recruitment of human flap endonuclease 1 to PCNA
-
S. Sakurai, K. Kitano, H. Yamaguchi, K. Hamada, K. Okada, K. Fukuda, M. Uchida, E. Ohtsuka, H. Morioka, and T. Hakoshima Structural basis for recruitment of human flap endonuclease 1 to PCNA EMBO J. 24 2005 683 693
-
(2005)
EMBO J.
, vol.24
, pp. 683-693
-
-
Sakurai, S.1
Kitano, K.2
Yamaguchi, H.3
Hamada, K.4
Okada, K.5
Fukuda, K.6
Uchida, M.7
Ohtsuka, E.8
Morioka, H.9
Hakoshima, T.10
-
59
-
-
84876902448
-
Transitions to catalytically inactive conformations in EGFR kinase
-
Y. Shan, A. Arkhipov, E.T. Kim, A.C. Pan, and D.E. Shaw Transitions to catalytically inactive conformations in EGFR kinase Proc. Natl. Acad. Sci. USA 110 2013 7270 7275
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 7270-7275
-
-
Shan, Y.1
Arkhipov, A.2
Kim, E.T.3
Pan, A.C.4
Shaw, D.E.5
-
60
-
-
68849094697
-
Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment
-
W. Strzalka, T. Oyama, K. Tori, and K. Morikawa Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment Protein Sci. 18 2009 1072 1080
-
(2009)
Protein Sci.
, vol.18
, pp. 1072-1080
-
-
Strzalka, W.1
Oyama, T.2
Tori, K.3
Morikawa, K.4
-
61
-
-
64849101493
-
Protein dynamism and evolvability
-
N. Tokuriki, and D.S. Tawfik Protein dynamism and evolvability Science 324 2009 203 207
-
(2009)
Science
, vol.324
, pp. 203-207
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
62
-
-
80055097282
-
Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
-
S.E. Tsutakawa, A.W. Van Wynsberghe, B.D. Freudenthal, C.P. Weinacht, L. Gakhar, M.T. Washington, Z. Zhuang, J.A. Tainer, and I. Ivanov Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA Proc. Natl. Acad. Sci. USA 108 2011 17672 17677
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 17672-17677
-
-
Tsutakawa, S.E.1
Van Wynsberghe, A.W.2
Freudenthal, B.D.3
Weinacht, C.P.4
Gakhar, L.5
Washington, M.T.6
Zhuang, Z.7
Tainer, J.A.8
Ivanov, I.9
-
63
-
-
9144258471
-
Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iota
-
A.E. Vidal, P. Kannouche, V.N. Podust, W. Yang, A.R. Lehmann, and R. Woodgate Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase iota J. Biol. Chem. 279 2004 48360 48368
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 48360-48368
-
-
Vidal, A.E.1
Kannouche, P.2
Podust, V.N.3
Yang, W.4
Lehmann, A.R.5
Woodgate, R.6
-
64
-
-
0037523309
-
The diverse spectrum of sliding clamp interacting proteins
-
J.B. Vivona, and Z. Kelman The diverse spectrum of sliding clamp interacting proteins FEBS Lett. 546 2003 167 172
-
(2003)
FEBS Lett.
, vol.546
, pp. 167-172
-
-
Vivona, J.B.1
Kelman, Z.2
-
65
-
-
33644761306
-
Hydrogen exchange mass spectrometry for the analysis of protein dynamics
-
T.E. Wales, and J.R. Engen Hydrogen exchange mass spectrometry for the analysis of protein dynamics Mass Spectrom. Rev. 25 2006 158 170
-
(2006)
Mass Spectrom. Rev.
, vol.25
, pp. 158-170
-
-
Wales, T.E.1
Engen, J.R.2
-
66
-
-
33645073892
-
Partial unfolding of diverse SH3 domains on a wide timescale
-
T.E. Wales, and J.R. Engen Partial unfolding of diverse SH3 domains on a wide timescale J. Mol. Biol. 357 2006 1592 1604
-
(2006)
J. Mol. Biol.
, vol.357
, pp. 1592-1604
-
-
Wales, T.E.1
Engen, J.R.2
-
67
-
-
51549121010
-
High-speed and high-resolution UPLC separation at zero degrees Celsius
-
T.E. Wales, K.E. Fadgen, G.C. Gerhardt, and J.R. Engen High-speed and high-resolution UPLC separation at zero degrees Celsius Anal. Chem. 80 2008 6815 6820
-
(2008)
Anal. Chem.
, vol.80
, pp. 6815-6820
-
-
Wales, T.E.1
Fadgen, K.E.2
Gerhardt, G.C.3
Engen, J.R.4
-
68
-
-
0036463721
-
Hydrogen exchange-mass spectrometry: Optimization of digestion conditions
-
L. Wang, H. Pan, and D.L. Smith Hydrogen exchange-mass spectrometry: optimization of digestion conditions Mol. Cell. Proteomics 1 2002 132 138
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 132-138
-
-
Wang, L.1
Pan, H.2
Smith, D.L.3
-
69
-
-
0032031972
-
PCNA binding through a conserved motif
-
E. Warbrick PCNA binding through a conserved motif Bioessays 20 1998 195 199
-
(1998)
Bioessays
, vol.20
, pp. 195-199
-
-
Warbrick, E.1
-
70
-
-
33749326831
-
Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis
-
D.D. Weis, T.E. Wales, J.R. Engen, M. Hotchko, and L.F. Ten Eyck Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis J. Am. Soc. Mass Spectrom. 17 2006 1498 1509
-
(2006)
J. Am. Soc. Mass Spectrom.
, vol.17
, pp. 1498-1509
-
-
Weis, D.D.1
Wales, T.E.2
Engen, J.R.3
Hotchko, M.4
Ten Eyck, L.F.5
-
71
-
-
33846847773
-
Conformational transitions of adenylate kinase: Switching by cracking
-
P.C. Whitford, O. Miyashita, Y. Levy, and J.N. Onuchic Conformational transitions of adenylate kinase: switching by cracking J. Mol. Biol. 366 2007 1661 1671
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
72
-
-
0029678248
-
Clamp loading, unloading and intrinsic stability of the PCNA, beta and gp45 sliding clamps of human, E. Coli and T4 replicases
-
N. Yao, J. Turner, Z. Kelman, P.T. Stukenberg, F. Dean, D. Shechter, Z.Q. Pan, J. Hurwitz, and M. O'Donnell Clamp loading, unloading and intrinsic stability of the PCNA, beta and gp45 sliding clamps of human, E. coli and T4 replicases Genes Cells 1 1996 101 113
-
(1996)
Genes Cells
, vol.1
, pp. 101-113
-
-
Yao, N.1
Turner, J.2
Kelman, Z.3
Stukenberg, P.T.4
Dean, F.5
Shechter, D.6
Pan, Z.Q.7
Hurwitz, J.8
O'Donnell, M.9
-
73
-
-
0027529263
-
Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation
-
Z. Zhang, and D.L. Smith Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation Protein Sci. 2 1993 522 531
-
(1993)
Protein Sci.
, vol.2
, pp. 522-531
-
-
Zhang, Z.1
Smith, D.L.2
|