-
1
-
-
0029893874
-
Mechanisms of helicase-catalyzed DNA unwinding
-
Lohman, T., and K. Bjornson. 1996. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:169-214.
-
(1996)
Annu. Rev. Biochem
, vol.65
, pp. 169-214
-
-
Lohman, T.1
Bjornson, K.2
-
3
-
-
0033987890
-
Helicases as nucleic acid unwinding machines
-
Waksman, G., E. Lanka, and J. Carazo. 2000. Helicases as nucleic acid unwinding machines. Nat. Struct. Biol. 7:20-22.
-
(2000)
Nat. Struct. Biol
, vol.7
, pp. 20-22
-
-
Waksman, G.1
Lanka, E.2
Carazo, J.3
-
4
-
-
0034479416
-
Crawling and wiggling on DNA: Structural insights to the mechanism of DNA unwinding by helicases
-
Marians, K. 2001. Crawling and wiggling on DNA: structural insights to the mechanism of DNA unwinding by helicases. Structure. 8:R227-R235.
-
(2001)
Structure
, vol.8
-
-
Marians, K.1
-
7
-
-
9144271294
-
Crystal structure of RecBCD reveals a machine for processing DNA breaks
-
Singleton, M., M. Dillingham, M. Gaudier, S. Kowalczykowski, and D. Wigley. 2004. Crystal structure of RecBCD reveals a machine for processing DNA breaks. Nature. 432:187-193.
-
(2004)
Nature
, vol.432
, pp. 187-193
-
-
Singleton, M.1
Dillingham, M.2
Gaudier, M.3
Kowalczykowski, S.4
Wigley, D.5
-
8
-
-
0033515425
-
Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism
-
Velankar, S., P. Soultanas, M. Dillingham, H. Subramanya, and D. Wigley. 1999. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell. 97:75-84.
-
(1999)
Cell
, vol.97
, pp. 75-84
-
-
Velankar, S.1
Soultanas, P.2
Dillingham, M.3
Subramanya, H.4
Wigley, D.5
-
9
-
-
0033428970
-
Helicase motifs: The engine that powers DNA unwinding
-
Hall, M., and S. Matson. 1999. Helicase motifs: the engine that powers DNA unwinding. Mol. Microbiol. 34:867-877.
-
(1999)
Mol. Microbiol
, vol.34
, pp. 867-877
-
-
Hall, M.1
Matson, S.2
-
10
-
-
0034635172
-
Demonstration of unidirectional single-stranded DNA translocatin by PcrA helicase: Measurement of step size and translocation speed
-
Dillingham, M., D. Wigley, and M. Webb. 2000. Demonstration of unidirectional single-stranded DNA translocatin by PcrA helicase: measurement of step size and translocation speed. Biochemistry. 39:205-212.
-
(2000)
Biochemistry
, vol.39
, pp. 205-212
-
-
Dillingham, M.1
Wigley, D.2
Webb, M.3
-
11
-
-
33748335314
-
Structure-based model of the stepping motor of PcrA helicase
-
Yu, J., T. Ha, and K. Schulten. 2006. Structure-based model of the stepping motor of PcrA helicase. Biophys. J. 91:2097-2114.
-
(2006)
Biophys. J
, vol.91
, pp. 2097-2114
-
-
Yu, J.1
Ha, T.2
Schulten, K.3
-
12
-
-
33748328253
-
PcrA helicase, a prototype ATP-driven molecular motor
-
Dittrich, M., and K. Schulten. 2006. PcrA helicase, a prototype ATP-driven molecular motor. Structure. 14:1345-1353.
-
(2006)
Structure
, vol.14
, pp. 1345-1353
-
-
Dittrich, M.1
Schulten, K.2
-
13
-
-
36849062952
-
PcrA helicase, a molecular motor studied from the electronic to the functional level
-
Dittrich, M., J. Yu, and K. Schulten. 2006. PcrA helicase, a molecular motor studied from the electronic to the functional level. Top. Curr. Chem. 268:319-347.
-
(2006)
Top. Curr. Chem
, vol.268
, pp. 319-347
-
-
Dittrich, M.1
Yu, J.2
Schulten, K.3
-
14
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
Isralewitz, B., M. Gao, and K. Schulten. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11:224-230.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 224-230
-
-
Isralewitz, B.1
Gao, M.2
Schulten, K.3
-
15
-
-
0003699033
-
-
Addison-Wesley, Reading, MA
-
Feynman, R., R. Leighton, and M. Sands. 1963. The Feynman lectures on physics. Addison-Wesley, Reading, MA.
-
(1963)
The Feynman lectures on physics
-
-
Feynman, R.1
Leighton, R.2
Sands, M.3
-
16
-
-
0031003997
-
Thermodynamics and kinetics of a Brownian motor
-
Astumian, R. 1997. Thermodynamics and kinetics of a Brownian motor. Science. 276:917-922.
-
(1997)
Science
, vol.276
, pp. 917-922
-
-
Astumian, R.1
-
17
-
-
0036681047
-
Ratchets, power strokes, and molecular motors
-
Wang, H., and G. Oster. 2002. Ratchets, power strokes, and molecular motors. App. Phys. A. 75:315-323.
-
(2002)
App. Phys. A
, vol.75
, pp. 315-323
-
-
Wang, H.1
Oster, G.2
-
18
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J., R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipote, R. Skeel, L. Kale, and K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipote, C.7
Skeel, R.8
Kale, L.9
Schulten, K.10
-
19
-
-
85031440652
-
-
MacKerell, A. D., Jr., C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry, 1. N. L. Allinger, T. Clark, J. Gasteiger, P. Kollman, and H. F. Schaefer III, editors, John Wiley & Sons, Chichester, UK. 271-277.
-
MacKerell, A. D., Jr., C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry, Vol. 1. N. L. Allinger, T. Clark, J. Gasteiger, P. Kollman, and H. F. Schaefer III, editors, John Wiley & Sons, Chichester, UK. 271-277.
-
-
-
-
20
-
-
0035449971
-
Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations
-
Batcho, P. F., D. A. Case, and T. Schlick. 2001. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J. Chem. Phys. 115:4003-4018.
-
(2001)
J. Chem. Phys
, vol.115
, pp. 4003-4018
-
-
Batcho, P.F.1
Case, D.A.2
Schlick, T.3
-
21
-
-
36449003554
-
Constant pressure molecular dynamics algorithms
-
Martyna, G. J., D. J. Tobias, and M. L. Klein. 1992. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 2:4177-4189.
-
(1992)
J. Chem. Phys
, vol.2
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
22
-
-
36449007836
-
Constant pressure molecular dynamics simulation - the Langevin piston method
-
Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation - the Langevin piston method. J. Chem. Phys. 103:4613-4621.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
23
-
-
85031441127
-
-
Brunger, A. T. 1992. X-PLOR, Version 3.1. A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT
-
Brunger, A. T. 1992. X-PLOR, Version 3.1. A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
-
-
-
-
24
-
-
0029092698
-
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations
-
Hünenberger, P. H., A. E. Mark, and W. F. van Gunsteren. 1995. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J. Mol. Biol. 252:492-503.
-
(1995)
J. Mol. Biol
, vol.252
, pp. 492-503
-
-
Hünenberger, P.H.1
Mark, A.E.2
van Gunsteren, W.F.3
-
25
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter atomic analysis
-
Tirion, M. 1996. Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys. Rev. Lett. 77:1905-1908.
-
(1996)
Phys. Rev. Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.1
-
26
-
-
0032533790
-
Analysis of domain motions in large proteins
-
Hinsen, K. 1998. Analysis of domain motions in large proteins. Proteins. 33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
27
-
-
13844276692
-
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
-
Zheng, W., and B. Brooks. 2005. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol. 346:745-759.
-
(2005)
J. Mol. Biol
, vol.346
, pp. 745-759
-
-
Zheng, W.1
Brooks, B.2
-
28
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless, S., and R. Ranganathan. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 286:295-299.
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.1
Ranganathan, R.2
-
29
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
Suel, G., S. Lockless, M. Wall, and R. Ranganathan. 2003. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10:59-69.
-
(2003)
Nat. Struct. Biol
, vol.10
, pp. 59-69
-
-
Suel, G.1
Lockless, S.2
Wall, M.3
Ranganathan, R.4
-
30
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S., W. Gish, W. Miller, E. Myers, and D. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
31
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S., T. Madden, A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schäffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
32
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J., D. Higgins, and T. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.1
Higgins, D.2
Gibson, T.3
-
33
-
-
0036211179
-
Modularity and specialization in superfamily 1 and 2 helicases
-
Singleton, M., and D. Wigley. 2002. Modularity and specialization in superfamily 1 and 2 helicases. J. Bacteriol. 184:1819-1826.
-
(2002)
J. Bacteriol
, vol.184
, pp. 1819-1826
-
-
Singleton, M.1
Wigley, D.2
-
34
-
-
0026743174
-
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
-
Russell, R., and G. Barton. 1992. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins. 14:309-323.
-
(1992)
Proteins
, vol.14
, pp. 309-323
-
-
Russell, R.1
Barton, G.2
-
37
-
-
85031446941
-
-
Web, S. C. A. http://www.hhmi.swmed.edu/Labs/rr/SCA.html.
-
, vol.100
, Issue.A
-
-
Web, S.1
-
38
-
-
25644452032
-
Evolutionary information for specifying a protein fold
-
Socolich, M., S. Lockless, W. P. Russ, H. Lee, K. Gardner, and R. Ranganathan. 2005. Evolutionary information for specifying a protein fold. Nature. 437:512-518.
-
(2005)
Nature
, vol.437
, pp. 512-518
-
-
Socolich, M.1
Lockless, S.2
Russ, W.P.3
Lee, H.4
Gardner, K.5
Ranganathan, R.6
-
39
-
-
25644442464
-
Natural-like function in artificial WW domains
-
Russ, W. P., D. M. Lowery, P. Mishra, M. B. Yaffe, and R. Ranganathan. 2005. Natural-like function in artificial WW domains. Nature. 437:579-583.
-
(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
-
40
-
-
0035427398
-
Protein flexibilty predictions using graph theory
-
Jacobs, D., A. Rader, M. Thorpe, and L. Kuhn. 2001. Protein flexibilty predictions using graph theory. Proteins Struct. Funct. Genet. 44:150-165.
-
(2001)
Proteins Struct. Funct. Genet
, vol.44
, pp. 150-165
-
-
Jacobs, D.1
Rader, A.2
Thorpe, M.3
Kuhn, L.4
-
41
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabási, A.-L., and R. Albert. 1999. Emergence of scaling in random networks. Science. 286:509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabási, A.-L.1
Albert, R.2
-
42
-
-
25844431698
-
Coarse-grained normal modes in structural biology
-
Bahar, I., and A. J. Rader. 2005. Coarse-grained normal modes in structural biology. Curr. Opin. Struct. Biol. 15:1-7.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 1-7
-
-
Bahar, I.1
Rader, A.J.2
-
43
-
-
33644517853
-
Functional modes of proteins are among the most robust
-
Nicolay, S., and Y.-H. Sanejouand. 2006. Functional modes of proteins are among the most robust. Phys. Rev. Lett. 96:078104.
-
(2006)
Phys. Rev. Lett
, vol.96
, pp. 078104
-
-
Nicolay, S.1
Sanejouand, Y.-H.2
-
44
-
-
61349160544
-
Normal Mode Analysis
-
Cui, Q, and I. Bahar, editors, Chapman and Hall/CRC. Boca Raton, FL
-
Cui, Q., and I. Bahar, editors. 2006. Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems. Chapman and Hall/CRC. Boca Raton, FL.
-
(2006)
Theory and Applications to Biological and Chemical Systems
-
-
-
45
-
-
22544482026
-
Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain
-
Brendza, K., W. Cheng, C. Fischer, M. Chesnik, A. Niedziela-Majka, and T. Lohman. 2005. Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain. Proc. Natl. Acad. Sci. USA. 102:10076-10081.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 10076-10081
-
-
Brendza, K.1
Cheng, W.2
Fischer, C.3
Chesnik, M.4
Niedziela-Majka, A.5
Lohman, T.6
-
46
-
-
27644514163
-
Repetitive shuttling of a motor protein on DNA
-
Myong, S., I. Rasnik, C. Joo, T. Lohman, and T. Ha. 2005. Repetitive shuttling of a motor protein on DNA. Nature. 322:1321-1325.
-
(2005)
Nature
, vol.322
, pp. 1321-1325
-
-
Myong, S.1
Rasnik, I.2
Joo, C.3
Lohman, T.4
Ha, T.5
-
47
-
-
9244235535
-
Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA
-
Fischer, C., N. Maluf, and T. Lohman. 2004. Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J. Mol. Biol. 344:1287-1309.
-
(2004)
J. Mol. Biol
, vol.344
, pp. 1287-1309
-
-
Fischer, C.1
Maluf, N.2
Lohman, T.3
-
48
-
-
0034679815
-
Uncoupling DNA translocation and helicase activity in PcrA: Direct evidence for an active mechanism
-
Soultanas, P., M. Dillingham, P. Wiley, M. Webb, and D. Wigley. 2000. Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism. EMBO J. 19:3799-3810.
-
(2000)
EMBO J
, vol.19
, pp. 3799-3810
-
-
Soultanas, P.1
Dillingham, M.2
Wiley, P.3
Webb, M.4
Wigley, D.5
-
49
-
-
33845657428
-
UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke
-
Lee, J., and W. Yang. 2006. UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell. 127:1349-1360.
-
(2006)
Cell
, vol.127
, pp. 1349-1360
-
-
Lee, J.1
Yang, W.2
-
50
-
-
0033566657
-
Site-directed mutagenesis of motif II in PcrA helicase reveals a role in coupling ATP hydrolysis to strand separation
-
Dillingham, M., P. Soultanas, and D. Wigley. 1999. Site-directed mutagenesis of motif II in PcrA helicase reveals a role in coupling ATP hydrolysis to strand separation. Nucleic Acids Res. 27:3310-3317.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3310-3317
-
-
Dillingham, M.1
Soultanas, P.2
Wigley, D.3
-
51
-
-
2942642183
-
Structure-specific DNA binding and bipolar helicase activities of PcrA
-
Anand, S., and S. Khan. 2004. Structure-specific DNA binding and bipolar helicase activities of PcrA. Nucleic Acids Res. 32:3190-3197.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3190-3197
-
-
Anand, S.1
Khan, S.2
-
52
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali, A., and T. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
-
(1993)
J. Mol. Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.2
-
53
-
-
0035902592
-
Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase
-
Dillingham, M. S., P. Soultanas, P. Wiley, M. R. Webb, and D. B. Wigley. 2001. Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase. Proc. Natl. Acad. Sci. USA. 98:8381-8387.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 8381-8387
-
-
Dillingham, M.S.1
Soultanas, P.2
Wiley, P.3
Webb, M.R.4
Wigley, D.B.5
|