-
1
-
-
84941485112
-
Das gleichgewicht zwischen hämoglobin und sauerstoff
-
Haurowitz F (1938) Das Gleichgewicht zwischen Hämoglobin und Sauerstoff. Z Physiol Chem 54:266-274
-
(1938)
Z Physiol Chem
, vol.54
, pp. 266-274
-
-
Haurowitz, F.1
-
3
-
-
0029981539
-
Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: Variation on common themes
-
Quiocho FA, Ledvin PS (1996) Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation on common themes. Mol Microbiol 20:17-25
-
(1996)
Mol Microbiol
, vol.20
, pp. 17-25
-
-
Quiocho, F.A.1
Ledvin, P.S.2
-
4
-
-
0037008011
-
Multiple conformational changes in enzyme catalysis
-
Hammes GG (2002) Multiple conformational changes in enzyme catalysis. Biochemistry 41:8221-8228
-
(2002)
Biochemistry
, vol.41
, pp. 8221-8228
-
-
Hammes, G.G.1
-
5
-
-
0041821836
-
A perspective on enzyme catalysis
-
Benkovic SJ, Hammes-Schiffer S (2003) A perspective on enzyme catalysis. Science 301:1196-1202
-
(2003)
Science
, vol.301
, pp. 1196-1202
-
-
Benkovic, S.J.1
Hammes-Schiffer, S.2
-
6
-
-
0037013143
-
The conformational plasticity of protein kinases
-
Huse M, Kuriyan J (2002) The conformational plasticity of protein kinases. Cell 109:275-282
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
7
-
-
2542464972
-
Structural changes during ion channel gating
-
Doyle DA (2004) Structural changes during ion channel gating. Trends Neurosci 27:298-302
-
(2004)
Trends Neurosci
, vol.27
, pp. 298-302
-
-
Doyle, D.A.1
-
8
-
-
9944226711
-
Towards a structural view of gating in potassium channels
-
Swartz KJ (2004) Towards a structural view of gating in potassium channels. Nature Rev Neurosci 5:905-916
-
(2004)
Nature Rev Neurosci
, vol.5
, pp. 905-916
-
-
Swartz, K.J.1
-
10
-
-
9244232349
-
Molecular motors: Strategies to get along
-
Mallik R, Gross SP (2004) Molecular motors: strategies to get along. Curr Biol 14:R971-R982
-
(2004)
Curr Biol
, vol.14
-
-
Mallik, R.1
Gross, S.P.2
-
11
-
-
0037452091
-
Molecular motors
-
Schliwa M, Woehlke G (2003) Molecular motors. Nature 422:759-765
-
(2003)
Nature
, vol.422
, pp. 759-765
-
-
Schliwa, M.1
Woehlke, G.2
-
13
-
-
0033617534
-
Chaperonin function: Folding by forced unfolding
-
Shtilerman M, Lorimer GH, Englander SW (1999) Chaperonin function: folding by forced unfolding. Science 284:822-825
-
(1999)
Science
, vol.284
, pp. 822-825
-
-
Shtilerman, M.1
Lorimer, G.H.2
Englander, S.W.3
-
14
-
-
3042856284
-
The unfolding action of GroEL on a protein substrate
-
van der Vaart A, Ma J, Karplus M (2004) The unfolding action of GroEL on a protein substrate. Biophys J 87:562-573
-
(2004)
Biophys J
, vol.87
, pp. 562-573
-
-
Van Der Vaart, A.1
Ma, J.2
Karplus, M.3
-
15
-
-
78651189765
-
On the nature of allosteric transitions - A plausible model
-
Monod M, Wyman J, Changeux JP (1965) On the nature of allosteric transitions - a plausible model. J Mol Biol 12:88-118
-
(1965)
J Mol Biol
, vol.12
, pp. 88-118
-
-
Monod, M.1
Wyman, J.2
Changeux, J.P.3
-
16
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
Koshland DE, Némethy G, Filmer D (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5:365-385
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland, D.E.1
Némethy, G.2
Filmer, D.3
-
17
-
-
0016437582
-
Ligand binding and enzymic catalysis coupled through subunits in tyrosyl-tRNA synthetase
-
Fersht AR, Mulvey RS, Koch GLE (1975) Ligand binding and enzymic catalysis coupled through subunits in tyrosyl-tRNA synthetase. Biochemistry 14:13-18
-
(1975)
Biochemistry
, vol.14
, pp. 13-18
-
-
Fersht, A.R.1
Mulvey, R.S.2
Koch, G.L.E.3
-
18
-
-
0029004759
-
Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL
-
Yifrach O, Horovitz A (1995) Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL. Biochemistry 34:5303-5308
-
(1995)
Biochemistry
, vol.34
, pp. 5303-5308
-
-
Yifrach, O.1
Horovitz, A.2
-
19
-
-
0025882959
-
Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: An analogue of the intermediate on the reaction pathway
-
Davenport RC, Bash PA, Seaton BA, Karplus M, Petsko GA, Ringe D (1991) Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway. Biochemistry 30:5821-5826
-
(1991)
Biochemistry
, vol.30
, pp. 5821-5826
-
-
Davenport, R.C.1
Bash, P.A.2
Seaton, B.A.3
Karplus, M.4
Petsko, G.A.5
Ringe, D.6
-
20
-
-
0033660312
-
Large-scale shape changes in proteins and macromolecular complexes
-
Wall ME, Gallagher SC, Trewhella J (2000) Large-scale shape changes in proteins and macromolecular complexes. Annu Rev Phys Chem 51:355-380
-
(2000)
Annu Rev Phys Chem
, vol.51
, pp. 355-380
-
-
Wall, M.E.1
Gallagher, S.C.2
Trewhella, J.3
-
21
-
-
0033813317
-
Conformational changes studied by cryo-electron microscopy
-
Saibil HR (2000) Conformational changes studied by cryo-electron microscopy. Nat Struct Biol 9:711-714
-
(2000)
Nat Struct Biol
, vol.9
, pp. 711-714
-
-
Saibil, H.R.1
-
22
-
-
0036089703
-
Single-particle imaging of macromolecules by cryo-electron microscopy
-
Frank J (2002) Single-particle imaging of macromolecules by cryo-electron microscopy. Annu Rev Biophys Biomol Struct 31:303-319
-
(2002)
Annu Rev Biophys Biomol Struct
, vol.31
, pp. 303-319
-
-
Frank, J.1
-
23
-
-
0031853060
-
Protein dynamics from NMR
-
Kay LE (1998) Protein dynamics from NMR. Nat Struct Biol 5:513-517
-
(1998)
Nat Struct Biol
, vol.5
, pp. 513-517
-
-
Kay, L.E.1
-
24
-
-
33748253186
-
Nuclear magnetic resonance methods for quantifying microsecond-to- millisecond motions in biological macromolecules
-
Palmer AG, Kroenke CD, Loria JP (2003) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 13:748-757
-
(2003)
Methods Enzymol
, vol.13
, pp. 748-757
-
-
Palmer, A.G.1
Kroenke, C.D.2
Loria, J.P.3
-
25
-
-
0141918782
-
Proteins in action: The physics of structural fluctuations and conformational changes
-
Parak FG (2003) Proteins in action: the physics of structural fluctuations and conformational changes. Curr Opin Struct Biol 13:552-557
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 552-557
-
-
Parak, F.G.1
-
26
-
-
0038047431
-
Watching a protein as it functions with 150-ps time-resolved X-ray crystallography
-
Schotte F, Lim MH, Jackson TA, Smirnov AV, Soman J, Olson JS, Phillips GN, Wulff M, Anfinrud PA (2003) Watching a protein as it functions with 150-ps time-resolved X-ray crystallography. Science 300:1944-1947
-
(2003)
Science
, vol.300
, pp. 1944-1947
-
-
Schotte, F.1
Lim, M.H.2
Jackson, T.A.3
Smirnov, A.V.4
Soman, J.5
Olson, J.S.6
Phillips, G.N.7
Wulff, M.8
Anfinrud, P.A.9
-
27
-
-
0344899932
-
Conformational analysis of proteins and peptides
-
Cai X, Dass C (2003) Conformational analysis of proteins and peptides. Curr Org Chem 7:1841-1854
-
(2003)
Curr Org Chem
, vol.7
, pp. 1841-1854
-
-
Cai, X.1
Dass, C.2
-
29
-
-
0343777458
-
Observing single biomolecules at work with the atomic force microscope
-
Engel A, Müller DJ (2000) Observing single biomolecules at work with the atomic force microscope. Nat Struct Biol 7:715-718
-
(2000)
Nat Struct Biol
, vol.7
, pp. 715-718
-
-
Engel, A.1
Müller, D.J.2
-
31
-
-
0036669824
-
Measuring protein conformational changes by FRET/LRET
-
Heyduk T (2002) Measuring protein conformational changes by FRET/LRET. Curr Opin Biotech 13:292-296
-
(2002)
Curr Opin Biotech
, vol.13
, pp. 292-296
-
-
Heyduk, T.1
-
32
-
-
0035354585
-
Changes in biomolecular conformation seen by small angle X-ray scattering
-
Doniach S (2001) Changes in biomolecular conformation seen by small angle X-ray scattering. Chem Rev 101:1763-1778
-
(2001)
Chem Rev
, vol.101
, pp. 1763-1778
-
-
Doniach, S.1
-
33
-
-
0031015737
-
Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductate: Crystallographic evidence
-
Sawaya MR, Kraut J (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductate: crystallographic evidence. Biochemistry 36:586-603
-
(1997)
Biochemistry
, vol.36
, pp. 586-603
-
-
Sawaya, M.R.1
Kraut, J.2
-
34
-
-
0028023726
-
Structure of influenza haemagglutinin at the pH of membrane fusion
-
Bullough PA, Hughson FM, Skehel JJ, Wiley DC (1994) Structure of influenza haemagglutinin at the pH of membrane fusion. Nature 371:37-43
-
(1994)
Nature
, vol.371
, pp. 37-43
-
-
Bullough, P.A.1
Hughson, F.M.2
Skehel, J.J.3
Wiley, D.C.4
-
35
-
-
0028335096
-
Structural mechanisms for domain movements in proteins
-
Gerstein M, Lesk AM, Chothia C (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749
-
(1994)
Biochemistry
, vol.33
, pp. 6739-6749
-
-
Gerstein, M.1
Lesk, A.M.2
Chothia, C.3
-
36
-
-
0032530836
-
A database of macromolecular motions
-
Gerstein M, Krebs W (1998) A database of macromolecular motions. Nucleic Acids Res 26:4280-4290
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
37
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern D, Zuiderweg ERP (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13:748-757
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.P.2
-
39
-
-
6344219895
-
Is allostery an intrinsic property of all dynamic proteins?
-
Gunasekaran K, Ma BY, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57:433-443
-
(2004)
Proteins
, vol.57
, pp. 433-443
-
-
Gunasekaran, K.1
Ma, B.Y.2
Nussinov, R.3
-
40
-
-
0023140044
-
Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
-
Elber R, Karplus M (1987) Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science 235:318-321
-
(1987)
Science
, vol.235
, pp. 318-321
-
-
Elber, R.1
Karplus, M.2
-
41
-
-
0242331659
-
The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
-
Millet O, Hudson RP, Kay LE (2003) The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc Natl Acad Sci USA 100:12700-12705
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12700-12705
-
-
Millet, O.1
Hudson, R.P.2
Kay, L.E.3
-
42
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion MM (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.M.1
-
43
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2:173-181
-
(1997)
Fold des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
44
-
-
24644483073
-
Large amplitude conformational change in proteins with a plastic network model: Adenylate kinase
-
Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins with a plastic network model: adenylate kinase. J Mol Biol 352:807-822
-
(2005)
J Mol Biol
, vol.352
, pp. 807-822
-
-
Maragakis, P.1
Karplus, M.2
-
45
-
-
0032006209
-
Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
-
Hayward S, Berendsen HJC (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 30:144-154
-
(1998)
Proteins
, vol.30
, pp. 144-154
-
-
Hayward, S.1
Berendsen, H.J.C.2
-
46
-
-
0034655949
-
The morph server: A standardized system for analyzing and visualizing macromolecular motions in a database framework
-
Krebs WG, Gerstein M (2000) The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res 28:1665-1675
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1665-1675
-
-
Krebs, W.G.1
Gerstein, M.2
-
47
-
-
0035966323
-
ATP-bound states of GroEL captured by cryo-electron microscopy
-
Ranson NA, Farr GW, Roseman AM, Gowen B, Fenton WA, Horwich AL, Saibil HR (2001) ATP-bound states of GroEL captured by cryo-electron microscopy. Cell 107:869-879
-
(2001)
Cell
, vol.107
, pp. 869-879
-
-
Ranson, N.A.1
Farr, G.W.2
Roseman, A.M.3
Gowen, B.4
Fenton, W.A.5
Horwich, A.L.6
Saibil, H.R.7
-
48
-
-
0034665864
-
A dynamic model for the allosteric mechanism of GroEL
-
Ma J, Sigler PB, Xu Z, Karplus M (2000) A dynamic model for the allosteric mechanism of GroEL. J Mol Biol 302:303-313
-
(2000)
J Mol Biol
, vol.302
, pp. 303-313
-
-
Ma, J.1
Sigler, P.B.2
Xu, Z.3
Karplus, M.4
-
49
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward S, Go N (1995) Collective variable description of native protein dynamics. Annu Rev Phys Chem 46:223-250
-
(1995)
Annu Rev Phys Chem
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
50
-
-
0034127361
-
Collective protein dynamics in relation to function
-
Berendsen HJC, Hayward S (2000) Collective protein dynamics in relation to function. CUIT Opin Struct Biol 10:165-169
-
(2000)
CUIT Opin Struct Biol
, vol.10
, pp. 165-169
-
-
Berendsen, H.J.C.1
Hayward, S.2
-
51
-
-
0034308140
-
Buildingblock approach for determining low-frequency normal modes of macromolecules
-
Tama F, Gadea FX, Marques O, Sanejouand Y-H (2000) Buildingblock approach for determining low-frequency normal modes of macromolecules. Proteins 41:1-7
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.-H.4
-
53
-
-
18144418170
-
Protein structural change upon ligand binding: Linear response theory
-
Ikeguchi M, Ueno J, Sato M, 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
-
54
-
-
0000055722
-
Diffusion-controlled reactions: A variational formula for the optimum reaction coordinate
-
Berkowitz M, Morgan JD, McCammon JA (1983) Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate. J Chem Phys 79:5563-5565
-
(1983)
J Chem Phys
, vol.79
, pp. 5563-5565
-
-
Berkowitz, M.1
Morgan, J.D.2
McCammon, J.A.3
-
55
-
-
0000603016
-
A method for determining reaction paths in large molecules: Application to myoglobin
-
Elber R, Karplus M (1987) A method for determining reaction paths in large molecules: application to myoglobin. Chem Phys Lett 139:375-380
-
(1987)
Chem Phys Lett
, vol.139
, pp. 375-380
-
-
Elber, R.1
Karplus, M.2
-
56
-
-
0000191981
-
Reaction path study of conformational transitions in flexible systems: Application to peptides
-
Czerminski R, Elber R (1990) Reaction path study of conformational transitions in flexible systems: application to peptides. J Chem Phys 92:5580-5601
-
(1990)
J Chem Phys
, vol.92
, pp. 5580-5601
-
-
Czerminski, R.1
Elber, R.2
-
57
-
-
78751663166
-
Bridging the gap between long time trajectories and reaction pathways
-
Elber R, Cárdenas A, Ghosh A, Stern HA (2003) Bridging the gap between long time trajectories and reaction pathways. Adv Chem Phys 126:93-129
-
(2003)
Adv Chem Phys
, vol.126
, pp. 93-129
-
-
Elber, R.1
Cárdenas, A.2
Ghosh, A.3
Stern, H.A.4
-
58
-
-
3042660129
-
A statistical method for identifying transition states in high dimensional problems
-
Pratt LR (1986) A statistical method for identifying transition states in high dimensional problems. J Chem Phys 85:5045-5048
-
(1986)
J Chem Phys
, vol.85
, pp. 5045-5048
-
-
Pratt, L.R.1
-
59
-
-
0000231955
-
Conjugate peak refinement: An algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom
-
Fischer S, Karplus M (1992) Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom. Chem Phys Lett 194:252-261
-
(1992)
Chem Phys Lett
, vol.194
, pp. 252-261
-
-
Fischer, S.1
Karplus, M.2
-
60
-
-
0031256658
-
The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature
-
Huo S, Straub JE (1997) The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature. J Chem Phys 107:5000-5006
-
(1997)
J Chem Phys
, vol.107
, pp. 5000-5006
-
-
Huo, S.1
Straub, J.E.2
-
61
-
-
0037326677
-
A concerted variational strategy for investigating rare events
-
Passerone D, Ceccarelli M, Parrinello M (2003) A concerted variational strategy for investigating rare events. J Chem Phys 118:2025-2032
-
(2003)
J Chem Phys
, vol.118
, pp. 2025-2032
-
-
Passerone, D.1
Ceccarelli, M.2
Parrinello, M.3
-
62
-
-
2442529095
-
Reduced gradient methods and their relation to reaction paths
-
Quapp W (2003) Reduced gradient methods and their relation to reaction paths. J Theor Comp Chem 2:385-417
-
(2003)
J Theor Comp Chem
, vol.2
, pp. 385-417
-
-
Quapp, W.1
-
63
-
-
0034700288
-
Pathway for large-scale conformational change in annexin V
-
Santos JSO, Fischer S, Guilbert C, Lewit-Bentley A, Smith JC (2000) Pathway for large-scale conformational change in annexin V. Biochem 39:14065-14074
-
(2000)
Biochem
, vol.39
, pp. 14065-14074
-
-
Santos, J.S.O.1
Fischer, S.2
Guilbert, C.3
Lewit-Bentley, A.4
Smith, J.C.5
-
64
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
with corrigenda in Nature Struct Biol 10:788-788, 2002
-
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat StructBiol 9:646-652 (with corrigenda in Nature Struct Biol 10:788-788, 2002)
-
(2002)
Nat StructBiol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
65
-
-
13544256698
-
Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS
-
Sotomayor M, Schulten K (2004) Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS. Biophys J 87:3050-3065
-
(2004)
Biophys J
, vol.87
, pp. 3050-3065
-
-
Sotomayor, M.1
Schulten, K.2
-
66
-
-
0033531973
-
Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
-
Paci E, Karplus M (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Biol 288:441-459
-
(1999)
J Mol Biol
, vol.288
, pp. 441-459
-
-
Paci, E.1
Karplus, M.2
-
67
-
-
0036073866
-
1-ATPase
-
with erratum in Structure 10:1285-1285, 2002
-
1-ATPase. Structure 10:921-931 (with erratum in Structure 10:1285-1285, 2002)
-
(2002)
Structure
, vol.10
, pp. 921-931
-
-
Ma, J.1
Flynn, T.C.2
Cui, Q.3
Leslie, A.G.W.4
Walker, J.E.5
Karplus, M.6
-
68
-
-
0027794972
-
Targeted molecular dynamics simulation of conformational change - Application to the T ↔ R transition in insulin
-
Schlitter J, Engels J, Krüger P, Jacoby E, Wollmer A (1993) Targeted molecular dynamics simulation of conformational change - application to the T ↔ R transition in insulin. Mol Sim 10:291-308
-
(1993)
Mol Sim
, vol.10
, pp. 291-308
-
-
Schlitter, J.1
Engels, J.2
Krüger, P.3
Jacoby, E.4
Wollmer, A.5
-
70
-
-
18644374892
-
Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method
-
van der Vaart A, Karplus M (2005) Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. J Chem Phys 122:114903
-
(2005)
J Chem Phys
, vol.122
, pp. 114903
-
-
Van Der Vaart, A.1
Karplus, M.2
-
71
-
-
0037197932
-
Conformational pathways in the gating of Escherichia coli mechanosensitive channel
-
Kong YF, Shen YF, Warth TE, Ma J (2002) Conformational pathways in the gating of Escherichia coli mechanosensitive channel. Proc Natl Acad Sci USA 99:5999-6004
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5999-6004
-
-
Kong, Y.F.1
Shen, Y.F.2
Warth, T.E.3
Ma, J.4
-
72
-
-
0035085863
-
Extending the capabilities of targeted molecular dynamics: Simulation of a large conformational transition in plasminogen activator inhibitor 1
-
Krüger P, Verheyden S, Declerck PJ, Engelborghs Y (2001) Extending the capabilities of targeted molecular dynamics: simulation of a large conformational transition in plasminogen activator inhibitor 1. Protein Sci 10:798-808
-
(2001)
Protein Sci
, vol.10
, pp. 798-808
-
-
Krüger, P.1
Verheyden, S.2
Declerck, P.J.3
Engelborghs, Y.4
-
73
-
-
9344250538
-
Simulation of the activation of alpha-chymotrypsin: Analysis of the pathway and role of the propeptide
-
Matrai J, Verheyden G, Krüger P, Engelborghs Y (2004) Simulation of the activation of alpha-chymotrypsin: analysis of the pathway and role of the propeptide. Protein Sci 13:3139-3150
-
(2004)
Protein Sci
, vol.13
, pp. 3139-3150
-
-
Matrai, J.1
Verheyden, G.2
Krüger, P.3
Engelborghs, Y.4
-
74
-
-
0032588951
-
Simulations of the T ↔ R conformational transition in aspartate transcarbamylase
-
Roche O, Field MJ (1999) Simulations of the T ↔ R conformational transition in aspartate transcarbamylase. Protein Eng 12:285-295
-
(1999)
Protein Eng
, vol.12
, pp. 285-295
-
-
Roche, O.1
Field, M.J.2
-
75
-
-
0037340698
-
Investigation of pathways for the low-pH conformational transition in influenza hemagglutinin
-
Madhusoodanan M, Lazaridis T (2003) Investigation of pathways for the low-pH conformational transition in influenza hemagglutinin. Biophys J 84:1926-1939
-
(2003)
Biophys J
, vol.84
, pp. 1926-1939
-
-
Madhusoodanan, M.1
Lazaridis, T.2
-
76
-
-
4444336426
-
In silico activation of Src tyrosine kinase reveals the molecular basis for intramolecular autophosphorylation
-
Mendieta J, Gago F (2004) In silico activation of Src tyrosine kinase reveals the molecular basis for intramolecular autophosphorylation. J Mol Graph Model 23:189-198
-
(2004)
J Mol Graph Model
, vol.23
, pp. 189-198
-
-
Mendieta, J.1
Gago, F.2
-
77
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
-
Grubmüller H, Heymann B, Tavan P (1996) Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 271:997-999
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmüller, H.1
Heymann, B.2
Tavan, P.3
-
78
-
-
0035003803
-
Steered molecular dynamics investigations of protein function
-
Isralewitz B, Baudry J, Gullingsrud J, Kosztin D, Schulten K (2001) Steered molecular dynamics investigations of protein function. J Mol Graph 19:13-25
-
(2001)
J Mol Graph
, vol.19
, pp. 13-25
-
-
Isralewitz, B.1
Baudry, J.2
Gullingsrud, J.3
Kosztin, D.4
Schulten, K.5
-
79
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
Isralewitz B, Gao M, Schulten K (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
-
80
-
-
0042885340
-
Free energy calculation for steered molecular dynamics simulations using Jarzynski's equality
-
Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K (2003) Free energy calculation for steered molecular dynamics simulations using Jarzynski's equality. J Chem Phys 119:3559-3566
-
(2003)
J Chem Phys
, vol.119
, pp. 3559-3566
-
-
Park, S.1
Khalili-Araghi, F.2
Tajkhorshid, E.3
Schulten, K.4
-
81
-
-
0036175994
-
Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in FL-ATP synthase
-
Böckmann RA, Grubmüller H (2002) Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in FL-ATP synthase. Nat Struct Biol 9:198-202
-
(2002)
Nat Struct Biol
, vol.9
, pp. 198-202
-
-
Böckmann, R.A.1
Grubmüller, H.2
-
82
-
-
0141754098
-
Gating of MscL studied by steered molecular dynamics
-
Gullingsrud J, Schulten K (2003) Gating of MscL studied by steered molecular dynamics. Biophys J 85:2087-2099
-
(2003)
Biophys J
, vol.85
, pp. 2087-2099
-
-
Gullingsrud, J.1
Schulten, K.2
-
83
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 53:291-318
-
(2002)
Annu Rev Phys Chem
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
84
-
-
0344270866
-
Atomistic understanding of kinetic pathways for single basepair binding and unbinding in DNA
-
Hagan MF, Dinner AR, Chandler D, Chakraborty AK (2003) Atomistic understanding of kinetic pathways for single basepair binding and unbinding in DNA. Proc Natl Acad Sci USA 100:13922-13927
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13922-13927
-
-
Hagan, M.F.1
Dinner, A.R.2
Chandler, D.3
Chakraborty, A.K.4
-
85
-
-
1942437505
-
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β's closing
-
Radhakrishnan R, Schlick T (2004) Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β's closing. Proc Natl Acad Sci USA 101:5970-5975
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 5970-5975
-
-
Radhakrishnan, R.1
Schlick, T.2
-
86
-
-
4143085014
-
Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "SOLAS"
-
Radhakrishnan R, Schlick T (2004) Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "SOLAS". J Chem Phys 121:2436-2444
-
(2004)
J Chem Phys
, vol.121
, pp. 2436-2444
-
-
Radhakrishnan, R.1
Schlick, T.2
-
87
-
-
14644441639
-
MM/PBSA analysis of molecular dynamics simulations of bovine β-lactoglobulin: Free energy gradients in conformational transitions?
-
Fogolari F, Moroni E, Wojciechowski M, Baginski M, Ragona L, Molinari H (2005) MM/PBSA analysis of molecular dynamics simulations of bovine β-lactoglobulin: free energy gradients in conformational transitions? Proteins 59:91-103
-
(2005)
Proteins
, vol.59
, pp. 91-103
-
-
Fogolari, F.1
Moroni, E.2
Wojciechowski, M.3
Baginski, M.4
Ragona, L.5
Molinari, H.6
-
88
-
-
0025294114
-
Conformational sampling using high-temperature molecular-dynamics
-
Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature molecular-dynamics Biopolymers 29:1847-1862
-
(1990)
Biopolymers
, vol.29
, pp. 1847-1862
-
-
Bruccoleri, R.E.1
Karplus, M.2
-
89
-
-
0025015392
-
Anatomy of a conformational change: Hinged "lid" motion of the triosephosphate isomerase loop
-
Joseph D, Petsko G A, Karplus M (1990) Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science 249:1425-1428
-
(1990)
Science
, vol.249
, pp. 1425-1428
-
-
Joseph, D.1
Petsko, G.A.2
Karplus, M.3
-
90
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: Conformational flooding
-
Grubmüller H (1995) Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys Rev E 52:2893-2906
-
(1995)
Phys Rev E
, vol.52
, pp. 2893-2906
-
-
Grubmüller, H.1
-
91
-
-
0040488445
-
Functional significance of hierarchical tiers in carbonmonoxy myglobin: Conformational substates and transitions studied by conformational flooding simulations
-
Schulze BG, Grubmüller H, Evanseck JD (2000) Functional significance of hierarchical tiers in carbonmonoxy myglobin: conformational substates and transitions studied by conformational flooding simulations J Am Chem Soc 122:8700-8711
-
(2000)
J Am Chem Soc
, vol.122
, pp. 8700-8711
-
-
Schulze, B.G.1
Grubmüller, H.2
Evanseck, J.D.3
-
92
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys 120:11919-11929
-
(2004)
J Chem Phys
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
93
-
-
13644250683
-
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: Accelerated molecular dynamics
-
Hamelberg D, Shen T, McCammon JA (2005) Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics. J Am Chem Soc 127:1969-1974
-
(2005)
J Am Chem Soc
, vol.127
, pp. 1969-1974
-
-
Hamelberg, D.1
Shen, T.2
McCammon, J.A.3
-
95
-
-
0041810451
-
Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics
-
Iannuzzi M, Laio A, Parrinello M (2003) Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics Phys Rev Lett 90:238302-238305
-
(2003)
Phys Rev Lett
, vol.90
, pp. 238302-238305
-
-
Iannuzzi, M.1
Laio, A.2
Parrinello, M.3
-
97
-
-
0029664944
-
The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγ S
-
Boisvert DC, Wang J, Otwinowski Z, Horwich AL, Sigler PB (1996) The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγ S. Nat Struct Biol 3:170-177
-
(1996)
Nat Struct Biol
, vol.3
, pp. 170-177
-
-
Boisvert, D.C.1
Wang, J.2
Otwinowski, Z.3
Horwich, A.L.4
Sigler, P.B.5
-
99
-
-
0028113299
-
Residues in chaperonin GroEL required for polypeptide binding and release
-
Fenton WA, Kashi Y, Furtak K, Horwich AL (1994) Residues in chaperonin GroEL required for polypeptide binding and release. Nature 371:614-619
-
(1994)
Nature
, vol.371
, pp. 614-619
-
-
Fenton, W.A.1
Kashi, Y.2
Furtak, K.3
Horwich, A.L.4
-
100
-
-
0030056969
-
Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction
-
Weissman JS, Rye HS, Fenton WA, Beechem JM, Horwich AL (1996) Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction Cell 84:481-490
-
(1996)
Cell
, vol.84
, pp. 481-490
-
-
Weissman, J.S.1
Rye, H.S.2
Fenton, W.A.3
Beechem, J.M.4
Horwich, A.L.5
-
101
-
-
0030804446
-
Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL
-
Rye HS, Burston SG, Fenton WA, Beechem JM, Xu Z, Sigler PB, Horwich AL (1997) Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL. Nature 388:792-798
-
(1997)
Nature
, vol.388
, pp. 792-798
-
-
Rye, H.S.1
Burston, S.G.2
Fenton, W.A.3
Beechem, J.M.4
Xu, Z.5
Sigler, P.B.6
Horwich, A.L.7
-
102
-
-
0033617129
-
GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings
-
Rye HS, Roseman AM, Chen S, Furtak K, Fenton WA, Saibil HR, Horwich AL (1999) GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. Cell 97:325-338
-
(1999)
Cell
, vol.97
, pp. 325-338
-
-
Rye, H.S.1
Roseman, A.M.2
Chen, S.3
Furtak, K.4
Fenton, W.A.5
Saibil, H.R.6
Horwich, A.L.7
-
103
-
-
0028027055
-
Location of a folding protein and shape changes in GroEL-GroES complexes imaged by cryoelectron microscopy
-
Chen S, Roseman AM, Hunter AS, Wood SP, Burston SG, Ranson NA, Clarke AR, Saibil HR (1994) Location of a folding protein and shape changes in GroEL-GroES complexes imaged by cryoelectron microscopy. Nature 371:261-264
-
(1994)
Nature
, vol.371
, pp. 261-264
-
-
Chen, S.1
Roseman, A.M.2
Hunter, A.S.3
Wood, S.P.4
Burston, S.G.5
Ranson, N.A.6
Clarke, A.R.7
Saibil, H.R.8
-
104
-
-
0030592538
-
The chaperonin ATPase cycle: Mechanism of allosteric switching and movements of substrate-binding domains in GroEL
-
Roseman AM, Chen S, White H, Braig K, Saibil HR (1996) The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell 87:241-251
-
(1996)
Cell
, vol.87
, pp. 241-251
-
-
Roseman, A.M.1
Chen, S.2
White, H.3
Braig, K.4
Saibil, H.R.5
-
105
-
-
0030726403
-
Conformational changes in the GroEL oligomer during the functional cycle
-
Llorca O, Marco S, Carrascosa JL, Valpuesta JM (1997) Conformational changes in the GroEL oligomer during the functional cycle. J Struct Biol 118:31-42
-
(1997)
J Struct Biol
, vol.118
, pp. 31-42
-
-
Llorca, O.1
Marco, S.2
Carrascosa, J.L.3
Valpuesta, J.M.4
-
106
-
-
0032555216
-
The allosteric mechanism of the chaperonin GroEL: A dynamic analysis
-
Ma J, Karplus M (1998) The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc Natl Acad Sci USA 95:8502-8507
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 8502-8507
-
-
Ma, J.1
Karplus, M.2
-
107
-
-
0028031345
-
Dynamics of the chaperonin ATPase cycle: Implications for facilitated protein folding
-
Todd MJ, Viitanen PV, Lorimer GH (1994) Dynamics of the chaperonin ATPase cycle: implications for facilitated protein folding. Science 265:659-666
-
(1994)
Science
, vol.265
, pp. 659-666
-
-
Todd, M.J.1
Viitanen, P.V.2
Lorimer, G.H.3
-
110
-
-
0035830681
-
Nucleotide binding to the chaperonin GroEL: Non-cooperative binding of ATP analogs and ADP and cooperative effect of ATP
-
Inobe T, Makio T, Takasu-Ishikawa E, Terada TP, Kuwajima K (2001) Nucleotide binding to the chaperonin GroEL: non-cooperative binding of ATP analogs and ADP and cooperative effect of ATP. Biochim Biophys Acta 1545:160-173
-
(2001)
Biochim Biophys Acta
, vol.1545
, pp. 160-173
-
-
Inobe, T.1
Makio, T.2
Takasu-Ishikawa, E.3
Terada, T.P.4
Kuwajima, K.5
-
111
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins 35:133-152
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
113
-
-
0033598941
-
The crystal structure of a GroEL/peptide complex: Plasticity as a basis for substrate diversity
-
Chen L, Sigler PB (1999) The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity. Cell 99:757-768
-
(1999)
Cell
, vol.99
, pp. 757-768
-
-
Chen, L.1
Sigler, P.B.2
-
114
-
-
0034598920
-
Multivalent binding of nonnative substrate proteins by the chaperonin GroEL
-
Farr GW, Furtak K, Rowland MB, Ranson NA, Saibil HR, Kirchhausen T, Horwich AL (2000) Multivalent binding of nonnative substrate proteins by the chaperonin GroEL. Cell 100:561-573
-
(2000)
Cell
, vol.100
, pp. 561-573
-
-
Farr, G.W.1
Furtak, K.2
Rowland, M.B.3
Ranson, N.A.4
Saibil, H.R.5
Kirchhausen, T.6
Horwich, A.L.7
-
115
-
-
0036435907
-
Determination of a transition state at atomic resolution from protein engineering data
-
Paci E, Vendruscolo M, Dobson CM, Karplus M (2002) Determination of a transition state at atomic resolution from protein engineering data. J Mol Biol 324:151-163
-
(2002)
J Mol Biol
, vol.324
, pp. 151-163
-
-
Paci, E.1
Vendruscolo, M.2
Dobson, C.M.3
Karplus, M.4
-
116
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Lindorff-Larsen K, Best RB, DePristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128-132
-
(2005)
Nature
, vol.433
, pp. 128-132
-
-
Lindorff-Larsen, K.1
Best, R.B.2
DePristo, M.A.3
Dobson, C.M.4
Vendruscolo, M.5
-
117
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria E, Fischer S, Karplus M (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105:1902-1921
-
(1996)
J Chem Phys
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
118
-
-
0024365336
-
Hidden thermodynamics of mutant proteins: A molecular dynamics analysis
-
Gao J, Kuczera K, Tidor B, Karplus M (1989) Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science 244:1069-1072
-
(1989)
Science
, vol.244
, pp. 1069-1072
-
-
Gao, J.1
Kuczera, K.2
Tidor, B.3
Karplus, M.4
|