-
3
-
-
0025763437
-
-
Knowles, J. R. Nature 1991, 350, 121-123.
-
(1991)
Nature
, vol.350
, pp. 121-123
-
-
Knowles, J.R.1
-
13
-
-
0034102419
-
-
Wu, N.; Mo, Y. R.; Gao, J. L.; Pai, E. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2017-2022.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 2017-2022
-
-
Wu, N.1
Mo, Y.R.2
Gao, J.L.3
Pai, E.F.4
-
14
-
-
0032475836
-
-
Cleland, W. W.; Frey, P. A.; Gerlt, J. A. J. Biol. Chem. 1998, 273, 25529.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 25529
-
-
Cleland, W.W.1
Frey, P.A.2
Gerlt, J.A.3
-
23
-
-
0037076062
-
-
Cui, Q.; Elstner, M.; Karplus, M. J. Phys. Chem. B 2002, 106, 2721-2740.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 2721-2740
-
-
Cui, Q.1
Elstner, M.2
Karplus, M.3
-
32
-
-
0017776823
-
-
McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature 1977, 267, 585-590.
-
(1977)
Nature
, vol.267
, pp. 585-590
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
-
33
-
-
0025015392
-
-
Joseph, D.; Petsko, G. A.; Karplus, M. Science 1990, 249, 1425-1428.
-
(1990)
Science
, vol.249
, pp. 1425-1428
-
-
Joseph, D.1
Petsko, G.A.2
Karplus, M.3
-
34
-
-
0032484096
-
-
Lu, H. P.; Xun, L.; Xie, X. Science 1998, 282, 1877.
-
(1998)
Science
, vol.282
, pp. 1877
-
-
Lu, H.P.1
Xun, L.2
Xie, X.3
-
35
-
-
0037461492
-
-
Xie, X. J. Chem. Phys. 2002, 117, 11024-11032.
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 11024-11032
-
-
Xie, X.1
-
38
-
-
0034919305
-
-
Palmer, A. G.; Kroenke, C. D.; Loria, J. P. Methods Enzymol. 2001, 339, 204-238.
-
(2001)
Methods Enzymol.
, vol.339
, pp. 204-238
-
-
Palmer, A.G.1
Kroenke, C.D.2
Loria, J.P.3
-
39
-
-
0034945906
-
-
Wang, L.; Pang, Y.; Holder, T.; Brender, J. R.; Kurochkin, A. V.; Zuiderweg, E. R. P. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 7684-7689.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 7684-7689
-
-
Wang, L.1
Pang, Y.2
Holder, T.3
Brender, J.R.4
Kurochkin, A.V.5
Zuiderweg, E.R.P.6
-
41
-
-
0037154884
-
-
Eisenmesser, E. Z.; Bosco, D. A.; Akke, M.; Kern, D. Science 2002, 295, 1520-1523.
-
(2002)
Science
, vol.295
, pp. 1520-1523
-
-
Eisenmesser, E.Z.1
Bosco, D.A.2
Akke, M.3
Kern, D.4
-
42
-
-
0037117555
-
-
Bosco, D. A.; Eisenmesser, E. Z.; Pochapsky, S.; Sundquist, W. I.; Kern, D. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5247-5252.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 5247-5252
-
-
Bosco, D.A.1
Eisenmesser, E.Z.2
Pochapsky, S.3
Sundquist, W.I.4
Kern, D.5
-
43
-
-
0027071803
-
-
Zydowsky, L. D.; Etzkorn, F. A.; Chang, H. Y.; Ferguson, S. B.; Stolz, L. A.; Ho, S. I.; Walsh, C. T. Protein Sci. 1992, 1, 1092-1099.
-
(1992)
Protein Sci.
, vol.1
, pp. 1092-1099
-
-
Zydowsky, L.D.1
Etzkorn, F.A.2
Chang, H.Y.3
Ferguson, S.B.4
Stolz, L.A.5
Ho, S.I.6
Walsh, C.T.7
-
44
-
-
0025868143
-
-
Kofron, J. L.; Kuzmic, P.; Kishore, V.; Colon-Bonilla, E.; Rich, D. H. Biochemistry 1991, 30, 6127-6134.
-
(1991)
Biochemistry
, vol.30
, pp. 6127-6134
-
-
Kofron, J.L.1
Kuzmic, P.2
Kishore, V.3
Colon-Bonilla, E.4
Rich, D.H.5
-
45
-
-
0030448994
-
-
Gamble, T. R.; Vajdos, F. F.; Yoo, S.; Worthylake, D. K.; Houseweart, M. ; Sundquist, W. I.; Hill, C. P. Cell 1996, 87, 1285-1294.
-
(1996)
Cell
, vol.87
, pp. 1285-1294
-
-
Gamble, T.R.1
Vajdos, F.F.2
Yoo, S.3
Worthylake, D.K.4
Houseweart, M.5
Sundquist, W.I.6
Hill, C.P.7
-
47
-
-
0028877264
-
-
Kern, D.; Kern, G.; Scherer, G.; Fischer, G.; Drakenberg, T. Biochemistry 1995, 34, 13594-13602.
-
(1995)
Biochemistry
, vol.34
, pp. 13594-13602
-
-
Kern, D.1
Kern, G.2
Scherer, G.3
Fischer, G.4
Drakenberg, T.5
-
48
-
-
0027742843
-
-
Fischer, S.; Michnick, S.; Karplus, M. Biochemistry 1993, 32, 13830-13837.
-
(1993)
Biochemistry
, vol.32
, pp. 13830-13837
-
-
Fischer, S.1
Michnick, S.2
Karplus, M.3
-
51
-
-
0041784950
-
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B. ; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Kraplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Kraplus, M.29
more..
-
53
-
-
84986513644
-
-
Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700-733.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
55
-
-
0003525155
-
-
John Wiley & Sons
-
Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics Structure, & Thermodynamics; John Wiley & Sons: 1988; Vol. LXXI.
-
(1988)
Proteins: A Theoretical Perspective of Dynamics Structure, & Thermodynamics
, vol.71
-
-
Brooks III, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
57
-
-
0022068152
-
-
Brooks, C. L., III; Brünger, A.; Karplus, M. Biopolymers 1985, 24, 843.
-
(1985)
Biopolymers
, vol.24
, pp. 843
-
-
Brooks III, C.L.1
Brünger, A.2
Karplus, M.3
-
58
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 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
-
59
-
-
0000036869
-
-
Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
60
-
-
0001763714
-
-
Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720-1735.
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 1720-1735
-
-
Reuter, N.1
Dejaegere, A.2
Maigret, B.3
Karplus, M.4
-
61
-
-
1542779956
-
-
Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seigert, G. Phys. Rev. 1998, B58, 7260-7268.
-
(1998)
Phys. Rev.
, vol.B58
, pp. 7260-7268
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Elsner, J.4
Haugk, M.5
Frauenheim, T.6
Suhai, S.7
Seigert, G.8
-
62
-
-
84986512474
-
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
63
-
-
0035138648
-
-
Cui, Q.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Karplus, M. J. Phys. Chem. B 2001, 105, 569-585.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
64
-
-
0030666230
-
-
Vajdos, F. F.; Yoo, S.; Houseweart, M.; Sundquist, W. I.; Hill, C. P. Protein Sci. 1997, 6, 2297.
-
(1997)
Protein Sci.
, vol.6
, pp. 2297
-
-
Vajdos, F.F.1
Yoo, S.2
Houseweart, M.3
Sundquist, W.I.4
Hill, C.P.5
-
68
-
-
0345491105
-
-
Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
72
-
-
26844534384
-
-
Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. J. Chem. Phys. 1980, 72, 650-654.
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 650-654
-
-
Krishnan, R.1
Binkley, J.S.2
Seeger, R.3
Pople, J.A.4
-
75
-
-
84986519238
-
-
Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
76
-
-
33646940952
-
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. J. Comput. Phys. 1977, 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.3
-
77
-
-
0038780573
-
-
Howard, B. R.; Vajdos, F. F.; Li, S.; Sundquist, W. I.; Hill, C. P. Nat. Struct. Biol. 2003, 10, 475-481.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 475-481
-
-
Howard, B.R.1
Vajdos, F.F.2
Li, S.3
Sundquist, W.I.4
Hill, C.P.5
-
81
-
-
0026723477
-
-
Meiering, E. M.; Serrano, L.; Fersht, A. R. J. Mol. Biol. 1992, 225, 585-589.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 585-589
-
-
Meiering, E.M.1
Serrano, L.2
Fersht, A.R.3
-
82
-
-
0028896311
-
-
Shoichet, B. K.; Baase, W. A.; Kuroki, R.; Matthews, B. W. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 452-456.
-
(1995)
Proc. Natl. Acad. Sci. U.S.A.
, vol.92
, pp. 452-456
-
-
Shoichet, B.K.1
Baase, W.A.2
Kuroki, R.3
Matthews, B.W.4
-
83
-
-
0030460727
-
-
Kanaya, S.; Oobatake, M.; Liu, Y. J. Biol. Chem. 1996, 271, 32729-32736.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 32729-32736
-
-
Kanaya, S.1
Oobatake, M.2
Liu, Y.3
-
86
-
-
0038810233
-
-
Rod, T. H.; Radkiewicz, J. L.; Brooks, C. L., III. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6980-6985.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 6980-6985
-
-
Rod, T.H.1
Radkiewicz, J.L.2
Brooks III, C.L.3
-
87
-
-
0037022683
-
-
Agarwal, P. K.; Billeter, S. R.; Rajagopalan, P. T. R.; Benkovic, S. J.; Hammes-Schiffer, S. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2794-2799.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 2794-2799
-
-
Agarwal, P.K.1
Billeter, S.R.2
Rajagopalan, P.T.R.3
Benkovic, S.J.4
Hammes-Schiffer, S.5
-
91
-
-
0345471293
-
-
note
-
After the present work was nearly ready for submission, we were informed that the Arg55Lys mutant was found experimentally to be largely inactive toward the proline isomerization (Kern, D., private communication).
-
-
-
-
92
-
-
0344609145
-
-
note
-
The authors also included the condition that the Pro(N)⋯Arg55(NH2) distance must be smaller than 4.0 Å. This was not included here because clearly no such condition can be defined for proline isomerization in solution.
-
-
-
|