-
1
-
-
0035471139
-
-
Lombardi, A.; Nastri, F.; Pavone, V. Chem. Rev. 2001, 101, 3165.
-
(2001)
Chem. Rev
, vol.101
, pp. 3165
-
-
Lombardi, A.1
Nastri, F.2
Pavone, V.3
-
2
-
-
13444302392
-
-
Cochran, F. V.; Wu, S. P.; Wang, W.; Nanda, V.; Saven, J. G.; Therien, M. J.; DeGrado, W. F. J. Am. Chem. Soc. 2005, 127, 1346.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 1346
-
-
Cochran, F.V.1
Wu, S.P.2
Wang, W.3
Nanda, V.4
Saven, J.G.5
Therien, M.J.6
DeGrado, W.F.7
-
3
-
-
24944475046
-
-
Ye, S.; Discher, B. M.; Strzalka, J.; Xu, T.; Wu, S. P.; Noy, D.; Kuzmenko, I.; Gog, T.; Therien, M. J.; Dutton, P. L.; Blasie, J. K. Nano Lett. 2005, 5, 1658.
-
(2005)
Nano Lett
, vol.5
, pp. 1658
-
-
Ye, S.1
Discher, B.M.2
Strzalka, J.3
Xu, T.4
Wu, S.P.5
Noy, D.6
Kuzmenko, I.7
Gog, T.8
Therien, M.J.9
Dutton, P.L.10
Blasie, J.K.11
-
5
-
-
33846121641
-
-
Xu, T.; Wu, S. P.; Miloradovic, I.; Therien, M. J.; Blasie, J. K. Nano Lett. 2006, 6, 2387.
-
(2006)
Nano Lett
, vol.6
, pp. 2387
-
-
Xu, T.1
Wu, S.P.2
Miloradovic, I.3
Therien, M.J.4
Blasie, J.K.5
-
6
-
-
0028281579
-
-
Robertson, D. E.; Farid, R. S.; Moser, C. C.; Urbauer, J. L.; Mulholland, S. E.; Pidikiti, R.; Lear, J. D.; Wand, A. J.; Degrade, W. F.; Dutton, P. L. Nature 1994, 368, 425.
-
(1994)
Nature
, vol.368
, pp. 425
-
-
Robertson, D.E.1
Farid, R.S.2
Moser, C.C.3
Urbauer, J.L.4
Mulholland, S.E.5
Pidikiti, R.6
Lear, J.D.7
Wand, A.J.8
Degrade, W.F.9
Dutton, P.L.10
-
7
-
-
0032836018
-
-
Dalton, L. R.; Steier, W. H.; Robinson, B. H.; Zhang, C.; Ren, A.; Garner, S.; Chen, A. T.; Londergan, T.; Irwin, L.; Carlson, B.; Fifield, L.; Phelan, G.; Kincaid, C.; Amend, J.; Jen, A. J. Mater. Chem. 1999, 9, 1905.
-
(1999)
J. Mater. Chem
, vol.9
, pp. 1905
-
-
Dalton, L.R.1
Steier, W.H.2
Robinson, B.H.3
Zhang, C.4
Ren, A.5
Garner, S.6
Chen, A.T.7
Londergan, T.8
Irwin, L.9
Carlson, B.10
Fifield, L.11
Phelan, G.12
Kincaid, C.13
Amend, J.14
Jen, A.15
-
8
-
-
3142662537
-
-
Ye, S.; Strzalka, J. W.; Discher, B. M.; Noy, D.; Zheng, S.; Dutton, P. L.; Blasie, J. K. Langmuir 2004, 20, 5897.
-
(2004)
Langmuir
, vol.20
, pp. 5897
-
-
Ye, S.1
Strzalka, J.W.2
Discher, B.M.3
Noy, D.4
Zheng, S.5
Dutton, P.L.6
Blasie, J.K.7
-
9
-
-
33846167452
-
-
Strzalka, J.; Xu, T.; Tronin, A.; Wu, S. P.; Miloradovic, I.; Kuzmenko, I.; Gog, T.; Therien, M. J.; Blasie, J. K. Nano Lett. 2006, 6, 2395.
-
(2006)
Nano Lett
, vol.6
, pp. 2395
-
-
Strzalka, J.1
Xu, T.2
Tronin, A.3
Wu, S.P.4
Miloradovic, I.5
Kuzmenko, I.6
Gog, T.7
Therien, M.J.8
Blasie, J.K.9
-
10
-
-
0035249679
-
-
Strzalka, J.; Chen, X. X.; Moser, C. C.; Dutton, P. L.; Bean, J. C.; Blasie, J. K. Langmuir 2001, 17, 1193.
-
(2001)
Langmuir
, vol.17
, pp. 1193
-
-
Strzalka, J.1
Chen, X.X.2
Moser, C.C.3
Dutton, P.L.4
Bean, J.C.5
Blasie, J.K.6
-
11
-
-
33646129682
-
-
Churbanova, I. Y.; Tronin, A.; Strzalka, J.; Gog, T.; Kuzmenko, I.; Johansson, J. S.; Blasie, J. K. Biophys. J. 2006, 90, 3255.
-
(2006)
Biophys. J
, vol.90
, pp. 3255
-
-
Churbanova, I.Y.1
Tronin, A.2
Strzalka, J.3
Gog, T.4
Kuzmenko, I.5
Johansson, J.S.6
Blasie, J.K.7
-
12
-
-
0037470553
-
-
Huang, S. S.; Gibney, B. R.; Stayrook, S. E.; Dutton, P. L.; Lewis, M. J. Mol. Biol. 2003, 326, 1219.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 1219
-
-
Huang, S.S.1
Gibney, B.R.2
Stayrook, S.E.3
Dutton, P.L.4
Lewis, M.5
-
13
-
-
0033516327
-
-
Skalicky, J. J.; Gibney, B. R.; Rabanal, F.; Urbauer, R. J. B.; Dutton, P. L.; Wand, A. J. J. Am. Chem. Soc. 1999, 121, 4941.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 4941
-
-
Skalicky, J.J.1
Gibney, B.R.2
Rabanal, F.3
Urbauer, R.J.B.4
Dutton, P.L.5
Wand, A.J.6
-
14
-
-
0000465377
-
-
Chen, X. X.; Moser, C. C.; Pilloud, D. L.; Dutton, P. L. J. Phys. Chem. B 1998, 102, 6425.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 6425
-
-
Chen, X.X.1
Moser, C.C.2
Pilloud, D.L.3
Dutton, P.L.4
-
19
-
-
7044224837
-
-
Ash, W. L.; Zlomislic, M. R.; Oloo, E. O.; Tieleman, D. P. Biochim. Biophys. Acta 2004, 1666, 158.
-
(2004)
Biochim. Biophys. Acta
, vol.1666
, pp. 158
-
-
Ash, W.L.1
Zlomislic, M.R.2
Oloo, E.O.3
Tieleman, D.P.4
-
20
-
-
23044476985
-
-
Gumbart, J.; Wang, Y.; Aksimentiev, A.; Tajkhorshid, E.; Schulten, K. Curr. Opin. Struct. Biol. 2005, 15, 423.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 423
-
-
Gumbart, J.1
Wang, Y.2
Aksimentiev, A.3
Tajkhorshid, E.4
Schulten, K.5
-
21
-
-
84906384980
-
-
MD simulation results indicate that the rmsd of the backbone atoms of the equilibrated structure compared to that of the crystal structure is 0.80 ± 0.09 Å. The average interhelix separation is ∼10.8 Å from the simulation result compared to ∼10.7 Å from the crystal structure
-
MD simulation results indicate that the rmsd of the backbone atoms of the equilibrated structure compared to that of the crystal structure is 0.80 ± 0.09 Å. The average interhelix separation is ∼10.8 Å from the simulation result compared to ∼10.7 Å from the crystal structure.
-
-
-
-
22
-
-
24944574297
-
-
Discher, B. M.; Noy, D.; Strzalka, J.; Ye, S. X.; Moser, C. C.; Lear, J. D.; Blasie, J. K.; Dutton, P. L. Biochemistry 2005, 44, 12329.
-
(2005)
Biochemistry
, vol.44
, pp. 12329
-
-
Discher, B.M.1
Noy, D.2
Strzalka, J.3
Ye, S.X.4
Moser, C.C.5
Lear, J.D.6
Blasie, J.K.7
Dutton, P.L.8
-
25
-
-
0032558105
-
-
Sharp, R. E.; Diers, J. R.; Bocian, D. F.; Dutton, P. L. J. Am. Chem. Soc. 1998, 120, 7103.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 7103
-
-
Sharp, R.E.1
Diers, J.R.2
Bocian, D.F.3
Dutton, P.L.4
-
26
-
-
0031961956
-
-
Zhong, Q. F.; Jiang, Q.; Moore, P. B.; Newns, D. M.; Klein, M. L. Biophys. J. 1998, 74, 3.
-
(1998)
Biophys. J
, vol.74
, pp. 3
-
-
Zhong, Q.F.1
Jiang, Q.2
Moore, P.B.3
Newns, D.M.4
Klein, M.L.5
-
27
-
-
0042415783
-
-
Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283.
-
(1999)
J. Comput. Phys
, vol.151
, pp. 283
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
28
-
-
0041784950
-
-
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; 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.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Starub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586
-
-
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
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, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Starub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
29
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
30
-
-
4444240014
-
-
Autenrieth, F.; Tajkhorshid, E.; Baudry, J.; Luthey-Schulten, Z. J. Comput. Chem. 2004, 25, 1613.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1613
-
-
Autenrieth, F.1
Tajkhorshid, E.2
Baudry, J.3
Luthey-Schulten, Z.4
-
31
-
-
0000868022
-
-
Zhang, Y. H.; Feller, S. E.; Brooks, B. R.; Pastor, R. W. J. Chem. Phys. 1995, 103, 10252.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 10252
-
-
Zhang, Y.H.1
Feller, S.E.2
Brooks, B.R.3
Pastor, R.W.4
-
32
-
-
33846823909
-
-
Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
33
-
-
33646940952
-
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
35
-
-
84906413587
-
-
The concept of crossing angle was borrowed from ref 31. For an idealized model of two short sections of a-helix, it is defined as the angle between the axes of the two helices. Our definition of crossing angles is the angle between the principal axes (i.e, using the coordinate axis of the principal moment of inertia) of two neighboring helices. This definition is an approximation, and it could be too coarse to be meaningful for coiled coils with several turns of the major helix or for substantially distorted helices such as the case for holo-AP0. However, first, the bundles in our case are short around one-third of the pitch of the major helix, so the assumption that the long principal axis of the helix is approximately the axis of the helix is acceptable. Second, our calculation of the crossing angle for the helices of holo-AP0 is only for comparison with that of the apo-form and to thereby show that the holo-form is not a coiled coil
-
The concept of crossing angle was borrowed from ref 31. For an idealized model of two short sections of a-helix, it is defined as the angle between the axes of the two helices. Our definition of crossing angles is the angle between the principal axes (i.e., using the coordinate axis of the principal moment of inertia) of two neighboring helices. This definition is an approximation, and it could be too coarse to be meaningful for coiled coils with several turns of the major helix or for substantially distorted helices such as the case for holo-AP0. However, first, the bundles in our case are short (around one-third of the pitch of the major helix), so the assumption that the long principal axis of the helix is approximately the axis of the helix is acceptable. Second, our calculation of the crossing angle for the helices of holo-AP0 is only for comparison with that of the apo-form and to thereby show that the holo-form is not a coiled coil.
-
-
-
-
36
-
-
33646359334
-
-
Tronin, A.; Xu, T.; Blasie, J. K. Langmuir 2005, 21, 7760.
-
(2005)
Langmuir
, vol.21
, pp. 7760
-
-
Tronin, A.1
Xu, T.2
Blasie, J.K.3
-
37
-
-
0034513345
-
-
Strzalka, J.; Chen, X. X.; Moser, C. C.; Dutton, P. L.; Ocko, B. M.; Blasie, J. K. Langmuir 2000, 16, 10404.
-
(2000)
Langmuir
, vol.16
, pp. 10404
-
-
Strzalka, J.1
Chen, X.X.2
Moser, C.C.3
Dutton, P.L.4
Ocko, B.M.5
Blasie, J.K.6
-
38
-
-
37649031208
-
-
Strzalka, J.; Gibney, B. R.; Satija, S.; Blasie, J. K. Phys. Rev. E 2004, 70, 061905.
-
(2004)
Phys. Rev. E
, vol.70
, pp. 061905
-
-
Strzalka, J.1
Gibney, B.R.2
Satija, S.3
Blasie, J.K.4
|