-
1
-
-
0000349003
-
NMR Evidence of a short linear peptide that folds into a β-hairpin in aqueous solution
-
Blanco F., Jiménez M., Herranz J., Rico M., Santoro J., and Nieto J. NMR Evidence of a short linear peptide that folds into a β-hairpin in aqueous solution. J. Am. Chem. Soc. 115 (1993) 5887-5888
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 5887-5888
-
-
Blanco, F.1
Jiménez, M.2
Herranz, J.3
Rico, M.4
Santoro, J.5
Nieto, J.6
-
2
-
-
0034635340
-
beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat
-
Bonvin A.M., and van Gunsteren W.F. beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. J. Mol. Biol. 296 (2000) 255-268
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 255-268
-
-
Bonvin, A.M.1
van Gunsteren, W.F.2
-
3
-
-
0034081255
-
Mechanical unfolding of a beta-hairpin using molecular dynamics
-
Bryant Z., Pande V.S., and Rokhsar D.S. Mechanical unfolding of a beta-hairpin using molecular dynamics. Biophys. J. 78 (2000) 584-589
-
(2000)
Biophys. J.
, vol.78
, pp. 584-589
-
-
Bryant, Z.1
Pande, V.S.2
Rokhsar, D.S.3
-
6
-
-
0038502170
-
Folding dynamics and mechanism of beta-hairpin formation
-
Munoz V., Thompson P.A., Hofrichter J., and Eaton W.A. Folding dynamics and mechanism of beta-hairpin formation. Nature 390 (1997) 196-199
-
(1997)
Nature
, vol.390
, pp. 196-199
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
8
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
-
Pande V.S., and Rokhsar D.S. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 9062-9067
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 9062-9067
-
-
Pande, V.S.1
Rokhsar, D.S.2
-
9
-
-
0032735468
-
Molecular dynamics simulations of beta-hairpin folding
-
Wang H., Varady J., Ng L., and Sung S.S. Molecular dynamics simulations of beta-hairpin folding. Proteins 37 (1999) 325-333
-
(1999)
Proteins
, vol.37
, pp. 325-333
-
-
Wang, H.1
Varady, J.2
Ng, L.3
Sung, S.S.4
-
10
-
-
0037093874
-
Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation
-
Wu X., Wang S., and Brooks B.R. Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation. J. Am. Chem. Soc. 124 (2002) 5282-5283
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5282-5283
-
-
Wu, X.1
Wang, S.2
Brooks, B.R.3
-
11
-
-
1942519803
-
Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water
-
Wu X., and Brooks B.R. Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water. Biophys. J. 86 (2004) 1946-1958
-
(2004)
Biophys. J.
, vol.86
, pp. 1946-1958
-
-
Wu, X.1
Brooks, B.R.2
-
12
-
-
1842334454
-
Refolding simulations of an isolated fragment of barnase into a native-like beta hairpin: evidence for compactness and hydrogen bonding as concurrent stabilizing factors
-
Prevost M., and Ortmans I. Refolding simulations of an isolated fragment of barnase into a native-like beta hairpin: evidence for compactness and hydrogen bonding as concurrent stabilizing factors. Proteins 29 (1997) 212-227
-
(1997)
Proteins
, vol.29
, pp. 212-227
-
-
Prevost, M.1
Ortmans, I.2
-
13
-
-
0028865129
-
A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin
-
Searle M.S., Williams D.H., and Packman L.C. A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin. Nat. Struct. Biol. 2 (1995) 999-1006
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 999-1006
-
-
Searle, M.S.1
Williams, D.H.2
Packman, L.C.3
-
14
-
-
0035850758
-
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic B., Sorin E.J., and Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313 (2001) 151-169
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.3
-
15
-
-
0024316597
-
The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A
-
Loll P.J., and Lattman E.E. The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A. Proteins 5 (1989) 183-201
-
(1989)
Proteins
, vol.5
, pp. 183-201
-
-
Loll, P.J.1
Lattman, E.E.2
-
16
-
-
0028008617
-
Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy
-
Jacobs M.D., and Fox R.O. Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 449-453
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 449-453
-
-
Jacobs, M.D.1
Fox, R.O.2
-
17
-
-
0036135965
-
Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange
-
Walkenhorst W.F., Edwards J.A., Markley J.L., and Roder H. Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange. Protein Sci. 11 (2002) 82-91
-
(2002)
Protein Sci.
, vol.11
, pp. 82-91
-
-
Walkenhorst, W.F.1
Edwards, J.A.2
Markley, J.L.3
Roder, H.4
-
18
-
-
2442565750
-
Measuring the refolding of beta-sheets with different turn sequences on a nanosecond time scale
-
Chen R.P., Huang J.J., Chen H.L., Jan H., Velusamy M., Lee C.T., Fann W., Larsen R.W., and Chan S.I. Measuring the refolding of beta-sheets with different turn sequences on a nanosecond time scale. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 7305-7310
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 7305-7310
-
-
Chen, R.P.1
Huang, J.J.2
Chen, H.L.3
Jan, H.4
Velusamy, M.5
Lee, C.T.6
Fann, W.7
Larsen, R.W.8
Chan, S.I.9
-
19
-
-
8644237364
-
Understanding the key factors that control the rate of beta-hairpin folding
-
Du D., Zhu Y., Huang C.Y., and Gai F. Understanding the key factors that control the rate of beta-hairpin folding. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 15915-15920
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 15915-15920
-
-
Du, D.1
Zhu, Y.2
Huang, C.Y.3
Gai, F.4
-
20
-
-
0038241788
-
Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments
-
Mu Y., Kosov D., and Stock G. Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments. J. Phys. Chem. B 107 (2003) 5064-5073
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5064-5073
-
-
Mu, Y.1
Kosov, D.2
Stock, G.3
-
21
-
-
0034818192
-
Isotope-edited two-dimensional vibrational spectroscopy of a short alpha-helix in water
-
Woutersen S., and Hamm P. Isotope-edited two-dimensional vibrational spectroscopy of a short alpha-helix in water. J. Chem. Phys. 114 (2001) 2727-2737
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 2727-2737
-
-
Woutersen, S.1
Hamm, P.2
-
22
-
-
0037021502
-
Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study
-
Eker F., Cao X., Nafie L., and Schweitzer-Stenner R. Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study. J. Am. Chem. Soc. 124 (2002) 14330-14341
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 14330-14341
-
-
Eker, F.1
Cao, X.2
Nafie, L.3
Schweitzer-Stenner, R.4
-
23
-
-
0037047134
-
Polyproline II structure in a sequence of seven alanine residues
-
Shi Z., Olson C.A., Rose G.D., Baldwin R.L., and Kallenbach N.R. Polyproline II structure in a sequence of seven alanine residues. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 9190-9195
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 9190-9195
-
-
Shi, Z.1
Olson, C.A.2
Rose, G.D.3
Baldwin, R.L.4
Kallenbach, N.R.5
-
24
-
-
1842500993
-
Unfolded state of polyalanine is a segmented polyproline II helix
-
Kentsis A., Mezei M., Gindin T., and Osman R. Unfolded state of polyalanine is a segmented polyproline II helix. Proteins 55 (2004) 493-501
-
(2004)
Proteins
, vol.55
, pp. 493-501
-
-
Kentsis, A.1
Mezei, M.2
Gindin, T.3
Osman, R.4
-
25
-
-
1842500992
-
Polyproline II helix is the preferred conformation for unfolded polyalanine in water
-
Mezei M., Fleming P.J., Srinivasan R., and Rose G.D. Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins 55 (2004) 502-507
-
(2004)
Proteins
, vol.55
, pp. 502-507
-
-
Mezei, M.1
Fleming, P.J.2
Srinivasan, R.3
Rose, G.D.4
-
26
-
-
0034692902
-
Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability
-
Chen J., Lu Z., Sakon J., and Stites W.E. Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability. J. Mol. Biol. 303 (2000) 125-130
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 125-130
-
-
Chen, J.1
Lu, Z.2
Sakon, J.3
Stites, W.E.4
-
27
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling
-
Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
28
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman B. (Ed), Reidel Publishing Company, Dordrecht, The Netherlands
-
Berendsen H., Postma J.P.M., van Gunsteren W.F., and Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B. (Ed). Inter Molecular Forces (1981), Reidel Publishing Company, Dordrecht, The Netherlands 331-342
-
(1981)
Inter Molecular Forces
, pp. 331-342
-
-
Berendsen, H.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Hermans, J.4
-
29
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U., Perera L., Berkowitz M., Darden T., Lee H., and Pedersen L. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.3
Darden, T.4
Lee, H.5
Pedersen, L.6
-
30
-
-
33846823909
-
Particle mesh Ewald: An N-log (N) method for Ewald sums in large systems
-
Darden T., York D., and Pedersen L. 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
-
31
-
-
0033024177
-
Molecular dynamics simulations of biomolecules: long-range electrostatic effects
-
Sagui C., and Darden T.A. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu. Rev. Biophys. Biomol. Struct. 28 (1999) 155-179
-
(1999)
Annu. Rev. Biophys. Biomol. Struct.
, vol.28
, pp. 155-179
-
-
Sagui, C.1
Darden, T.A.2
-
34
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H., Postma J., DiNola A., and Haak J. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
DiNola, A.3
Haak, J.4
-
35
-
-
0035789518
-
Gromacs 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E., Hess B., and van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317
-
(2001)
J. Mol. Mod.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
36
-
-
33747886172
-
-
W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H. Hünenberger, P. Krüger, A.E. Mark, W.R.P. Scott, I.G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide, Zürich, Switzerland, Hochschulverlag AG an der ETH Zürich, 1996.
-
-
-
-
37
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott W.R.P., Huenenberger P., Tironi I., Mark A., Billeter S., Fennen J., Torda A., Huber T., Krueger P., and van Gunsteren W. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 103 (1999) 3596-3607
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Huenenberger, P.2
Tironi, I.3
Mark, A.4
Billeter, S.5
Fennen, J.6
Torda, A.7
Huber, T.8
Krueger, P.9
van Gunsteren, W.10
-
38
-
-
0033556236
-
Peptide folding: when simulation meets experiment
-
Daura X., Gademann K., Jaun B., Seebach D., Van Gunsteren W.F., and Mark A.E. Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. 38 (1999) 236-240
-
(1999)
Angew. Chem. Int. Ed.
, vol.38
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
Van Gunsteren, W.F.5
Mark, A.E.6
-
40
-
-
0033557181
-
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations
-
Daura X., van Gunsteren W.F., and Mark A.E. Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins 34 (1999) 269-280
-
(1999)
Proteins
, vol.34
, pp. 269-280
-
-
Daura, X.1
van Gunsteren, W.F.2
Mark, A.E.3
-
41
-
-
0037382258
-
Atom depth as a descriptor of the protein interior
-
Pintar A., Carugo O., and Pongor S. Atom depth as a descriptor of the protein interior. Biophys. J. 84 (2003) 2553-2561
-
(2003)
Biophys. J.
, vol.84
, pp. 2553-2561
-
-
Pintar, A.1
Carugo, O.2
Pongor, S.3
-
43
-
-
0025729007
-
A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution
-
Pedersen T.G., Sigurskjold B.W., Andersen K.V., Kjaer M., Poulsen F.M., Dobson C.M., and Redfield C. A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution. J. Mol. Biol. 218 (1991) 413-426
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 413-426
-
-
Pedersen, T.G.1
Sigurskjold, B.W.2
Andersen, K.V.3
Kjaer, M.4
Poulsen, F.M.5
Dobson, C.M.6
Redfield, C.7
-
44
-
-
0029786620
-
A fragment of staphylococcal nuclease with an OB-fold structure shows hydrogen-exchange protection factors in the range reported for "molten globules"
-
Alexandrescu A.T., Dames S.A., and Wiltscheck R. A fragment of staphylococcal nuclease with an OB-fold structure shows hydrogen-exchange protection factors in the range reported for "molten globules". Protein Sci. 5 (1996) 1942-1946
-
(1996)
Protein Sci.
, vol.5
, pp. 1942-1946
-
-
Alexandrescu, A.T.1
Dames, S.A.2
Wiltscheck, R.3
-
45
-
-
3042848873
-
Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics
-
Deechongkit S., Nguyen H., Powers E.T., Dawson P.E., Gruebele M., and Kelly J.W. Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics. Nature 430 (2004) 101-105
-
(2004)
Nature
, vol.430
, pp. 101-105
-
-
Deechongkit, S.1
Nguyen, H.2
Powers, E.T.3
Dawson, P.E.4
Gruebele, M.5
Kelly, J.W.6
-
46
-
-
0029044324
-
NMR structure of a stable "OB-fold" sub-domain isolated from staphylococcal nuclease
-
Alexandrescu A.T., Gittis A.G., Abeygunawardana C., and Shortle D. NMR structure of a stable "OB-fold" sub-domain isolated from staphylococcal nuclease. J. Mol. Biol. 250 (1995) 134-143
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 134-143
-
-
Alexandrescu, A.T.1
Gittis, A.G.2
Abeygunawardana, C.3
Shortle, D.4
-
47
-
-
0031908874
-
Hydrogen exchange studies of protein structure
-
Raschke T.M., and Marqusee S. Hydrogen exchange studies of protein structure. Curr. Opin. Biotechnol. 9 (1998) 80-86
-
(1998)
Curr. Opin. Biotechnol.
, vol.9
, pp. 80-86
-
-
Raschke, T.M.1
Marqusee, S.2
-
48
-
-
0027384196
-
Hydrogen exchange in unligated and ligated staphylococcal nuclease
-
Loh S.N., Prehoda K.E., Wang J., and Markley J.L. Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry 32 (1993) 11022-11028
-
(1993)
Biochemistry
, vol.32
, pp. 11022-11028
-
-
Loh, S.N.1
Prehoda, K.E.2
Wang, J.3
Markley, J.L.4
-
49
-
-
0028866620
-
Different subdomains are most protected from hydrogen exchange in the molten globule and native states of human alpha-lactalbumin
-
Schulman B.A., Redfield C., Peng Z.Y., Dobson C.M., and Kim P.S. Different subdomains are most protected from hydrogen exchange in the molten globule and native states of human alpha-lactalbumin. J. Mol. Biol. 253 (1995) 651-657
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 651-657
-
-
Schulman, B.A.1
Redfield, C.2
Peng, Z.Y.3
Dobson, C.M.4
Kim, P.S.5
-
50
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel beta-sheet peptide
-
Ferrara P., and Caflisch A. Folding simulations of a three-stranded antiparallel beta-sheet peptide. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 10780-10785
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
51
-
-
0037372211
-
Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study
-
Colombo G., De Mori G.M., and Roccatano D. Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study. Protein Sci. 12 (2003) 538-550
-
(2003)
Protein Sci.
, vol.12
, pp. 538-550
-
-
Colombo, G.1
De Mori, G.M.2
Roccatano, D.3
-
52
-
-
0034598946
-
Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces
-
Ma B., and Nussinov R. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. J. Mol. Biol. 296 (2000) 1091-1104
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1091-1104
-
-
Ma, B.1
Nussinov, R.2
-
53
-
-
0032881707
-
A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G
-
Roccatano D., Amadei A., Di Nola A., and Berendsen H.J. A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G. Protein Sci. 8 (1999) 2130-2143
-
(1999)
Protein Sci.
, vol.8
, pp. 2130-2143
-
-
Roccatano, D.1
Amadei, A.2
Di Nola, A.3
Berendsen, H.J.4
|