-
1
-
-
0037397987
-
Peptide folding simulations
-
Gnanakaran, S., Nymeyer, H., Portman, J., Sanbonmatsu, K. Y., and Garcia, A. E. (2003) Peptide folding simulations, Curr. Opin. Struct. Biol. 13, 168-174.
-
(2003)
Curr. Opin. Struct. Biol
, vol.13
, pp. 168-174
-
-
Gnanakaran, S.1
Nymeyer, H.2
Portman, J.3
Sanbonmatsu, K.Y.4
Garcia, A.E.5
-
2
-
-
0027364930
-
Dissecting the structure of a partially folded protein. Circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin
-
Cox, J. P., Evans, P. A., Packman, L. C., Williams, D. H., and Woolfson, D. N. (1993) Dissecting the structure of a partially folded protein. Circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin, J. Mol. Biol. 234, 483-492.
-
(1993)
J. Mol. Biol
, vol.234
, pp. 483-492
-
-
Cox, J.P.1
Evans, P.A.2
Packman, L.C.3
Williams, D.H.4
Woolfson, D.N.5
-
3
-
-
0022804939
-
Stabilization of the ribonuclease S-peptide alpha-helix by trifluoroethanol
-
Nelson, J. W., and Kallenbach, N. R. (1986) Stabilization of the ribonuclease S-peptide alpha-helix by trifluoroethanol, Proteins 1, 211-217.
-
(1986)
Proteins
, vol.1
, pp. 211-217
-
-
Nelson, J.W.1
Kallenbach, N.R.2
-
4
-
-
0008501653
-
A thermostable 35-residue subdomain within villin headpiece
-
McKnight, C. J., Doering, D. S., Matsudaira, P. T., and Kim, P. S. (1996) A thermostable 35-residue subdomain within villin headpiece, J. Mol. Biol. 260, 126-134.
-
(1996)
J. Mol. Biol
, vol.260
, pp. 126-134
-
-
McKnight, C.J.1
Doering, D.S.2
Matsudaira, P.T.3
Kim, P.S.4
-
5
-
-
1542533572
-
Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: The villin headpiece subdomain
-
Tang, Y., Rigotti, D. J., Fairman, R., and Raleigh, D. P. (2004) Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: the villin headpiece subdomain, Biochemistry 43, 3264-3272.
-
(2004)
Biochemistry
, vol.43
, pp. 3264-3272
-
-
Tang, Y.1
Rigotti, D.J.2
Fairman, R.3
Raleigh, D.P.4
-
6
-
-
33644880010
-
Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage
-
Bunagan, M. R., Yang, X., Saven, J. G., and Gai, F. (2006) Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage, J. Phys. Chem. B 110, 3759-3763.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3759-3763
-
-
Bunagan, M.R.1
Yang, X.2
Saven, J.G.3
Gai, F.4
-
7
-
-
0036264492
-
Designing a 20-residue protein
-
Neidigh, J. W., Fesinmeyer, R. M., and Andersen, N. H. (2002) Designing a 20-residue protein, Nat. Struct. Biol. 9, 425-430.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 425-430
-
-
Neidigh, J.W.1
Fesinmeyer, R.M.2
Andersen, N.H.3
-
8
-
-
0037032225
-
Smaller and faster: The 20-residue Trp-cage protein folds in 4 μs
-
Qiu, L., Pabit, S. A., Roitberg, A. E., and Hagen, S. J. (2002) Smaller and faster: the 20-residue Trp-cage protein folds in 4 μs, J. Am. Chem. Soc. 124, 12952-12953.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 12952-12953
-
-
Qiu, L.1
Pabit, S.A.2
Roitberg, A.E.3
Hagen, S.J.4
-
9
-
-
28044460071
-
A microscopic view of miniprotein folding: Enhanced folding efficiency through formation of an intermediate
-
Neuweiler, H., Doose, S., and Sauer, M. (2005) A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate, Proc. Natl. Acad. Sci. U.S.A. 102, 16650-16655.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 16650-16655
-
-
Neuweiler, H.1
Doose, S.2
Sauer, M.3
-
10
-
-
0037065310
-
The Trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
-
Snow, C. D., Zagrovic, B., and Pande, V. S. (2002) The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations, J. Am. Chem. Soc. 124, 14548-14549.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 14548-14549
-
-
Snow, C.D.1
Zagrovic, B.2
Pande, V.S.3
-
11
-
-
0037470691
-
Ab initio folding simulation of the Tip-cage mini-protein approaches NMR resolution
-
Chowdhury, S., Lee, M. C., Xiong, G., and Duan, Y. (2003) Ab initio folding simulation of the Tip-cage mini-protein approaches NMR resolution, J. Mol. Biol. 327, 711-717.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 711-717
-
-
Chowdhury, S.1
Lee, M.C.2
Xiong, G.3
Duan, Y.4
-
12
-
-
0037934616
-
Understanding folding and design: Replica-exchange simulations of "Trp-cage" miniproteins
-
Pitera, J. W., and Swope, W. (2003) Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins, Proc. Natl. Acad. Sci. U.S.A. 100, 7587-7592.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A
, vol.100
, pp. 7587-7592
-
-
Pitera, J.W.1
Swope, W.2
-
13
-
-
0037661296
-
Possible locally driven folding pathways of TC5b, a 20-residue protein
-
Nikiforovich, G. V., Andersen, N. H., Fesinmeyer, R. M., and Frieden, C. (2003) Possible locally driven folding pathways of TC5b, a 20-residue protein, Proteins 52, 292-302.
-
(2003)
Proteins
, vol.52
, pp. 292-302
-
-
Nikiforovich, G.V.1
Andersen, N.H.2
Fesinmeyer, R.M.3
Frieden, C.4
-
14
-
-
0042561888
-
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
-
Zagrovic, B., and Pande, V. (2003) Solvent viscosity dependence of the folding rate of a small protein: distributed computing study, J. Comput. Chem. 24, 1432-1436.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1432-1436
-
-
Zagrovic, B.1
Pande, V.2
-
15
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
Zhou, R. (2003) Trp-cage: folding free energy landscape in explicit water, Proc. Natl. Acad. Sci. U.S.A. 100, 13280-13285.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A
, vol.100
, pp. 13280-13285
-
-
Zhou, R.1
-
16
-
-
1942455253
-
Exploring the protein folding free energy landscape: Coupling replica exchange method with P3ME/RESPA algorithm
-
Zhou, R. (2004) Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm, J. Mol. Graphics Modell. 22, 451-463.
-
(2004)
J. Mol. Graphics Modell
, vol.22
, pp. 451-463
-
-
Zhou, R.1
-
17
-
-
11244291006
-
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model
-
Ding, F., Buldyrev, S. V., and Dokholyan, N. V. (2005) Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model, Biophys. J. 88, 147-155.
-
(2005)
Biophys. J
, vol.88
, pp. 147-155
-
-
Ding, F.1
Buldyrev, S.V.2
Dokholyan, N.V.3
-
18
-
-
21244495332
-
Folding thermodynamics of peptides
-
Irback, A., and Mohanty, S. (2005) Folding thermodynamics of peptides, Biophys. J. 88, 1560-1569.
-
(2005)
Biophys. J
, vol.88
, pp. 1560-1569
-
-
Irback, A.1
Mohanty, S.2
-
19
-
-
33744816177
-
An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein 120
-
Schug, A., and Wenzel, W. (2006) An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein 120, Biophys. J. 90, 4273-4280.
-
(2006)
Biophys. J
, vol.90
, pp. 4273-4280
-
-
Schug, A.1
Wenzel, W.2
-
20
-
-
21444457267
-
Energy landscape paving simulations of the Trp-cage protein
-
Schug, A., Wenzel, W., and Hansmann, U. H. (2005) Energy landscape paving simulations of the Trp-cage protein, J. Chem. Phys. 122, 194711-194717.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 194711-194717
-
-
Schug, A.1
Wenzel, W.2
Hansmann, U.H.3
-
21
-
-
33645408056
-
Balancing solvation and intramolecular interactions: Toward a consistent generalized Born force field
-
Chen, J., Im, W., and Brooks, C. L., III (2006) Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field, J. Am. Chem. Soc. 128, 3728-3736.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 3728-3736
-
-
Chen, J.1
Im, W.2
Brooks III, C.L.3
-
22
-
-
33750468665
-
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
-
Juraszek, J., and Bolhuis, P. G. (2006) Sampling the multiple folding mechanisms of Trp-cage in explicit solvent, Proc. Natl. Acad. Sci.U.S.A. 103, 15859-15864.
-
(2006)
Proc. Natl. Acad. Sci.U.S.A
, vol.103
, pp. 15859-15864
-
-
Juraszek, J.1
Bolhuis, P.G.2
-
24
-
-
33947211608
-
Advances in the analysis of conformational transitions in peptides using differential scanning calorimetry
-
Streicher, W. W., and Makhatadze, G. I. (2007) Advances in the analysis of conformational transitions in peptides using differential scanning calorimetry, Methods Mol. Biol. 350, 105-113.
-
(2007)
Methods Mol. Biol
, vol.350
, pp. 105-113
-
-
Streicher, W.W.1
Makhatadze, G.I.2
-
25
-
-
0025610122
-
Partial molar volumes of polypeptides and their constituent groups in aqueous solution over a broad temperature range
-
Makhatadze, G. I., Medvedkin, V. N., and Privalov, P. L. (1990) Partial molar volumes of polypeptides and their constituent groups in aqueous solution over a broad temperature range, Biopolymers 30, 1001-1010.
-
(1990)
Biopolymers
, vol.30
, pp. 1001-1010
-
-
Makhatadze, G.I.1
Medvedkin, V.N.2
Privalov, P.L.3
-
26
-
-
0022555893
-
Scanning microcalorimetry in studying temperature-induced changes in proteins
-
Privalov, P. L., and Potekhin, S. A. (1986) Scanning microcalorimetry in studying temperature-induced changes in proteins, Methods Enzymol. 131, 4-51.
-
(1986)
Methods Enzymol
, vol.131
, pp. 4-51
-
-
Privalov, P.L.1
Potekhin, S.A.2
-
27
-
-
0018063963
-
Thermodynamic characterization of conformational states of biological macromolecules using differential scanning calorimetry
-
Biltonen, R. L., and Freire, E. (1978) Thermodynamic characterization of conformational states of biological macromolecules using differential scanning calorimetry, CRC Crit. Rev. Biochem. 5, 85-124.
-
(1978)
CRC Crit. Rev. Biochem
, vol.5
, pp. 85-124
-
-
Biltonen, R.L.1
Freire, E.2
-
28
-
-
0027006840
-
Alpha-helix to random coil transitions: Determination of peptide concentration from the CD at the isodichroic point
-
Holtzer, M. E., and Holtzer, A. (1992) Alpha-helix to random coil transitions: determination of peptide concentration from the CD at the isodichroic point, Biopolymers 32, 1675-1677.
-
(1992)
Biopolymers
, vol.32
, pp. 1675-1677
-
-
Holtzer, M.E.1
Holtzer, A.2
-
29
-
-
0032776418
-
Heat capacity change for ribonuclease A folding
-
Pace, C. N., Grimsley, G. R., Thomas, S. T., and Makhatadze, G. I. (1999) Heat capacity change for ribonuclease A folding, Protein Sci. 8, 1500-1504.
-
(1999)
Protein Sci
, vol.8
, pp. 1500-1504
-
-
Pace, C.N.1
Grimsley, G.R.2
Thomas, S.T.3
Makhatadze, G.I.4
-
30
-
-
0018588511
-
Stability of proteins: Small globular proteins
-
Privalov, P. L. (1979) Stability of proteins: small globular proteins, Adv. Protein Chem. 33, 167-241.
-
(1979)
Adv. Protein Chem
, vol.33
, pp. 167-241
-
-
Privalov, P.L.1
-
31
-
-
0024602854
-
Heat capacity and conformation of proteins in the denatured state
-
Privalov, P. L., Tiktopulo, E. I., Venyaminov, S., Griko Yu, V., Makhatadze, G. I., and Khechinashvili, N. N. (1989) Heat capacity and conformation of proteins in the denatured state, J. Mol. Biol. 205, 737-750.
-
(1989)
J. Mol. Biol
, vol.205
, pp. 737-750
-
-
Privalov, P.L.1
Tiktopulo, E.I.2
Venyaminov, S.3
Griko Yu, V.4
Makhatadze, G.I.5
Khechinashvili, N.N.6
-
32
-
-
0025287103
-
Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects
-
Privalov, P. L., and Makhatadze, G. I. (1990) Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects, J. Mol. Biol. 213, 385-391.
-
(1990)
J. Mol. Biol
, vol.213
, pp. 385-391
-
-
Privalov, P.L.1
Makhatadze, G.I.2
-
33
-
-
0027482286
-
Thermodynamics of BPTI folding
-
Makhatadze, G. I., Kim, K. S., Woodward, C., and Privalov, P. L. (1993) Thermodynamics of BPTI folding, Protein Sci. 2, 2028-2036.
-
(1993)
Protein Sci
, vol.2
, pp. 2028-2036
-
-
Makhatadze, G.I.1
Kim, K.S.2
Woodward, C.3
Privalov, P.L.4
-
34
-
-
0036364804
-
Differential scanning calorimetry
-
Lopez, M. M., and Makhatadze, G. I. (2002) Differential scanning calorimetry, Methods Mol. Biol. 173, 113-119.
-
(2002)
Methods Mol. Biol
, vol.173
, pp. 113-119
-
-
Lopez, M.M.1
Makhatadze, G.I.2
-
35
-
-
0025360593
-
Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect
-
Makhatadze, G. I., and Privalov, P. L. (1990) Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect, J. Mol. Biol. 213, 375-384.
-
(1990)
J. Mol. Biol
, vol.213
, pp. 375-384
-
-
Makhatadze, G.I.1
Privalov, P.L.2
-
36
-
-
0000368236
-
Some specific ion effects on the conformation and thermal stability of ribonuclease
-
Ginsburg, A., and Carroll, W. R. (1965) Some specific ion effects on the conformation and thermal stability of ribonuclease, Biochemistry 4, 2159-2174.
-
(1965)
Biochemistry
, vol.4
, pp. 2159-2174
-
-
Ginsburg, A.1
Carroll, W.R.2
-
37
-
-
0032317156
-
Deciphering rules of helix stability in peptides
-
Rohl, C. A., and Baldwin, R. L. (1998) Deciphering rules of helix stability in peptides, Methods Enzymol. 295, 1-26.
-
(1998)
Methods Enzymol
, vol.295
, pp. 1-26
-
-
Rohl, C.A.1
Baldwin, R.L.2
-
38
-
-
0347753737
-
Temperature dependence of the thermodynamics of helix-coil transition
-
Richardson, J. M., and Makhatadze, G. I. (2004) Temperature dependence of the thermodynamics of helix-coil transition, J. Mol. Biol. 335, 1029-1037.
-
(2004)
J. Mol. Biol
, vol.335
, pp. 1029-1037
-
-
Richardson, J.M.1
Makhatadze, G.I.2
-
39
-
-
0027298784
-
Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities
-
Chakrabartty, A., Kortemme, T., Padmanabhan, S., and Baldwin, R. L. (1993) Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities, Biochemistry 32, 5560-5565.
-
(1993)
Biochemistry
, vol.32
, pp. 5560-5565
-
-
Chakrabartty, A.1
Kortemme, T.2
Padmanabhan, S.3
Baldwin, R.L.4
-
40
-
-
0027527209
-
Circular dichroism studies of barnase and its mutants: Characterization of the contribution of aromatic side chains
-
Vuilleumier, S., Sancho, J., Loewenthal, R., and Fersht, A. R. (1993) Circular dichroism studies of barnase and its mutants: characterization of the contribution of aromatic side chains, Biochemistry 32, 10303-10313.
-
(1993)
Biochemistry
, vol.32
, pp. 10303-10313
-
-
Vuilleumier, S.1
Sancho, J.2
Loewenthal, R.3
Fersht, A.R.4
-
41
-
-
0032550183
-
Heat capacities of amino acids, peptides and proteins
-
Makhatadze, G. I. (1998) Heat capacities of amino acids, peptides and proteins, Biophys. Chem. 71, 133-156.
-
(1998)
Biophys. Chem
, vol.71
, pp. 133-156
-
-
Makhatadze, G.I.1
-
42
-
-
30744462335
-
Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4
-
Streicher, W. W., and Makhatadze, G. I. (2006) Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4, J. Am. Chem. Soc. 128, 30-31.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 30-31
-
-
Streicher, W.W.1
Makhatadze, G.I.2
-
43
-
-
33947248825
-
Microcalorimetry of biological macromolecules
-
in press
-
Privalov, P. L., and Dragan, A. I. (2006) Microcalorimetry of biological macromolecules, Biophys. Chem. (in press).
-
(2006)
Biophys. Chem
-
-
Privalov, P.L.1
Dragan, A.I.2
-
44
-
-
0028204537
-
Thermodynamics of barnase unfolding
-
Griko, Y. V., Makhatadze, G. I., Privalov, P. L., and Hartley, R. W. (1994) Thermodynamics of barnase unfolding, Protein Sci. 3, 669-676.
-
(1994)
Protein Sci
, vol.3
, pp. 669-676
-
-
Griko, Y.V.1
Makhatadze, G.I.2
Privalov, P.L.3
Hartley, R.W.4
-
45
-
-
0020348367
-
Stability of proteins. Proteins which do not present a single cooperative system
-
Privalov, P. L. (1982) Stability of proteins. Proteins which do not present a single cooperative system, Adv. Protein Chem. 35, 1-104.
-
(1982)
Adv. Protein Chem
, vol.35
, pp. 1-104
-
-
Privalov, P.L.1
-
46
-
-
1842559515
-
Equilibrium thermal transitions of collagen model peptides
-
Persikov, A. V., Xu, Y., and Brodsky, B. (2004) Equilibrium thermal transitions of collagen model peptides, Protein Sci. 13, 893-902.
-
(2004)
Protein Sci
, vol.13
, pp. 893-902
-
-
Persikov, A.V.1
Xu, Y.2
Brodsky, B.3
-
47
-
-
0033613218
-
MEARA sequence repeat of human CstF-64 polyadenylation factor is helical in solution. A spectroscopic and calorimetric study
-
Richardson, J. M., McMahon, K. W., MacDonald, C. C., and Makhatadze, G. I. (1999) MEARA sequence repeat of human CstF-64 polyadenylation factor is helical in solution. A spectroscopic and calorimetric study, Biochemistry 38, 12869-12875.
-
(1999)
Biochemistry
, vol.38
, pp. 12869-12875
-
-
Richardson, J.M.1
McMahon, K.W.2
MacDonald, C.C.3
Makhatadze, G.I.4
-
48
-
-
13444279887
-
Enthalpy of helix-coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues
-
Richardson, J. M., Lopez, M. M., and Makhatadze, G. I. (2005) Enthalpy of helix-coil transition: missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues, Proc. Natl. Acad. Sci. U.S.A. 102, 1413-1418.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 1413-1418
-
-
Richardson, J.M.1
Lopez, M.M.2
Makhatadze, G.I.3
-
49
-
-
0037022332
-
The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation
-
Lopez, M. M., Chin, D. H., Baldwin, R. L., and Makhatadze, G. I. (2002) The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation, Proc. Natl. Acad. Sci. U.S.A. 99, 1298-1302.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A
, vol.99
, pp. 1298-1302
-
-
Lopez, M.M.1
Chin, D.H.2
Baldwin, R.L.3
Makhatadze, G.I.4
|