-
1
-
-
73949154012
-
Molecular simulations of peptides: A useful tool for the development of new drugs and for the study of molecular recognition
-
M. Meli, G. Colombo, Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition, Methods Mol. Biol. 570 (2009) 77-153.
-
(2009)
Methods Mol. Biol.
, vol.570
, pp. 77-153
-
-
Meli, M.1
Colombo, G.2
-
2
-
-
23244452958
-
Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization
-
DOI 10.1529/biophysj.105.061978
-
A. Caballero-Herrera, K. Nordstrand, K.D. Berndt, L. Nilsson, Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization, Biophys. J. 89 (2005) 842-857. (Pubitemid 41098971)
-
(2005)
Biophysical Journal
, vol.89
, Issue.2
, pp. 842-857
-
-
Caballero-Herrera, A.1
Nordstrand, K.2
Berndt, K.D.3
Nilsson, L.4
-
3
-
-
45849084663
-
Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations
-
C. Camilloni, A.G. Rocco, I. Eberini, E. Gianazza, R.A. Broglia, G. Tiana, Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations, Biophys. J. 94 (2008) 4654-4661.
-
(2008)
Biophys. J.
, vol.94
, pp. 4654-4661
-
-
Camilloni, C.1
Rocco, A.G.2
Eberini, I.3
Gianazza, E.4
Broglia, R.A.5
Tiana, G.6
-
4
-
-
34250869055
-
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism
-
DOI 10.1021/ja069232+
-
E.P. O'Brien, R.I. Dima, B. Brooks, D. Thirumalai, Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism, J. Am. Chem. Soc. 129 (2007) 7346-7353. (Pubitemid 46980813)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.23
, pp. 7346-7353
-
-
O'Brien, E.P.1
Dima, R.I.2
Brooks, B.3
Thirumalai, D.4
-
5
-
-
55949131241
-
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
-
L. Hua, R. Zhou, D. Thirumalai, B.J. Berne, Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding, Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 16928-16933.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 16928-16933
-
-
Hua, L.1
Zhou, R.2
Thirumalai, D.3
Berne, B.J.4
-
6
-
-
46149109506
-
The multiscale coarse-graining method.I. A rigorous bridge between atomistic and coarse-grained models
-
W.G. Noid, J.W. Chu, G.S. Ayton, V. Krishna, S. Izvekov, G.A. Voth, A. Das, H.C. Andersen, The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models, J. Chem. Phys. 128 (2008) 244114.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 244114
-
-
Noid, W.G.1
Chu, J.W.2
Ayton, G.S.3
Krishna, V.4
Izvekov, S.5
Voth, G.A.6
Das, A.7
Andersen, H.C.8
-
7
-
-
47749106779
-
Atomistic mechanism of protein denaturation by urea
-
A. Das, C. Mukhopadhyay, Atomistic mechanism of protein denaturation by urea, J. Phys. Chem. B 112 (2008) 7903-7908.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 7903-7908
-
-
Das, A.1
Mukhopadhyay, C.2
-
8
-
-
44049099949
-
Characterization of the protein unfolding processes induced by urea and temperature
-
A.G. Rocco, L. Mollica, P. Ricchiuto, A.M. Baptista, E. Gianazza, I. Eberini, Characterization of the protein unfolding processes induced by urea and temperature, Biophys. J. 94 (2008) 2241-2251.
-
(2008)
Biophys. J.
, vol.94
, pp. 2241-2251
-
-
Rocco, A.G.1
Mollica, L.2
Ricchiuto, P.3
Baptista, A.M.4
Gianazza, E.5
Eberini, I.6
-
9
-
-
57149110439
-
Polar or apolar- The role of polarity for ureainduced protein denaturation
-
M.C. Stumpe, H. Grubmuller, Polar or apolar-the role of polarity for ureainduced protein denaturation, PLoS Comput. Biol. 4 (2008) e1000221.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Stumpe, M.C.1
Grubmuller, H.2
-
10
-
-
67650363919
-
Urea impedes the hydrophobic collapse of partially unfolded proteins
-
M.C. Stumpe, H. Grubmuller, Urea impedes the hydrophobic collapse of partially unfolded proteins, Biophys. J. 96 (2009) 3744-3752.
-
(2009)
Biophys. J.
, vol.96
, pp. 3744-3752
-
-
Stumpe, M.C.1
Grubmuller, H.2
-
11
-
-
63149153986
-
Urea's action on hydrophobic interactions
-
R. Zangi, R.H. Zhou, B.J. Berne, Urea's action on hydrophobic interactions, J. Am. Chem. Soc. 131 (2009) 1535-1541.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 1535-1541
-
-
Zangi, R.1
Zhou, R.H.2
Berne, B.J.3
-
12
-
-
77749285768
-
Equilibrium study of protein denaturation by urea
-
D.R. Canchi, D. Paschek, A.E. Garcia, Equilibrium study of protein denaturation by urea, J. Am. Chem. Soc. 132 (2010) 2338-2344.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 2338-2344
-
-
Canchi, D.R.1
Paschek, D.2
Garcia, A.E.3
-
13
-
-
0029294696
-
Multiple molecular recognition properties of the lipocalin protein family
-
D.R. Flower, Multiple molecular recognition properties of the lipocalin protein family, J. Mol. Recognit. 8 (1995) 185-195.
-
(1995)
J. Mol. Recognit.
, vol.8
, pp. 185-195
-
-
Flower, D.R.1
-
14
-
-
0032491188
-
Structural basis of the tanford transition of bovine β-lactoglobulin
-
DOI 10.1021/bi981016t
-
B.Y. Qin, M.C. Bewley, L.K. Creamer, H.M. Baker, E.N. Baker, G.B. Jameson, Structural basis of the Tanford transition of bovine beta-lactoglobulin, Biochemistry-US 37 (1998) 14014-14023. (Pubitemid 28471234)
-
(1998)
Biochemistry
, vol.37
, Issue.40
, pp. 14014-14023
-
-
Qin, B.Y.1
Bewley, M.C.2
Creamer, L.K.3
Baker, H.M.4
Baker, E.N.5
Jameson, G.B.6
-
15
-
-
0004907667
-
Bovine β-lactoglobulin at 1.8 A resolution - Still an enigmatic lipocalin
-
S. Brownlow, J.H. Morais Cabral, R. Cooper, D.R. Flower, S.J. Yewdall, I. Polikarpov, A.C. North, L. Sawyer, Bovine beta-lactoglobulin at 1.8A resolution-still an enigmatic lipocalin, Structure 5 (1997) 481-495. (Pubitemid 27191225)
-
(1997)
Structure
, vol.5
, Issue.4
, pp. 481-495
-
-
Brownlow, S.1
Morais Cabral, J.H.2
Cooper, R.3
Flower, D.R.4
Yewdall, S.J.5
Polikarpov, I.6
North, A.C.T.7
Sawyer, L.8
-
16
-
-
0029944773
-
Partially folded structure of monomeric bovine β-lactoglobulin
-
DOI 10.1016/0014-5793(96)00100-7
-
H. Molinari, L. Ragona, L. Varani, G. Musco, R. Consonni, L. Zetta, H.L. Monaco, Partially folded structure of monomeric bovine beta-lactoglobulin, FEBS Lett. 381 (1996) 237-243. (Pubitemid 26080343)
-
(1996)
FEBS Letters
, vol.381
, Issue.3
, pp. 237-243
-
-
Molinari, H.1
Ragona, L.2
Varani, L.3
Musco, G.4
Consonni, R.5
Zetta, L.6
Monaco, H.L.7
-
17
-
-
0032475891
-
Monomeric bovine β-lactoglobulin adopts a β-barrel fold at pH 2
-
DOI 10.1016/S0014-5793(98)00936-3, PII S0014579398009363
-
F. Fogolari, L. Ragona, L. Zetta, S. Romagnoli, K.G. De Kruif, H. Molinari, Monomeric bovine beta-lactoglobulin adopts a beta-barrel fold at pH 2, FEBS Lett. 436 (1998) 149-154. (Pubitemid 28468545)
-
(1998)
FEBS Letters
, vol.436
, Issue.2
, pp. 149-154
-
-
Fogolari, F.1
Ragona, L.2
Zetta, L.3
Romagnoli, S.4
De Kruif, K.G.5
Molinari, H.6
-
18
-
-
0030635208
-
Identification of a conserved Hydrophobie cluster in partially folded bovine β-lactoglobulin at pH 2
-
L. Ragona, F. Pusterla, L. Zetta, H.L. Monaco, H. Molinari, Identification of a conserved hydrophobic cluster in partially folded bovine beta-lactoglobulin at pH 2, Fold. Des. 2 (1997) 281-290. (Pubitemid 127740550)
-
(1997)
Folding and Design
, vol.2
, Issue.5
, pp. 281-290
-
-
Ragona, L.1
Pusterla, F.2
Zetta, L.3
Monaco, H.L.4
Molinari, H.5
-
19
-
-
0032741871
-
Solution structure and dynamics of bovine β-lactoglobulin A
-
K. Kuwata, M. Hoshino, V. Forge, S. Era, C.A. Batt, Y. Goto, Solution structure and dynamics of bovine beta-lactoglobulin A, Protein Sci. 8 (1999) 2541-2545. (Pubitemid 29536426)
-
(1999)
Protein Science
, vol.8
, Issue.11
, pp. 2541-2545
-
-
Kuwata, K.1
Hoshino, M.2
Forge, V.3
Era, S.4
Batt, C.A.5
Goto, Y.6
-
20
-
-
0033135870
-
Equilibrium unfolding cd studies of bovine β-lactoglobulin and its 14- 52 fragment at acidic pH
-
DOI 10.1002/(SICI)1097-0282(199905)49:6<441::AID-BIP2>3.0.CO;2-A
-
L. Ragona, L. Confalonieri, L. Zetta, K.G. De Kruif, S. Mammi, E. Peggion, R. Longhi, H. Molinari, Equilibrium unfolding CD studies of bovine beta-lactoglobulin and its 14-52 fragment at acidic pH, Biopolymers 49 (1999) 441-450. (Pubitemid 29157356)
-
(1999)
Biopolymers
, vol.49
, Issue.6
, pp. 441-450
-
-
Ragona, L.1
Confalonieri, L.2
Zetta, L.3
De Kruif, K.G.4
Mammi, S.5
Peggion, E.6
Longhi, R.7
Molinari, H.8
-
21
-
-
0033527582
-
Unfolding and refolding of bovine β-lactoglobulin monitored by hydrogen exchange measurements
-
DOI 10.1006/jmbi.1999.3191
-
L. Ragona, F. Fogolari, S. Romagnoli, L. Zetta, J.L. Maubois, H. Molinari, Unfolding and refolding of bovine beta-lactoglobulin monitored by hydrogen exchange measurements, J. Mol. Biol. 293 (1999) 953-969. (Pubitemid 29527676)
-
(1999)
Journal of Molecular Biology
, vol.293
, Issue.4
, pp. 953-969
-
-
Ragona, L.1
Fogolari, F.2
Romagnoli, S.3
Zetta, L.4
Maubois, J.L.5
Molinari, H.6
-
22
-
-
67349093283
-
Structural dynamics and folding of beta-lactoglobulin probed by heteronuclear NMR
-
K. Sakurai, T. Konuma, M. Yagi, Y. Goto, Structural dynamics and folding of beta-lactoglobulin probed by heteronuclear NMR, Biochim. Biophys. Acta 1790 (2009) 527-537.
-
(2009)
Biochim. Biophys. Acta
, vol.1790
, pp. 527-537
-
-
Sakurai, K.1
Konuma, T.2
Yagi, M.3
Goto, Y.4
-
23
-
-
10844294270
-
Porcine beta-lactoglobulin chemical unfolding: Identification of a non-native α-helical intermediate
-
DOI 10.1002/prot.20309
-
L. D'Alfonso, M. Collini, L. Ragona, R. Ugolini, G. Baldini, H. Molinari, Porcine beta-lactoglobulin chemical unfolding: identification of a non-native alphahelical intermediate, Proteins 58 (2005) 70-79. (Pubitemid 39665617)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.58
, Issue.1
, pp. 70-79
-
-
D'Alfonso, L.1
Collini, M.2
Ragona, L.3
Ugolini, R.4
Baldini, G.5
Molinari, H.6
-
24
-
-
0035150938
-
Structural and kinetic characterization of early folding events in β-lactoglobulin
-
DOI 10.1038/84145
-
K. Kuwata, R. Shastry, H. Cheng, M. Hoshino, C.A. Batt, Y. Goto, H. Roder, Structural and kinetic characterization of early folding events in beta-lactoglobulin, Nat. Struct. Biol. 8 (2001) 151-155. (Pubitemid 32116068)
-
(2001)
Nature Structural Biology
, vol.8
, Issue.2
, pp. 151-155
-
-
Kuwata, K.1
Shastry, R.2
Cheng, H.3
Hoshino, M.4
Batt, C.A.5
Goto, Y.6
Roder, H.7
-
25
-
-
0034598947
-
Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix
-
V. Forge, M. Hoshino, K. Kuwata, M. Arai, K. Kuwajima, C.A. Batt, Y. Goto, Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix, J. Mol. Biol. 296 (2000) 1039-1051.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1039-1051
-
-
Forge, V.1
Hoshino, M.2
Kuwata, K.3
Arai, M.4
Kuwajima, K.5
Batt, C.A.6
Goto, Y.7
-
26
-
-
0038392577
-
Trehalose influence on beta-lactoglobulin stability and hydration by time resolved fluorescence
-
DOI 10.1046/j.1432-1033.2003.03621.x
-
L. D'Alfonso, M. Collini, G. Baldini, Trehalose influence on beta-lactoglobulin stability and hydration by time resolved fluorescence, Eur. J. Biochem. 270 (2003) 2497-2504. (Pubitemid 36645368)
-
(2003)
European Journal of Biochemistry
, vol.270
, Issue.11
, pp. 2497-2504
-
-
D'Alfonso, L.1
Collini, M.2
Baldini, G.3
-
27
-
-
0346668369
-
PH and ionic strength dependence of protein (Un)folding and ligand binding to bovine β-lactoglobulins A and B
-
DOI 10.1021/bi020493f
-
T. Beringhelli, I. Eberini, M. Galliano, A. Pedoto, M. Perduca, A. Sportiello, E. Fontana, H.L. Monaco, E. Gianazza, pH and ionic strength dependence of protein (un)folding and ligand binding to bovine beta-lactoglobulins A and B, Biochemistry-US 41 (2002) 15415-15422. (Pubitemid 36008153)
-
(2002)
Biochemistry
, vol.41
, Issue.51
, pp. 15415-15422
-
-
Beringhelli, T.1
Eberini, I.2
Galliano, M.3
Pedoto, A.4
Perduca, M.5
Sportiello, A.6
Fontana, E.7
Monaco, H.L.8
Gianazza, E.9
-
28
-
-
0034825616
-
1: Structural differences between genetic variants A and B and features of the Tanford transition
-
DOI 10.1046/j.1432-1327.2001.01918.x
-
K.M. Oliveira, V.L. Valente-Mesquita, M.M. Botelho, L. Sawyer, S.T. Ferreira, I. Polikarpov, Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transition, Eur. J. Biochem. 268 (2001) 477-483. (Pubitemid 32862681)
-
(2001)
European Journal of Biochemistry
, vol.268
, Issue.2
, pp. 477-483
-
-
Oliveira, K.M.G.1
Valente-Mesquita, V.L.2
Botelho, M.M.3
Sawyer, L.4
Ferreira, S.T.5
Polikarpov, I.6
-
29
-
-
0000371745
-
Do denaturants interact with aromatic-hydrocarbons in water
-
E.M. Duffy, P.J. Kowalczyk, W.L. Jorgensen, Do denaturants interact with aromatic-hydrocarbons in water, J. Am. Chem. Soc. 115 (1993) 9271-9275.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9271-9275
-
-
Duffy, E.M.1
Kowalczyk, P.J.2
Jorgensen, W.L.3
-
30
-
-
32044466479
-
Urea parametrization for molecular dynamics simulations
-
A. Caballero-Herrera, L. Nilsson, Urea parametrization for molecular dynamics simulations, J. Mol. Struct.: Theochem 758 (2006) 139-148.
-
(2006)
J. Mol. Struct.: Theochem
, vol.758
, pp. 139-148
-
-
Caballero-Herrera, A.1
Nilsson, L.2
-
31
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
DOI 10.1002/jcc.20291
-
D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, H.J. Berendsen, GROMACS: fast, flexible, and free, J. Comput. Chem. 26 (2005) 1701-1718. (Pubitemid 43076182)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
32
-
-
35748935079
-
Wordom: A program for efficient analysis of molecular dynamics simulations
-
DOI 10.1093/bioinformatics/btm378
-
M. Seeber, M. Cecchini, F. Rao, G. Settanni, A. Caflisch, Wordom: a program for efficient analysis of molecular dynamics simulations, Bioinformatics 23 (2007) 2625-2627. (Pubitemid 350048368)
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2625-2627
-
-
Seeber, M.1
Cecchini, M.2
Rao, F.3
Settanni, G.4
Caflisch, A.5
-
33
-
-
0033134665
-
Structural details of urea binding to barnase: A molecular dynamics analysis
-
DOI 10.1016/S0969-2126(99)80064-1
-
A. Caflisch, M. Karplus, Structural details of urea binding to barnase: amolecular dynamics analysis, Structure 7 (1999) 477-488. (Pubitemid 29230482)
-
(1999)
Structure
, vol.7
, Issue.5
, pp. 477-488
-
-
Caflisch, A.1
Karplus, M.2
-
35
-
-
0035816223
-
Native-like β-hairpin retained in the cold-denatured state of bovine β-lactoglobulin
-
DOI 10.1006/jmbi.2001.4777
-
H. Katou, M. Hoshino, H. Kamikubo, C.A. Batt, Y. Goto, Native-like beta-hairpin retained in the cold-denatured state of bovine beta-lactoglobulin, J. Mol. Biol. 310 (2001) 471-484. (Pubitemid 32664880)
-
(2001)
Journal of Molecular Biology
, vol.310
, Issue.2
, pp. 471-484
-
-
Katou, H.1
Hoshino, M.2
Kamikubo, H.3
Batt, C.A.4
Goto, Y.5
-
36
-
-
0037176830
-
Peptide models of folding initiation sites of bovine β- lactoglobulin: Identification of nativelike hydrophobic interactions involving G and H strands
-
DOI 10.1021/bi011615r
-
L. Ragona, M. Catalano, L. Zetta, R. Longhi, F. Fogolari, H. Molinari, Peptide models of folding initiation sites of bovine beta-lactoglobulin: identification of nativelike hydrophobic interactions involving G and H strands, Biochemistry- US 41 (2002) 2786-2796. (Pubitemid 34168948)
-
(2002)
Biochemistry
, vol.41
, Issue.8
, pp. 2786-2796
-
-
Ragona, L.1
Catalano, M.2
Zetta, L.3
Longhi, R.4
Fogolari, F.5
Molinari, H.6
-
37
-
-
0028168283
-
Tryptophan-19 of beta-lactoglobulin, the only residue completely conserved in the lipocalin superfamily, is not essential for binding retinol, but relevant to stabilizing bound retinol and maintaining its structure
-
Y. Katakura, M. Totsuka, A. Ametani, S. Kaminogawa, Tryptophan-19 of beta-lactoglobulin, the only residue completely conserved in the lipocalin superfamily, is not essential for binding retinol, but relevant to stabilizing bound retinol and maintaining its structure, Biochim. Biophys. Acta 1207 (1994) 58-67.
-
(1994)
Biochim. Biophys. Acta
, vol.1207
, pp. 58-67
-
-
Katakura, Y.1
Totsuka, M.2
Ametani, A.3
Kaminogawa, S.4
-
38
-
-
77955365355
-
On the stability of chymotrypsin inhibitor 2 in a 10M urea solution. The role of interaction energies for urea-induced protein denaturation
-
M. Lindgren, P.O. Westlund, On the stability of chymotrypsin inhibitor 2 in a 10M urea solution. The role of interaction energies for urea-induced protein denaturation, Phys. Chem. Chem. Phys. 12 (2010) 9358-9366.
-
Phys. Chem. Chem. Phys.
, vol.12
, Issue.2010
, pp. 9358-9366
-
-
Lindgren, M.1
Westlund, P.O.2
-
39
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22 (1983) 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|