-
1
-
-
28644451763
-
Comparative molecular dynamics-similar folds and similar motions?
-
Pang A, Arinaminpathy Y, Sansom MS, Biggin PC. Comparative molecular dynamics-similar folds and similar motions? Proteins 2005; 61: 809-822.
-
(2005)
Proteins
, vol.61
, pp. 809-822
-
-
Pang, A.1
Arinaminpathy, Y.2
Sansom, M.S.3
Biggin, P.C.4
-
2
-
-
35048866000
-
Characterization of protein conformational states by normal-mode frequencies
-
Hall BA, Kaye SL, Pang A, Perera R, Biggin PC. Characterization of protein conformational states by normal-mode frequencies. J Am Chem Soc 2007; 129: 11394-11401.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 11394-11401
-
-
Hall, B.A.1
Kaye, S.L.2
Pang, A.3
Perera, R.4
Biggin, P.C.5
-
3
-
-
27744606438
-
A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein
-
Stockner T, Vogel H, Tieleman D. A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein. Biophys J 2005; 89: 3362-3371.
-
(2005)
Biophys J
, vol.89
, pp. 3362-3371
-
-
Stockner, T.1
Vogel, H.2
Tieleman, D.3
-
4
-
-
4143115810
-
Periplasmic binding proteins: a versatile superfamily for protein engineering
-
Dwyer MA, Hellinga HW. Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr Opin Struct Biol 2004; 14: 495-504.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 495-504
-
-
Dwyer, M.A.1
Hellinga, H.W.2
-
5
-
-
0011729692
-
Two periplasmic transport proteins which interact with a common membrane receptor show extensive homology: complete nucleotide sequences
-
Higgins CF, Ames GF. Two periplasmic transport proteins which interact with a common membrane receptor show extensive homology: complete nucleotide sequences. Proc Natl Acad Sci USA 1981; 78: 6038-6042.
-
(1981)
Proc Natl Acad Sci USA
, vol.78
, pp. 6038-6042
-
-
Higgins, C.F.1
Ames, G.F.2
-
6
-
-
0037052565
-
The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism
-
Locher KP, Lee AT, Rees DC. The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 2002; 296: 1091-1098.
-
(2002)
Science
, vol.296
, pp. 1091-1098
-
-
Locher, K.P.1
Lee, A.T.2
Rees, D.C.3
-
7
-
-
0028063379
-
Structural basis for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein
-
Oh BH, Ames GF, Kim SH. Structural basis for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein. J Biol Chem 1994; 269: 26323-26330.
-
(1994)
J Biol Chem
, vol.269
, pp. 26323-26330
-
-
Oh, B.H.1
Ames, G.F.2
Kim, S.H.3
-
8
-
-
0028067178
-
The bacterial periplasmic histidine-binding protein. structure/function analysis of the ligand-binding site and comparison with related proteins
-
Oh BH, Kang CH, De Bondt H, Kim SH, Nikaido K, Joshi AK, Ames GF. The bacterial periplasmic histidine-binding protein. structure/function analysis of the ligand-binding site and comparison with related proteins. J Biol Chem 1994; 269: 4135-4143.
-
(1994)
J Biol Chem
, vol.269
, pp. 4135-4143
-
-
Oh, B.H.1
Kang, C.H.2
De Bondt, H.3
Kim, S.H.4
Nikaido, K.5
Joshi, A.K.6
Ames, G.F.7
-
9
-
-
0026630610
-
Purification and characterization of the periplasmic lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium
-
Nikaido K, Ames GF. Purification and characterization of the periplasmic lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium. J Biol Chem 1992; 267: 20706-20712.
-
(1992)
J Biol Chem
, vol.267
, pp. 20706-20712
-
-
Nikaido, K.1
Ames, G.F.2
-
10
-
-
0026321096
-
Crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium at 2.7-\AA resolution
-
Kang CH, Shin WC, Yamagata Y, Gokcen S, Ames GF, Kim SH. Crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium at 2.7-\AA resolution. J Biol Chem 1991; 266: 23893-23899.
-
(1991)
J Biol Chem
, vol.266
, pp. 23893-23899
-
-
Kang, C.H.1
Shin, W.C.2
Yamagata, Y.3
Gokcen, S.4
Ames, G.F.5
Kim, S.H.6
-
11
-
-
0029787272
-
Ligand-dependent conformational plasticity of the periplasmic histidine-binding protein HisJ. Involvement in transport specificity
-
Wolf A, Lee KC, Kirsch JF, Ames GF. Ligand-dependent conformational plasticity of the periplasmic histidine-binding protein HisJ. Involvement in transport specificity. J Biol Chem 1996; 271: 21243-21250.
-
(1996)
J Biol Chem
, vol.271
, pp. 21243-21250
-
-
Wolf, A.1
Lee, K.C.2
Kirsch, J.F.3
Ames, G.F.4
-
12
-
-
65249098263
-
Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence
-
Cao J, Huang S, Qian J, Huang J, Jin L, Su Z, Yang J, Liu J. Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence. BMC Evol Biol 2009; 9: 67.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 67
-
-
Cao, J.1
Huang, S.2
Qian, J.3
Huang, J.4
Jin, L.5
Su, Z.6
Yang, J.7
Liu, J.8
-
13
-
-
66249089158
-
A new family of receptor tyrosine kinases with a venus flytrap binding domain in insects and other invertebrates activated by aminoacids
-
Ahier A, Rondard P, Gouignard N, Khayath N, Huang S, Trolet J, Donoghue DJ, Gauthier M, Pin JP, Dissous C. A new family of receptor tyrosine kinases with a venus flytrap binding domain in insects and other invertebrates activated by aminoacids. PLoS One 2009; 4: e5651.
-
(2009)
PLoS One
, vol.4
-
-
Ahier, A.1
Rondard, P.2
Gouignard, N.3
Khayath, N.4
Huang, S.5
Trolet, J.6
Donoghue, D.J.7
Gauthier, M.8
Pin, J.P.9
Dissous, C.10
-
14
-
-
70349333363
-
Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins
-
Cheung J, Le-Khac M, Hendrickson WA. Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins. Proteins 2009; 77: 235-241.
-
(2009)
Proteins
, vol.77
, pp. 235-241
-
-
Cheung, J.1
Le-Khac, M.2
Hendrickson, W.A.3
-
15
-
-
72249085220
-
Collective dynamics of periplasmic glutamine binding protein upon domain closure
-
Loeffler HH, Kitao A. Collective dynamics of periplasmic glutamine binding protein upon domain closure. Biophys J 2009; 97: 2541-2549.
-
(2009)
Biophys J
, vol.97
, pp. 2541-2549
-
-
Loeffler, H.H.1
Kitao, A.2
-
16
-
-
0027235488
-
Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand
-
Oh BH, Pandit J, Kang CH, Nikaido K, Gokcen S, Ames GF, Kim SH. Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand. J Biol Chem 1993; 268: 11348-11355.
-
(1993)
J Biol Chem
, vol.268
, pp. 11348-11355
-
-
Oh, B.H.1
Pandit, J.2
Kang, C.H.3
Nikaido, K.4
Gokcen, S.5
Ames, G.F.6
Kim, S.H.7
-
17
-
-
0031718310
-
Homology modeling, model and software evaluation: three related resources
-
Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G. Homology modeling, model and software evaluation: three related resources. Bioinformatics 1998; 14: 523-528.
-
(1998)
Bioinformatics
, vol.14
, pp. 523-528
-
-
Rodriguez, R.1
Chinea, G.2
Lopez, N.3
Pons, T.4
Vriend, G.5
-
18
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001; 7: 306-317.
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
19
-
-
27344454932
-
GROMACS: fast, flexible, and free
-
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem 2005; 26: 1701-1718.
-
(2005)
J Comput Chem
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
-
20
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman B, editor. The Netherlands: Reidel, Dordrecht;.
-
Berendsen H, Postma J, Van Gunsteren W, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. The Netherlands: Reidel, Dordrecht; 1981. 331-342 p.
-
(1981)
Intermolecular forces
, pp. 331-342
-
-
Berendsen, H.1
Postma, J.2
Van Gunsteren, W.3
Hermans, J.4
-
22
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H, Postma J, Van Gunsteren W, DiNola A, Haak J. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Van Gunsteren, W.3
DiNola, A.4
Haak, J.5
-
23
-
-
84986440341
-
SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto S, Kollman P. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 1992; 13: 952-962.
-
(1992)
J Comput Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.2
-
24
-
-
33846823909
-
Particle mesh Ewald: an N log (N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J Chem Phys 1993; 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
25
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz M, Darden T, Lee H, Pedersen L. A smooth particle mesh Ewald method. J Chem Phys 1995; 103: 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
-
27
-
-
0037671391
-
Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein
-
Pang A, Arinaminpathy Y, Sansom MS, Biggin PC. Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein. FEBS Lett 2003; 550: 168-174.
-
(2003)
FEBS Lett
, vol.550
, pp. 168-174
-
-
Pang, A.1
Arinaminpathy, Y.2
Sansom, M.S.3
Biggin, P.C.4
-
28
-
-
33544461370
-
The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors
-
Felder CB, Graul RC, Lee AY, Merkle HP, Sadee W. The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors. AAPS Pharm Sci 1999; 1: 7-26.
-
(1999)
AAPS Pharm Sci
, vol.1
, pp. 7-26
-
-
Felder, C.B.1
Graul, R.C.2
Lee, A.Y.3
Merkle, H.P.4
Sadee, W.5
-
29
-
-
35548976322
-
Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
-
Tang C, Schwieters CD, Clore GM. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 2007; 449: 1078-1082.
-
(2007)
Nature
, vol.449
, pp. 1078-1082
-
-
Tang, C.1
Schwieters, C.D.2
Clore, G.M.3
-
30
-
-
69949132012
-
Structural stability of electrosprayed proteins: temperature and hydration effects
-
Marklund EG, Larsson DSD, van der Spoel D, Patriksson A, Caleman C. Structural stability of electrosprayed proteins: temperature and hydration effects. Phys Chem Chem Phys 2009; 11: 8069-8078.
-
(2009)
Phys Chem Chem Phys
, vol.11
, pp. 8069-8078
-
-
Marklund, E.G.1
Larsson, D.S.D.2
van der Spoel, D.3
Patriksson, A.4
Caleman, C.5
-
31
-
-
34249799922
-
Cation-pi interactions involving aromatic amino acids
-
discussion1516S-1517S.
-
Dougherty DA. Cation-pi interactions involving aromatic amino acids. J Nutr 2007; 137(6 Suppl 1): 1504S-1508S; discussion1516S-1517S.
-
(2007)
J Nutr
, vol.137
, Issue.6 SUPPL. 1
-
-
Dougherty, D.A.1
-
32
-
-
33344456354
-
Molecular determinants for substrate specificity of the ligand-binding protein OpuAC from Bacillus subtilis for the compatible solutes glycine betaine and proline betaine
-
Horn C, Sohn-Bösser L, Breed J, Welte W, Schmitt L, Bremer E. Molecular determinants for substrate specificity of the ligand-binding protein OpuAC from Bacillus subtilis for the compatible solutes glycine betaine and proline betaine. J Mol Biol 2006; 357: 592-606.
-
(2006)
J Mol Biol
, vol.357
, pp. 592-606
-
-
Horn, C.1
Sohn-Bösser, L.2
Breed, J.3
Welte, W.4
Schmitt, L.5
Bremer, E.6
|