-
1
-
-
0037450782
-
Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression
-
doi:10.1093/emboj/cdg085
-
Mok KC, Wingreen NS, Bassler BL, (2003) Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression. EMBO J 22: 870-881. doi:10.1093/emboj/cdg085. PubMed: 12574123.
-
(2003)
EMBO J
, vol.22
, pp. 870-881
-
-
Mok, K.C.1
Wingreen, N.S.2
Bassler, B.L.3
-
2
-
-
0036157549
-
Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm
-
doi:10.1128/jb.184.4.1140-1154.2002
-
Sauer K, Camper AK, Ehrlich GD, Costerton JW, Davies DG, (2002) Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J Bacteriol 184: 1140-1154. doi:10.1128/jb.184.4.1140-1154.2002. PubMed: 11807075.
-
(2002)
J Bacteriol
, vol.184
, pp. 1140-1154
-
-
Sauer, K.1
Camper, A.K.2
Ehrlich, G.D.3
Costerton, J.W.4
Davies, D.G.5
-
3
-
-
0032989877
-
Active efflux and diffusion are involved in transport of Pseudomonas aeruginosa cell-to-cell signals
-
PubMed: 9973347
-
Pearson JP, Van Delden C, Iglewski BH, (1999) Active efflux and diffusion are involved in transport of Pseudomonas aeruginosa cell-to-cell signals. J Bacteriol 181: 1203-1210. PubMed: 9973347.
-
(1999)
J Bacteriol
, vol.181
, pp. 1203-1210
-
-
Pearson, J.P.1
Van Delden, C.2
Iglewski, B.H.3
-
4
-
-
51149109323
-
Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis
-
doi:10.1099/mic.0.2008/019281-0
-
Willcox MD, Zhu H, Conibear TC, Hume EB, Givskov M, et al. (2008) Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis. Microbiology 154: 2184-2194. doi:10.1099/mic.0.2008/019281-0. PubMed: 18667552.
-
(2008)
Microbiology
, vol.154
, pp. 2184-2194
-
-
Willcox, M.D.1
Zhu, H.2
Conibear, T.C.3
Hume, E.B.4
Givskov, M.5
-
5
-
-
1842791546
-
Specificity and enzyme kinetics of the quorum-quenching N-Acyl homoserine lactone lactonase (AHL-lactonase)
-
doi:10.1074/jbc.M311194200
-
Wang LH, Weng LX, Dong YH, Zhang LH, (2004) Specificity and enzyme kinetics of the quorum-quenching N-Acyl homoserine lactone lactonase (AHL-lactonase). J Biol Chem 279: 13645-13651. doi:10.1074/jbc.M311194200. PubMed: 14734559.
-
(2004)
J Biol Chem
, vol.279
, pp. 13645-13651
-
-
Wang, L.H.1
Weng, L.X.2
Dong, Y.H.3
Zhang, L.H.4
-
6
-
-
0034770056
-
Quorum sensing in bacteria
-
doi:10.1146/annurev.micro.55.1.165
-
Miller MB, Bassler BL, (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55: 165-199. doi:10.1146/annurev.micro.55.1.165. PubMed: 11544353.
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 165-199
-
-
Miller, M.B.1
Bassler, B.L.2
-
7
-
-
0030985995
-
Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa
-
PubMed: 9150205
-
Pesci EC, Pearson JP, Seed PC, Iglewski BH, (1997) Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa. J Bacteriol 179: 3127-3132. PubMed: 9150205.
-
(1997)
J Bacteriol
, vol.179
, pp. 3127-3132
-
-
Pesci, E.C.1
Pearson, J.P.2
Seed, P.C.3
Iglewski, B.H.4
-
8
-
-
15944383000
-
Quorum sensing and quorum-quenching enzymes
-
Spec No: 101-109
-
Dong YH, Zhang LH, (2005) Quorum sensing and quorum-quenching enzymes. J Microbiol 43Spec No: 101-109.
-
(2005)
J Microbiol
, vol.43
-
-
Dong, Y.H.1
Zhang, L.H.2
-
9
-
-
84884229310
-
-
EnzymesABreslowR. Wiley-VCH Verlag., Wiley-VCH Verlag
-
(2005) Enzymes A, Breslow R, eds. Wiley-VCH Verlag.
-
(2005)
-
-
-
10
-
-
29144497867
-
The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase
-
doi:10.1073/pnas.0504996102
-
Kim MH, Choi WC, Kang HO, Lee JS, Kang BS, et al. (2005) The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase. Proc Natl Acad Sci U S A 102: 17606-17611. doi:10.1073/pnas.0504996102. PubMed: 16314577.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 17606-17611
-
-
Kim, M.H.1
Choi, W.C.2
Kang, H.O.3
Lee, J.S.4
Kang, B.S.5
-
11
-
-
64349108338
-
Reaction mechanism of the dinuclear zinc enzyme N-acyl-L-homoserine lactone hydrolase: a quantum chemical study
-
doi:10.1021/ic801531n
-
Liao RZ, Yu JG, Himo F, (2009) Reaction mechanism of the dinuclear zinc enzyme N-acyl-L-homoserine lactone hydrolase: a quantum chemical study. Inorg Chem 48: 1442-1448. doi:10.1021/ic801531n. PubMed: 19159270.
-
(2009)
Inorg Chem
, vol.48
, pp. 1442-1448
-
-
Liao, R.Z.1
Yu, J.G.2
Himo, F.3
-
12
-
-
23844552796
-
Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis
-
doi:10.1073/pnas.0505255102
-
Liu D, Lepore BW, Petsko GA, Thomas PW, Stone EM, et al. (2005) Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis. Proc Natl Acad Sci U S A 102: 11882-11887. doi:10.1073/pnas.0505255102. PubMed: 16087890.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 11882-11887
-
-
Liu, D.1
Lepore, B.W.2
Petsko, G.A.3
Thomas, P.W.4
Stone, E.M.5
-
13
-
-
47649131677
-
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures
-
Liu D, Momb J, Thomas PW, Moulin A, Petsko GA, et al. (2008) Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures. Biochemistry 47: 7706-7714.
-
(2008)
Biochemistry
, vol.47
, pp. 7706-7714
-
-
Liu, D.1
Momb, J.2
Thomas, P.W.3
Moulin, A.4
Petsko, G.A.5
-
14
-
-
0032868673
-
Metallo-beta-lactamase: structure and mechanism
-
doi:10.1016/S1367-5931(99)00017-4
-
Wang Z, Fast W, Valentine AM, Benkovic SJ, (1999) Metallo-beta-lactamase: structure and mechanism. Curr Opin Chem Biol 3: 614-622. doi:10.1016/S1367-5931(99)00017-4. PubMed: 10508665.
-
(1999)
Curr Opin Chem Biol
, vol.3
, pp. 614-622
-
-
Wang, Z.1
Fast, W.2
Valentine, A.M.3
Benkovic, S.J.4
-
15
-
-
60749124902
-
QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A
-
doi:10.1016/j.theochem.2008.06.033
-
Szeto M, Mujika JI, Zurek J, Mulholland AJ, Harvey JN, (2009) QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A. J Mol Struct THEOCHEM 898: 106-114. doi:10.1016/j.theochem.2008.06.033.
-
(2009)
J Mol Struct THEOCHEM
, vol.898
, pp. 106-114
-
-
Szeto, M.1
Mujika, J.I.2
Zurek, J.3
Mulholland, A.J.4
Harvey, J.N.5
-
16
-
-
84884242737
-
-
Spartan 06 for Macintosh, Irvine, Califiornia. Wavefunction, Inc., Wavefunction, Inc
-
Spartan, 06 for Macintosh, Irvine, Califiornia (2006). Wavefunction, Inc.
-
(2006)
-
-
-
17
-
-
7544226311
-
PRODRG - a tool for high-throughput crystallography of protein-ligand complexes
-
Schuettelkopf AW, van Aalten DMF, (2004) PRODRG- a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D60: 1335-1363.
-
(2004)
Acta Crystallogr
, vol.D60
, pp. 1335-1363
-
-
Schuettelkopf, A.W.1
van Aalten, D.M.F.2
-
18
-
-
0000945505
-
Computing the ionization states of proteins with a detailed charge model
-
doi:10.1002/(SICI)1096-987X(19961115)17:14
-
Antosiewicz J, Briggs JM, Elcock AH, Gilson MK, McCammon JA, (1996) Computing the ionization states of proteins with a detailed charge model. J Comput Chem 17: 1633-1644. doi:10.1002/(SICI)1096-987X(19961115)17:14.
-
(1996)
J Comput Chem
, vol.17
, pp. 1633-1644
-
-
Antosiewicz, J.1
Briggs, J.M.2
Elcock, A.H.3
Gilson, M.K.4
McCammon, J.A.5
-
19
-
-
0028305457
-
Prediction of pH-dependent properties of proteins
-
doi:10.1006/jmbi.1994.1301
-
Antosiewicz J, McCammon JA, Gilson MK, (1994) Prediction of pH-dependent properties of proteins. J Mol Biol 238: 415-436. doi:10.1006/jmbi.1994.1301. PubMed: 8176733.
-
(1994)
J Mol Biol
, vol.238
, pp. 415-436
-
-
Antosiewicz, J.1
McCammon, J.A.2
Gilson, M.K.3
-
20
-
-
0029633152
-
Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program
-
Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, et al. (1995) Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program. Comp Phys Commun 91: 57-95.
-
(1995)
Comp Phys Commun
, vol.91
, pp. 57-95
-
-
Madura, J.D.1
Briggs, J.M.2
Wade, R.C.3
Davis, M.E.4
Luty, B.A.5
-
21
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
doi:10.1021/jp973084f
-
Mackerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616. doi:10.1021/jp973084f.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
-
22
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
doi:10.1002/jcc.21287
-
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, et al. (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30: 1545-1614. doi:10.1002/jcc.21287. PubMed: 19444816.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks 3rd, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
-
23
-
-
28644432877
-
Very Fast Empirical Prediction and Interpretation of Protein pKa Values
-
doi:10.1002/prot.20660
-
Li H, Robertson AD, Jensen JH, (2005) Very Fast Empirical Prediction and Interpretation of Protein pKa Values. Proteins 61: 704-721. doi:10.1002/prot.20660. PubMed: 16231289.
-
(2005)
Proteins
, vol.61
, pp. 704-721
-
-
Li, H.1
Robertson, A.D.2
Jensen, J.H.3
-
24
-
-
57349090665
-
Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes
-
doi:10.1002/prot.22102
-
Bas DC, Rogers DM, Jensen JH, (2008) Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes. Proteins 73: 765-783. doi:10.1002/prot.22102. PubMed: 18498103.
-
(2008)
Proteins
, vol.73
, pp. 765-783
-
-
Bas, D.C.1
Rogers, D.M.2
Jensen, J.H.3
-
25
-
-
54049083045
-
Effects of antibiotics on quorum sensing in Pseudomonas aeruginosa
-
doi:10.1128/AAC.01230-07
-
Skindersoe ME, Alhede M, Phipps R, Yang L, Jensen PO, et al. (2008) Effects of antibiotics on quorum sensing in Pseudomonas aeruginosa. Antimicrob Agents Chemother 52: 3648-3663. doi:10.1128/AAC.01230-07. PubMed: 18644954.
-
(2008)
Antimicrob Agents Chemother
, vol.52
, pp. 3648-3663
-
-
Skindersoe, M.E.1
Alhede, M.2
Phipps, R.3
Yang, L.4
Jensen, P.O.5
-
26
-
-
79951476387
-
PROPKA3: Consistent Treatment of Internal and SurfaceResidues in Empirical pKa predictions
-
doi:10.1021/ct100578z
-
Olsson MHM, Sondergaard CR, Rostkowski M, Jensen JH, (2011) PROPKA3: Consistent Treatment of Internal and SurfaceResidues in Empirical pKa predictions. J Chem Theory Computation 7: 525-537. doi:10.1021/ct100578z.
-
(2011)
J Chem Theory Computation
, vol.7
, pp. 525-537
-
-
Olsson, M.H.M.1
Sondergaard, C.R.2
Rostkowski, M.3
Jensen, J.H.4
-
27
-
-
27344454932
-
GROMACS: Fast, Flexible and Free
-
doi:10.1002/jcc.20291
-
van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: Fast, Flexible and Free. J Comput Chem 26: 1701-1718. doi:10.1002/jcc.20291. PubMed: 16211538.
-
(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
-
28
-
-
0008819754
-
The GROMOS Biomolecular Simulation Program Package
-
103: 3596-3607
-
Scott WRP, Huenenberger IG, Tironi AE, Mark SR, Billeter SR, et al. (2001) The GROMOS Biomolecular Simulation Program Package. Phys Chem A, 103: 3596-3607.
-
(2001)
Phys Chem A
-
-
Scott, W.R.P.1
Huenenberger, I.G.2
Tironi, A.E.3
Mark, S.R.4
Billeter, S.R.5
-
29
-
-
84986519235
-
Parameterization and evaluation of a flexible water model
-
doi:10.1002/jcc.540160413
-
Ferguson DM, (1995) Parameterization and evaluation of a flexible water model. J Comput Chem 16: 501-511. doi:10.1002/jcc.540160413.
-
(1995)
J Comput Chem
, vol.16
, pp. 501-511
-
-
Ferguson, D.M.1
-
30
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
doi:10.1002/(SICI)1096-987X(199709)18:12
-
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM, (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18: 1463-1472. doi:10.1002/(SICI)1096-987X(199709)18:12.
-
(1997)
J Comput Chem
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
31
-
-
33750587438
-
Molecular Dynamics with coupling to an external bath
-
doi:10.1063/1.448118
-
Berendsen HJC, Postma JPM, DiNola A, Haak JR, (1984) Molecular Dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690. doi:10.1063/1.448118.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
DiNola, A.3
Haak, J.R.4
-
32
-
-
0032232405
-
Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
-
261
-
Marelius J, Kolmodin K, Feierberg I, Aqvist J, (1998) Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J Mol Graph Model 16: 213-225, 261.
-
(1998)
J Mol Graph Model
, vol.16
, pp. 213-225
-
-
Marelius, J.1
Kolmodin, K.2
Feierberg, I.3
Aqvist, J.4
-
33
-
-
84884239302
-
-
Wallingford CT: Gaussian, Inc., 2004 (2004) Gaussian 03, Revision C.02., Wallingford CT, Gaussian, Inc., 2004
-
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al. Wallingford CT: Gaussian, Inc., 2004 (2004) Gaussian 03, Revision C.02.
-
(2004)
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
-
34
-
-
84864473993
-
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
-
doi:10.1093/nar/gks375
-
Anandakrishnan R, Aguilar B, Onufriev AV, (2012) H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 40: W537-W541. doi:10.1093/nar/gks375. PubMed: 22570416.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Anandakrishnan, R.1
Aguilar, B.2
Onufriev, A.V.3
-
35
-
-
23144457576
-
H++: a server for estimating pKas and adding missing hydrogens to macromolecules
-
doi:10.1093/nar/gki464
-
Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, et al. (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33: W368-W371. doi:10.1093/nar/gki464. PubMed: 15980491.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
-
36
-
-
33646794930
-
A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
-
doi:10.1002/prot.20922
-
Myers J, Grothaus G, Narayanan S, Onufriev A, (2006) A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules. Proteins 63: 928-938. doi:10.1002/prot.20922. PubMed: 16493626.
-
(2006)
Proteins
, vol.63
, pp. 928-938
-
-
Myers, J.1
Grothaus, G.2
Narayanan, S.3
Onufriev, A.4
-
37
-
-
0014799161
-
Alpha-chymotrypsin: a case study of substituent constants and regression analysis in enzymic structure--activity relationships
-
doi:10.1002/jps.2600590602
-
Hansch C, Coats E, (1970) Alpha-chymotrypsin: a case study of substituent constants and regression analysis in enzymic structure--activity relationships. J Pharmacol Sci 59: 731-743. doi:10.1002/jps.2600590602. PubMed: 4912447.
-
(1970)
J Pharmacol Sci
, vol.59
, pp. 731-743
-
-
Hansch, C.1
Coats, E.2
-
38
-
-
47649125426
-
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations
-
Momb J, Wang C, Liu D, Thomas PW, Petsko GA, et al. (2008) Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations. Biochemistry 47: 7715-7725.
-
(2008)
Biochemistry
, vol.47
, pp. 7715-7725
-
-
Momb, J.1
Wang, C.2
Liu, D.3
Thomas, P.W.4
Petsko, G.A.5
-
39
-
-
69049101137
-
Motion of the zinc ions in catalysis by a dizinc metallo-beta-lactamase
-
doi:10.1021/ja902534b
-
Breece RM, Hu Z, Bennett B, Crowder MW, Tierney DL, (2009) Motion of the zinc ions in catalysis by a dizinc metallo-beta-lactamase. J Am Chem Soc 131: 11642-11643. doi:10.1021/ja902534b. PubMed: 19653676.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 11642-11643
-
-
Breece, R.M.1
Hu, Z.2
Bennett, B.3
Crowder, M.W.4
Tierney, D.L.5
-
40
-
-
0040036304
-
Who Knows the Ka Values of Water and the Hydronium Ion?
-
doi:10.1021/ed063p473
-
Starkey R, Norman J, Hintzw M, (1986) Who Knows the Ka Values of Water and the Hydronium Ion? J Chem Educ 63: 473-474. doi:10.1021/ed063p473.
-
(1986)
J Chem Educ
, vol.63
, pp. 473-474
-
-
Starkey, R.1
Norman, J.2
Hintzw, M.3
-
41
-
-
2442496666
-
Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase
-
doi:10.1021/bi0497805
-
Aubert SD, Li Y, Raushel FM, (2004) Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase. Biochemistry 43: 5707-5715. doi:10.1021/bi0497805. PubMed: 15134445.
-
(2004)
Biochemistry
, vol.43
, pp. 5707-5715
-
-
Aubert, S.D.1
Li, Y.2
Raushel, F.M.3
-
42
-
-
0034709838
-
Reactivity of mu-Hydroxodizinc(II) Centers in Enzymatic Catalysis through Model Studies
-
doi:10.1021/ic000169d
-
Kaminskaia NV, He C, Lippard SJ, (2000) Reactivity of mu-Hydroxodizinc(II) Centers in Enzymatic Catalysis through Model Studies. Inorg Chem 39: 3365-3373. doi:10.1021/ic000169d. PubMed: 11196876.
-
(2000)
Inorg Chem
, vol.39
, pp. 3365-3373
-
-
Kaminskaia, N.V.1
He, C.2
Lippard, S.J.3
|