Insight into the binding of the wild type and mutated alginate lyase (AlyVI) with its substrate: A computational and experimental study

Gacesa, 1988, Alginates, Carbohydr. Polym., 8, 161, 10.1016/0144-8617(88)90001-X

Skjakbraek, 1985, The role of o-acetyl groups in the biosynthesis of alginate by azotobacter-vinelandii, Carbohydr. Res., 145, 169, 10.1016/S0008-6215(00)90427-0

Wong, 2000, Alginate lyase: review of major sources and enzyme characteristics, structure–function analysis, biological roles, and applications, Annu. Rev. Microbiol., 54, 289, 10.1146/annurev.micro.54.1.289

Zhang, 2004, Preparation and structure elucidation of alginate oligosaccharides degraded by alginate lyase from Vibro sp 510, Carbohydr. Res., 339, 1475, 10.1016/j.carres.2004.03.010

Hattori, 1997, Functional improvement of beta-lactoglobulin by conjugating with alginate lyase-lysate, J. Agric. Food Chem., 45, 703, 10.1021/jf960431u

Hatch, 1998, Alginate lyase promotes diffusion of aminoglycosides through the extracellular polysaccharide of mucoid Pseudomonas aeruginosa, Antimicrob. Agents Chemother., 42, 974, 10.1128/AAC.42.4.974

Boyd, 1994, Role of alginate lyase in cell detachment of pseudomonas-aeruginosa, Appl. Environ. Microbiol., 60, 2355, 10.1128/AEM.60.7.2355-2359.1994

Bayer, 1992, Effects of alginase on the natural-history and antibiotic-therapy of experimental endocarditis caused by mucoid pseudomonas-aeruginosa, Infect. Immun., 60, 3979, 10.1128/IAI.60.10.3979-3985.1992

Mai, 1993, Inhibition of adherence of mucoid pseudomonas-aeruginosa by alginase, specific monoclonal-antibodies, and antibiotics, Infect. Immun., 61, 4338, 10.1128/IAI.61.10.4338-4343.1993

Cross, 1983, Nosocomial infections due to pseudomonas-aeruginosa—review of recent trends, Rev. Infect. Dis., 5, S837, 10.1093/clinids/5.Supplement_5.S837

George, 1987, Pseudomonas infections in cystic-fibrosis, Arch. Dis. Child., 62, 438, 10.1136/adc.62.5.438

Sferra, 1993, The molecular-biology of cystic-fibrosis, Annu. Rev. Med., 44, 133, 10.1146/annurev.me.44.020193.001025

Wood, 1976, Cystic-fibrosis, Am. Rev. Respir. Dis., 113, 833

Sawabe, 2001, Cloning, sequence analysis and expression of Pseudoalteromonas elyakovii IAM 14594 gene (alyPEEC) encoding the extracellular alginate lyase, Carbohydr. Res., 335, 11, 10.1016/S0008-6215(01)00198-7

Miyake, 2003, An exotype alginate lyase in Sphingomonas sp Al: overexpression in Escherichia coli, purification, and characterization of alginate lyase IV (A1-IV), Protein Expr. Purif., 29, 33, 10.1016/S1046-5928(03)00018-4

Caswell, 1989, Molecular-cloning and heterologous expression of a klebsiella-pneumoniae gene encoding alginate lyase, Gene, 75, 127, 10.1016/0378-1119(89)90389-2

Han, 2004, Cloning, sequence analysis and expression of gene alyVI encoding alginate lyase from marine bacterium Vibrio sp QY101, DNA Seq., 15, 344, 10.1080/10425170400019300

Fujiyama, 1995, Purification and characterization of the recombinant alginate lyase from pseudomonas sp leaked by escherichia-coli upon addition of glycine, FEMS Microbiol. Lett., 126, 19, 10.1111/j.1574-6968.1995.tb07384.x

Weissbach, 1959, Formation of 2-keto-3-deoxyheptonic acid in extracts of escherichia-coli-b.1. identification, J. Biol. Chem., 234, 705, 10.1016/S0021-9258(18)70158-0

Benson, 1999, GenBank, Nucleic Acids Res., 27, 12, 10.1093/nar/27.1.12

Berman, 2000, The protein Data Bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235

Schwede, 2003, SWISS-MODEL: an automated protein homology-modeling server, Nucleic Acids Res., 31, 3381, 10.1093/nar/gkg520

Guex, 1997, Swiss-Model and the Swiss-PdbViewer: an environment for comparative protein modelling, Electrophoresis, 18, 2714, 10.1002/elps.1150181505

Gunsteren, 1996

Hooft, 1996, Verification of protein structures: side-chain planarity, J. Appl. Crystallogr., 29, 714, 10.1107/S0021889896008631

Sippl, 1993, Recognition of errors in three-dimensional structures of proteins, Proteins, 17, 355, 10.1002/prot.340170404

Melo, 1998, Assessing protein structures with a non-local atomic interaction energy, J. Mol. Biol., 277, 1141, 10.1006/jmbi.1998.1665

Eisenberg, 1997, VERIFY3D: assessment of protein models with three-dimensional profiles, Macromol. Crystallogr., Pt B, 277, 396, 10.1016/S0076-6879(97)77022-8

Frisch, 2003

Cieplak, 1995, Application of the multimolecule and multiconformational resp methodology to biopolymers—charge derivation for DNA, RNA, and proteins, J. Comput. Chem., 16, 1357, 10.1002/jcc.540161106

Bayly, 1993, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges—the resp model, J. Phys. Chem., 97, 10269, 10.1021/j100142a004

Case, 2006

Hamza, 2006, How can (−)-epigallocatechin gallate from green tea prevent HIV-1 infection? Mechanistic insights from computational modeling and the implication for rational design of anti-HIV-1 entry inhibitors, J. Phys. Chem. B, 110, 2910, 10.1021/jp0550762

Zhang, 2008, A novel Hsp90 inhibitor to disrupt Hsp90/Cdc37 complex against pancreatic cancer cells, Mol. Cancer Ther., 7, 162, 10.1158/1535-7163.MCT-07-0484

Kuntz, 1994, Structure-based molecular design, Acc. Chem. Res., 27, 117, 10.1021/ar00041a001

Gatchell, 2000, Discrimination of near-native protein structures from misfolded models by empirical free energy functions, Proteins-Struct. Funct. Genet., 41, 518, 10.1002/1097-0134(20001201)41:4<518::AID-PROT90>3.0.CO;2-6

Naim, 2007, Solvated interaction energy (SIE) for scoring protein–ligand binding affinities. 1. Exploring the parameter space, J. Chem. Inf. Model., 47, 122, 10.1021/ci600406v

Kollman, 2000, Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models, Acc. Chem. Res., 33, 889, 10.1021/ar000033j

Purisima, 1998, Fast summation boundary element method for calculating solvation free energies of macromolecules, J. Comput. Chem., 19, 1494, 10.1002/(SICI)1096-987X(199810)19:13<1494::AID-JCC6>3.0.CO;2-L

Yang, 2010, Computational determination of binding structures and free energies of phosphodiesterase-2 with benzo 1,4 diazepin-2-one derivatives, J. Phys. Chem. B, 114, 16020, 10.1021/jp1086416

Hamza, 2009, Determination of the structure of human phosphodiesterase-2 in a bound state and its binding with inhibitors by molecular modeling, docking, and dynamics simulation, J. Phys. Chem. B, 113, 2896, 10.1021/jp8082612

Hamza, 2010, Understanding microscopic binding of human microsomal prostaglandin E synthase-1 (mPGES-1) trimer with substrate PGH2 and cofactor GSH: insights from computational alanine scanning and site-directed mutagenesis, J. Phys. Chem. B, 114, 5605, 10.1021/jp100668y

Martin, 1997, Assessment of comparative modeling in CASP2, Proteins-Struct. Funct. Bioinf., 14, 10.1002/(SICI)1097-0134(1997)1+<14::AID-PROT4>3.0.CO;2-O

Chothia, 1986, The relation between the divergence of sequence and structure in proteins, EMBO J., 5, 823, 10.1002/j.1460-2075.1986.tb04288.x

Creighton, 1993

Hamza, 2010, Understanding microscopic binding of human microsomal prostaglandin E synthase-1 (mPGES-1) trimer with substrate PGH2 and cofactor GSH: insights from computational alanine scanning and site-directed mutagenesis, J. Phys. Chem., 114, 5605, 10.1021/jp100668y

Zoete, 2005, Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition, Proteins: Structure, Function, and Bioinformation, 61, 79, 10.1002/prot.20528

Gohlke, 2003, Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes, J. Mol. Biol., 330, 891, 10.1016/S0022-2836(03)00610-7