References
- Gribble GW. Naturally occurring organohalogen compounds. Acc Chem Res. 1998;31:141–152.
- Gribble GW. Natural organohalogens. Sci Dossier Eur Chlor. 2004;17:1–79. Available from: http://www.eurochlor.org/media/41291/sd6-organohalogens-final.pdf
- Cairns SS, Cornish A, Cooper RA. Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. Eur J Biochem. 1996;235:744–749.
- Slater JH, Bull AT, Hardman DJ. Microbial dehalogenation. Biodegradation. 1995;6:181–189.
- Hill KE, Marchesi JR, Weightman AJ. Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J Bacteriol. 1999;181:2535–2547.
- Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30:2785–2791.
- Motosugi K, Esaki N, Soda K. Purification and properties of a new enzyme, DL-2-haloacid dehalogenase, from Pseudomonas sp. J Bacteriol. 1982;150:522–527.
- Barth PT, Bolton L, Thomson JC. Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity. J Bacteriol. 1992;174:2612–2619.
- Schmidberger JW, Wilce JA, Weightman A J, Whisstock JC, Wilce MCJ. The crystal structure of DehI reveals a new α-haloacid dehalogenase fold and active-site mechanism. J Mol Biol. 2008;378:284–294.
- Slater JH, Bull AT, Hardman DJ. Microbial dehalogenation of halogenated alkanoic acids, alcohols and alkanes. In: Poole RK, editor. Advances in microbial physiology. Vol. 38. Massachusetts, USA: Academic Press; 1996. p. 133–176.
- Burgess CM, Quiroga RM. Assessment of the safety and efficacy of poly-L-lactic acid for the treatment of HIV-associated facial lipoatrophy. J Am Acad Dermatol. 2005;52:233–239.
- Middleton JC, Tipton AJ. Synthetic biodegradable polymers as orthopedic devices. Biomater. 2000;21:2335–2346.
- Vochelle D. The use of poly-L-lactic acid in the management of soft-tissue augmentation: a five-year experience. Sem Cut Med Surg. 2004;23:223–226.
- Taylor SC. Darlington (GB2); Imperial Chemical Industries PLC, London (GB2). D-2-Haloalkanoic acid halidohydrolase. United States Patent US 4,758,518. 1988 Jul 19.
- Ordaz E, Garrido-Pertierra A, Gallego M, Puyet A. Covalent and metal–chelate immobilization of a modified 2-haloacid dehalogenase for the enzymatic resolution of optically active chloropropionic acid. Biotechnol Prog. 2000;16:287–291.
- Vallee BL, Riordan JF. Chemical approaches to the properties of active sites of enzymes. Annu Rev Biochem. 1969;38:733–794.
- Chaplin MF, Bucke C. Enzyme technology. New York (NY): Cambridge University Press; 1990.
- Kmuníček J, Boháč M, Luengo S, Gago F, Wade RC, Damborský J. Comparative binding energy analysis of haloalkane dehalogenase substrates: modeling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. J Comput Aided Mol Des. 2003;17:299–311.
- Sudi IY, Wong E, Joyce-Tan K, Shamsir M, Jamaluddin H, Huyop F. Structure prediction, molecular dynamics simulation and docking studies of D-specific dehalogenase from Rhizobium sp. RCI. Int J Mol Sci. 2012;13:15724–15754.
- Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem. 1998;19:1639–1662.
- Sanner MF. Python: a programming language for software integration and development. J Mol Graphics Model. 1999;17:57–61.
- van der Spoel, D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: fast, flexible, and free. J Comput Chem. 2005;26:1701–1718.
- Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004;25:1656–1676.
- Schuttelkopf AW, van Aalten DMF. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. 2004;60:1355–1363.
- Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593.
- Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: a linear constraint solver for molecular simulations. J Comput Chem. 1997;18:1463–1472.
- Thallapally PK, Nangia A. A Cambridge structural database analysis of the C–HCl interaction: C–HCl− and C–HCl–M often behave as hydrogen bonds but C–HCl–C is generally a van der Waals interaction. Cryst Eng Comm. 2001;3:114–119.
- Chowdhury S, Zhang W, Wu C, Xion G, Duan Y. Breaking non native hydrophobic clusters is the rate-limiting step in folding of an alanine-based peptide. Biopolymers. 2003;68:63–75.
- Petsko GA, Ringe D. Protein structure and function: from sequence to consequence. London: New Science Press; 2004.
- Liu Y. Computational modeling of protein knases: molecular basis for inhibition and catalysis [Thesis]. Philadelphia: University of Pennsylvania; 2010.
- Luo L, Taylor KL, Xiang H, Wei Y, Zhang W, Dunaway-Mariano D. Role of active site binding interactions in 4-chlorobenzoyl-coenzyme A dehalogenase catalysis. Biochemistry. 2001;40:15684–15692.
- Huyop FZ, Cooper RA. A potential use of dehalogenase D (DehD) from Rhizobium sp. for industrial process. J Teknologi. 2003;38:69–75.
- Kokkinidis M, Glykos NM, Fadouloglou VE. Protein flexibility and enzymatic catalysis. Adv Prot Chem Struct Biol. 2012;87:181–218.
- Hartmann MD, Ridderbusch O, Zeth K, Albrecht R, Testa O, Woolfson DN, Sauer G, Dunin-Horkawicz S, Lupas AN, Alvarez BH. A coiled-coil motif that sequesters ions to the hydrophobic core. Proc Natl Acad Sci. 2009;106:16950–16955.
- Betts MJ, Russell RB. Amino acid properties and consequences of subsitutions. In: Barnes MR, Gray IC, editors. Bioinformatics for geneticists. Vol. 387. John Wiley & Sons; 2003.p. 289–316.
- Xiong JP, Stehle T, Zhang R, Joachimiak A, Frech M, Goodman SL, Arnaout MA. Crystal structure of the extracellular segment of integrin αVβ3 in complex with an Arg-Gly-Asp ligand. Science. 2002;296:151–155.
- McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977;267:585–590.
- McCammon JA, Harvey SC. Dynamics of proteins and nucleic acids. Georgia Institute of Technology: Cambridge University Press; 1987.
- Tuengler P, Stein TN, Long GL. Studies on the active center of D-and L-lactate dehydrogenases using oxamate-diaminohexyl-sepharose affinity chromatography. Proc Natl Acad Sci. 1980;77:5832–5836.
- Nardi-Dei V, Kurihara T, Park C, Miyagi M, Tsunasawa S, Soda K, Esaki N. DL-2-haloacid dehalogenase from Pseudomonas sp. 113 is a new class of dehalogenase catalyzing hydrolytic dehalogenation not involving enzyme-substrate ester intermediate. J Biol Chem. 1999;274:20977–20981.
- Omi R, Kurokawa S, Mihara H, Hayashi H, Goto M, Miyahara I, Kurihara T, Hirotsu K, Esaki N. Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase. J Biol Chem. 2010;285:12133–12139.