Molecular dynamics simulations of the enzyme Catechol-O-Methyltransferase: methodological issuesFootnote1

¹Presented at CMTPI 2007: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Moscow, Russia, September 1–5, 2007).

References

• Guldberg , HC and Marsden , CA . 1975 . Catechol-O-methyltransferase: pharmacological aspects and physiological role . Pharm. Rev. , 27 : 135 – 206 .
   PubMed Web of Science ®Google Scholar
• Poewe , W . 2004 . The role of COMT inhibition in the treatment of Parkinson's disease . Neurology , 62 : S31 – S38 .
   PubMed Web of Science ®Google Scholar
• Männistö , PT and Kaakkola , S . 1999 . Catechol-O-methyltransferase (COMT): biochemistry, molecular biology, pharmacology, and clinical efficacy of the new selective COMT inhibitors . Pharm. Rev. , 51 : 593 – 628 .
   PubMed Web of Science ®Google Scholar
• Vidgren , J , Svensson , LA and Liljas , A . 1994 . Crystal structure of catechol O-methyltransferase . Nature. , 368 : 354 – 358 .
   PubMed Web of Science ®Google Scholar
• et , CLerner . 2001 . Angew. Chem. Int. Ed. 40 . X-ray crystal structure of a bisubstrate inhibitor bound to the enzyme catechol-O-methyltransferase: a dramatic effect of inhibitor preorganization on binding affinity , : 4040 – 4042 .
   Google Scholar
• et , MJBonifácio . 2002 . Kinetics and crystal structure of Catechol-O-methyltransferase complex with co-substrate and a novel inhibitor with potential therapeutic application . Mol. Pharm. , 62 : 795 – 805 .
   Google Scholar
• Palma , PN . 2006 . Comparative study of ortho- and meta-nitrated inhibitors of catechol-O-methyltransferase: interactions with the active site and regioselectivity of O-methylation . Mol. Pharm. 70 , : 143 – 153 .
   Google Scholar
• Männistö , PT . 1994 . Catechol O-methyltransferase (COMT), and COMT inhibitors, in Design of Enzyme Inhibitors as Drugs , Edited by: Sandler , M and Smith , HJ . Vol. 2 , Oxford : Oxford University Press .
   Google Scholar
• et , JRMin . The crystal structure of human catecho-O-metyltransferase domain containing 1 in complex S-adenosyl-L-methionine , to be published.
   Google Scholar
• Kuhn , B and Kollman , PA . 2000 . QM-FE and molecular dynamics calculations on catechol O-methyltransferase: free energy of activation in the enzyme and in aqueous solution and regioselectivity of the enzyme-catalyzed reactionJ. Am. Chem. Soc. . J. Am. Chem. Soc. , 122 : 2586 – 2596 .
   Web of Science ®Google Scholar
• Lau , EY and Bruice , TC . 2000 . Comparison of the dynamics for ground-state and transition-state structures in the active site of catechol O-methyltransferase . J. Am. Chem. Soc. , 122 : 7165 – 7171 .
   Google Scholar
• et , PNPalma . 2003 . Drug Metab. Dispos. . Molecular modeling and metabolic studies of the interaction of catechol-O-methyltransferase and a new nitrocatechol inhibitor , 31 : 250 – 258 .
   Google Scholar
• et , MRoca . 2003 . Theoretical modeling of enzyme catalytic power: analysis of “cratic” and electrostatic factors in catechol O-methyltransferase . J. Am. Chem. Soc. , 125 : 7726 – 7737 .
   Google Scholar
• et , MRoca . 2005 . On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations . J. Am. Chem. Soc. , 127 : 10648 – 10655 .
   Google Scholar
• Rod , TH and Ryde , U . 2005 . Accurate QM/MM free energy calculations of enzyme reactions: methylation by catechol O-methyltransferase . J. Chem. Theory Comput. , 1 : 1240 – 1251 .
   PubMed Web of Science ®Google Scholar
• et , AJTervo . 2003 . A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods . J. Comput. Aided Mol. Des. , 17 : 797 – 810 .
   Google Scholar
• Vattulainen , I and Karttunen , M . 2005 . Modeling of biologically motivated soft matter systems in Computational Nanotechnology , Edited by: Rieth , M and Schommers , W . New york : American Scientific Press .
   Google Scholar
• et , SAhna . 2001 . The “open” and “closed” structures of the type-C inorganic pyrophosphatases from bacillus subtilis and streptococcus gordonii . J. Mol. Biol. , 313 : 797 – 811 .
   Google Scholar
• et , MCMerckel . 2001 . Crystal structure of streptococcus mutans pyrophosphatase: a new fold for an old mechanism. Structure , 9 : 289 – 297 .
   Google Scholar
• et , NDeshpande . 2005 . The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema . Nucl. Acids Res. , 33 : D233 – D237 .
   Google Scholar
• Jorgensen , W and Tirado-Rives , J . 1988 . The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin . J. Am. Chem. Soc. , 110 : 1657 – 1666 .
   PubMed Web of Science ®Google Scholar
• Murzyn , K . 2006 . Proteins . Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome , 62 : 1088 – 1100 .
   Google Scholar
• et , TRóg . 2007 . Non-polar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies . J. Pep. Sci. , in press: Doi: 10.1002/psc.936.
   Google Scholar
• et , CIBayly . 1993 . A Well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model . J. Phys. Chem. , 97 : 10269 – 10280 .
   Google Scholar
• et , MWSchmidt . 1993 . The General atomic and molecular electronic structure system . J. Comp. Chem. , 14 : 1347 – 1362 .
   Google Scholar
• et , WLJorgensen . 1983 . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys. , 79 : 926 – 935 .
   Google Scholar
• Lindahl , E , Hess , B and Spoel , D vander . 2001 . GROMACS 3.0: a package for molecular simulation and trajectory analysis . J. Mol. Mod. , 7 : 306 – 317 .
   Web of Science ®Google Scholar
• Frenkel , D and Smit , B . 2002 . Understanding molecular simulation: from algorithms to applications, , 2nd ed. , San Diego : Academic Press .
   Google Scholar
• Parrinello , M and Rahman , A . 1981 . Polymorphic transitions in single crystals: a new molecular dynamics method . J. Appl. Phys. , 52 : 7182 – 7190 .
   Web of Science ®Google Scholar
• Darden , T , York , D and Pedersen , L . 1993 . Particle mesh Ewald: an N log(N) method for Ewald sums in large systems . J. Chem. Phys. , 98 : 10089 – 10092 .
   Web of Science ®Google Scholar
• Lee , B and Richards , FM . 1971 . The interpretation of protein structures: estimation of static accessibility . J. Mol. Biol. , 55 : 379 – 380 .
   PubMed Web of Science ®Google Scholar
• Connolly , ML . 1983 . Analytical molecular surface calculation . J. Appl. Cryst. , 16 : 548 – 558 .
   Web of Science ®Google Scholar
• Connolly , ML . 1992 . The molecular surface package . J. Mol. Graph. , 11 : 139 – 141 .
   Google Scholar
• Kabsch , W and Sander , C . 1983 . Biopolymers . Definition of secondary structure of protein given a set of 3D coordinates , 22 : 2577 – 2637 .
   Google Scholar
• Humphrey , W , Dalke , A and Schulten , K . 1996 . VMD: visual molecular dynamics . J. Mol. Graph. , 14 : 33 – 38 .
   PubMed Web of Science ®Google Scholar
• et , MPatra . 2004 . Lipid bilayers driven to a wrong lane in molecular dynamics simulations by truncation of long-range electrostatic interactions . J. Phys. Chem. B , 108 : 4485 – 4494 .
   Google Scholar
• Gurtovenko , AA . 2005 . Effect of monovalent salt on cationic lipid membranes as revealed by molecular dynamics simulations . z J. Phys. Chem. B , 109 : 21126 – 21134 .
   Google Scholar