Molecular Dynamics Simulation of the Human Apo-dihydrofolate Reductase: An Investigation of an Unstable Enzyme

References

• McCammon , J.A. and Harvey , S.C. 1987 . Dynamics of Proteins and Nudeic Acids , Cambridge : Cambridge University Press .
   Google Scholar
• Brooks , C.L. , K. , M. and Pettitt , B.M. 1988 . Protein: A Theoretical Perspective of Dynamic Structure and Thermodynamics , Canada : Wiley .
   Google Scholar
• Schweitzer , B.I. , Dicker , A.P. , B. and J.R. 1990 . "Dihydrofolate reductase as a therapeutic target" . FASEB J. , 4 : 2441
   PubMed Web of Science ®Google Scholar
• Knighton , D.R. , Kan , C-G , Rowland , E. , Janson , C.A. , Hostomska , Z. , Welsh , K.M. and Matthews , D.A. 1994 . "Structure and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase" . Net. Struct. Biol. , 1 : 186
   PubMedGoogle Scholar
• Bolin , J.T. , F.D. , J. , Matthews , D.A. , Hamlin , R.C. and Kraut , J. 1982 . "Crystal structures of Escherichia colt and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. I. General features and binding of methotrexate" . J. Biol. Chem. , 257 : 13650
   PubMed Web of Science ®Google Scholar
• Birdsail , B. , R , J. , Tendier , S.J. , Hammond , S.J. and Roberts , G.C. 1989 . "Dihydrofloate reductase multiple conformations and alternative modes of substrate binding" . Biochemistry , 28 : 2297
   PubMed Web of Science ®Google Scholar
• Bystroff , C , O. , S.J. and Kraut , J. 1990 . "Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state" . Biochemistry , 29 : 3293
   Web of Science ®Google Scholar
• Bystroff , C. , J. and K. 1991 . "Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding" . Biochemistry , 30 : 2227
   PubMed Web of Science ®Google Scholar
• Champness , J.N. , A. , A. , Ballantine , S.P. , Bryant , P.K. , Delves , C.J. and Stammers , O.K. 1994 . "The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 A resolution" . Structure , 2 : 915
   PubMed Web of Science ®Google Scholar
• Volz , K.W. , M. , DA. , Alden , R.A. , Freer , S.T. , Hansch , C. , Kaufman , B.T. and Kraut , J. 1982 . "Crystal structure of avian dihydrofolate reductase containing phenyltriazine and NADPH" . J. Biol. Chem. , 257 : 2528
   PubMed Web of Science ®Google Scholar
• Matthews , D.A. , Bolin , J.T. , Burridge , J.M. , Filman , D.J. , VoIz , K.W. and Kraut , J. 1985 . "Dihydrofblate reductase the stereocheniistry of inhibitor selectivity" . J. Biol. Chem. , 260 : 392
   PubMed Web of Science ®Google Scholar
• McTigue , M.A. , D. , J.F. , Kaufman , B.T. and Kraut , J. 1992 . "Crystal structure of chicken liver dihydrofolate reductase complexed with NADP+ and biopterin" . Biochemistry , 31 : 7264
   PubMed Web of Science ®Google Scholar
• McTigue , M.A. , D. , J.F. , Kaufman , B.T. and Kraut , J. 1993 . "Crystal structures of chicken liver dihydrofolate reductase: binary thioNADP+ and ternary thioNADP+biopterin complexes" . Biochemistry , 32 : 6855
   PubMed Web of Science ®Google Scholar
• Oefner , C. , D. , A.A. and Winkler , F.K. 1988 . "Crystal structure of human dihydrofolate reductase complexed with folate" . Eur. J. Biochem. , 174 : 377
   PubMedGoogle Scholar
• Davies , J.F. , Delcamp , T.J. , Prendergast , N.J. , A. , V.A. , Freisheim , J.H. and Kraut , J. 1990 . "Crystal structure of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate" . Biochemistry , 29 : 9467
   PubMed Web of Science ®Google Scholar
• Cody , V , Galitsky , N. , Luft , J.R. , Pangborn , W. , Blakley , RX. and Gangjee , A. 1981 . "Comparison of ternary crystal complexes of F31 variants of human dihydrofolate reductase with NADPH and a classical antitumor furopyrimidine" . Anti-Cancer Drug Des. , 13 : 307
   Google Scholar
• Matthews , H.R. , Matthews , K.S. and Opella , S.J. 1977 . "Selectively deuterated amino acid analoguest syntesis, incorporation into proteins and NMR properties" . Biochim. Biophys. Acta , 497 : 1
   PubMedGoogle Scholar
• Stockman , B.J. , N. , N. , Wagner , G. , Delcamp , T.J. , De Yannan , M.T. and Freisheim , J.H. 1992 . "Sequence-specific 1H and 15N resonance assignments for human dihydrofolate reductase in solution" . Biochemistry , 31 : 218
   PubMed Web of Science ®Google Scholar
• Johnson , J.M. , Meiering , E.M. , Wright , J.E. , Pardo , J. , Rosowsky , A. and Wagner , G. 1997 . "NMR solution structure of the antitumor compound PT523 and NADPH in the ternary complex with human dihydrofolate reductase" . Biochemistry , 36 : 4399
   PubMed Web of Science ®Google Scholar
• Cornell , W.D. , Cieplak , P. , Bayly , C.J. , Gould , LR. , Merz , K.M. Jr , Ferguson , D.M. Jr , Spellmeyer , D.C. Jr , Fox , T Jr , Caldwell , J.W. Jr and Kollman , P.A. Jr . 1995 . "A second generation force field for the simulation of proteins, nucleic acid, and organic molecules" . J. Am. Chem. Soc. , 117 : 5179
   Web of Science ®Google Scholar
• Jorgensen , W.L. , Chandrasekhar , J. , Madura , J. , Impey , R.W. and Klein , M.L. 1983 . "Comparison of simple potential functions for simulating liquid water" . J. Chem. Phys. , 79 : 926
   Web of Science ®Google Scholar
• Berendsen , H.J.C. , Postma , J.P.M. , van Gunsteren , W.F. , DiNoIa , A. and Haak , J.R. 1984 . "Molecular dynamics with coupling to an external bath" . J. Chem. Phys. , 81 : 3684
   Web of Science ®Google Scholar
• Case , D.A. 1997 . AMBER 5 , San Francisco : University of California .
   Google Scholar
• Guex , N. , P. and M. 1997 . "SWISS-MODEL, and the SwissPdbViewer: an environment for comparative protein modeling" . Electrophoresis , 18 : 2714
   PubMed Web of Science ®Google Scholar
• Sayle , R. 1994 . Rasmol , 2.6 edit. , Greenford, Middlesex , , UK : Biomolecular Structure Department, Glaxo Research and Development .
   Google Scholar
• Koradi , R. , Billeter , M. and Wuthrich , K. 1996 . "MOLMOL: a program for display and analysis of macromolecular structures" . J. Mol. Graph. , 14 : 51
   PubMedGoogle Scholar
• Kraulis , P.J. 1991 . "MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures" . J. Appl. Crystallog. , 24 : 946
   Web of Science ®Google Scholar
• Laskowski , R.A. , MacArthur , M.W. , Moss , D.S. and Thornton , J.M. 1993 . "PROCHECK: a program to check the stereochemical quality of protein structures" . J. Appl. Crystallog. , 26 : 283
   Web of Science ®Google Scholar
• McCammon , AJ. and H.S. , eds. 1987 . Dynamics of Proteins and Nucleic Acids , Cambridge , , UK : Cambridge university press .
   Google Scholar
• Kabsh , W. and Sander , C. 1983 . "Dictionary of protein secondary structure; pattern recognition of hydrogen-bonded and geometrical features" . Biopolymers , 22 : 2577
   PubMed Web of Science ®Google Scholar
• Connolly , M.L. 1983 . "Solvent-accessible surfaces of proteins and nucleic acids" . Science , 221 : 709
   PubMed Web of Science ®Google Scholar
• Sawaya , MR. and Kraut , J. 1997 . "Loop and sundomain movements in the mechanism of Escherichia colt dihydrofolate reductase: crystallographic evidence" . Biochemistry , 36 : 586
   PubMed Web of Science ®Google Scholar
• Chunduru , S.K. , Cody , V. , Luft , J.R. , Pangborn , W. , Appleman , J.R. and Blakley , R.L. 1994 . "Methotrexateresistant variants of human dihydrofolate reductase: effects of Phe31 substitutions" . J. Biol. chem. , 269 : 9547
   PubMed Web of Science ®Google Scholar
• Nakano , T. , Spencer , H.T. , Appleman , J.R. and Blakley , R.L. 1994 . "Critical role of phenylalanine 34 of human dihydrofolate reductase in substrate and inhibitor binding and in catalysis" . Biochemistry , 33 : 9945
   PubMed Web of Science ®Google Scholar