메뉴 건너뛰기




Volumn 47, Issue 6, 2007, Pages 2358-2365

Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CRYSTAL STRUCTURE; DRUG DELIVERY; ENZYMES; ESCHERICHIA COLI; MOLECULAR STRUCTURE; SOLVENTS;

EID: 37249000795     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700167n     Document Type: Article
Times cited : (34)

References (37)
  • 1
    • 0013615206 scopus 로고
    • Amino acid metabolism
    • 2nd ed, John Wiley & Sons, Inc, New York
    • Voet, D.; Voet, J. Amino acid metabolism. In Biochemistry, 2nd ed.; John Wiley & Sons, Inc.: New York, 1995; p 762.
    • (1995) Biochemistry , pp. 762
    • Voet, D.1    Voet, J.2
  • 2
    • 0025361947 scopus 로고
    • Dihydrofolate Reductase as a Therapeutic Target
    • Schweitzer, B. I.; Dicker, A. P.; Bertino, J. R. Dihydrofolate Reductase as a Therapeutic Target. FASEB J. 1990, 4, 2441-2452.
    • (1990) FASEB J , vol.4 , pp. 2441-2452
    • Schweitzer, B.I.1    Dicker, A.P.2    Bertino, J.R.3
  • 3
    • 26944489929 scopus 로고    scopus 로고
    • University Data-Mining and Docking Competition - Computational Models on the Catwalk
    • Parker, C. N. McMaster University Data-Mining and Docking Competition - Computational Models on the Catwalk. J. Biomol. Screen. 2005, 10, 647-648.
    • (2005) J. Biomol. Screen , vol.10 , pp. 647-648
    • Parker, C.1    McMaster, N.2
  • 5
    • 0033955055 scopus 로고    scopus 로고
    • Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase
    • Radkiewicz, J. L.; Brooks, C. L., III Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase. J. Am. Chem. Soc. 2000, 122, 225-231.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 225-231
    • Radkiewicz, J.L.1    Brooks III, C.L.2
  • 7
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis
    • Agarwal, P. K.; Billeter, S. R.; Hammes-Schiffer, S. Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis. J. Phys. Chem. B 2002, 106, 3283-3293.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 3283-3293
    • Agarwal, P.K.1    Billeter, S.R.2    Hammes-Schiffer, S.3
  • 8
    • 0034677111 scopus 로고    scopus 로고
    • Feeney, J. NMR Studies of Ligand Binding to Dihydrofolate Reductase. Angew. Chem. Int. Ed. 2000, 39, 290-312.
    • Feeney, J. NMR Studies of Ligand Binding to Dihydrofolate Reductase. Angew. Chem. Int. Ed. 2000, 39, 290-312.
  • 9
    • 33748781457 scopus 로고    scopus 로고
    • The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis
    • Boehr, D. D.; McElheny, D.; Dyson, H. J.; Wright, P. E. The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis. Science 2006, 313, 1638-1642.
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 10
    • 0035928796 scopus 로고    scopus 로고
    • Backbone Dynamics in Dihydrofolate Reductase Complexes: Role of Loop Flexibility in the Catalytic Mechanism
    • Osborne, M. J.; Schnell, J.; Benkovic, S. J.; Dyson, H. J.; Wright, P. E. Backbone Dynamics in Dihydrofolate Reductase Complexes: Role of Loop Flexibility in the Catalytic Mechanism. Biochemistry 2001, 40, 9846-9859.
    • (2001) Biochemistry , vol.40 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 11
    • 0031015737 scopus 로고    scopus 로고
    • Loop and Subdomain Movements in the Mechanism of Escherichia Coli Dihydrofolate Reductase: Crystallographic Evidence
    • Sawaya, M. R.; Kraut, J. Loop and Subdomain Movements in the Mechanism of Escherichia Coli Dihydrofolate Reductase: Crystallographic Evidence. Biochemistry 1997, 36, 586-603.
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 13
    • 0031808658 scopus 로고    scopus 로고
    • Stretching Exercises - Flexibility in Dihydrofolate Reductase Catalysis
    • Miller, G. P.; Benkovic, S. J. Stretching Exercises - Flexibility in Dihydrofolate Reductase Catalysis. Chem. Biol. 1998, 5, R105-R113.
    • (1998) Chem. Biol , vol.5
    • Miller, G.P.1    Benkovic, S.J.2
  • 14
    • 3042660150 scopus 로고    scopus 로고
    • Structure, Dynamics, and Catalytic Function of Dihydrofolate Reductase
    • Schnell, J. R.; Dyson, H. J.; Wright, P. E. Structure, Dynamics, and Catalytic Function of Dihydrofolate Reductase. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 119-140.
    • (2004) Annu. Rev. Biophys. Biomol. Struct , vol.33 , pp. 119-140
    • Schnell, J.R.1    Dyson, H.J.2    Wright, P.E.3
  • 15
    • 0001105311 scopus 로고    scopus 로고
    • Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design
    • Carlson, H. A.; Masukawa, K. M.; McCammon, J. A. Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design. J. Phys. Chem. A 1999, 103, 10213-10219.
    • (1999) J. Phys. Chem. A , vol.103 , pp. 10213-10219
    • Carlson, H.A.1    Masukawa, K.M.2    McCammon, J.A.3
  • 17
    • 6344245774 scopus 로고    scopus 로고
    • Meagher, K. L.; Carlson, H. A. Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case. J. Am. Chem. Soc. 2004, 126, 13276-13281.
    • Meagher, K. L.; Carlson, H. A. Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case. J. Am. Chem. Soc. 2004, 126, 13276-13281.
  • 18
    • 33745123314 scopus 로고    scopus 로고
    • Refining the Multiple Protein Structure Pharmacophore Method: Consistency Across Three Independem HIV-1 Protease Models
    • Meagher, K. L.; Lerner, M. G.; Carlson, H. A. Refining the Multiple Protein Structure Pharmacophore Method: Consistency Across Three Independem HIV-1 Protease Models. J. Med. Chem. 2006, 49, 3478-3484.
    • (2006) J. Med. Chem , vol.49 , pp. 3478-3484
    • Meagher, K.L.1    Lerner, M.G.2    Carlson, H.A.3
  • 19
    • 33947662384 scopus 로고    scopus 로고
    • Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System
    • Bowman, A. L.; Lerner, M. G.; Carlson, H. A. Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System. J. Am. Chem. Soc. 2007, 129, 3634-3640.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 3634-3640
    • Bowman, A.L.1    Lerner, M.G.2    Carlson, H.A.3
  • 20
    • 34447271743 scopus 로고    scopus 로고
    • Exploring Sources of Multiple Protein Conformations in Structure-Based Drug Design
    • Damm, K. L.; Carlson, H. A. Exploring Sources of Multiple Protein Conformations in Structure-Based Drug Design. J. Am. Chem. Soc. 2007, 129, 8225-8235.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 8225-8235
    • Damm, K.L.1    Carlson, H.A.2
  • 22
    • 0029633186 scopus 로고
    • AMBER, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules
    • Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; Debolt, S.; Ferguson, D. M.; Seibel, G. L.; Kollman, P. A. AMBER, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules. Comput. Phys. Commun. 1995, 91, 1-41.
    • (1995) Comput. Phys. Commun , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham III, T.E.5    Debolt, S.6    Ferguson, D.M.7    Seibel, G.L.8    Kollman, P.A.9
  • 23
    • 0032744506 scopus 로고    scopus 로고
    • Redesign of the Coenzyme Specificity in L-Lactate Dehydrogenase from Bacillus Stearothermophilus using Site-Directed Mutagenesis and Media Engineering
    • Holmberg, N.; Ryde, U.; Bulow, L. Redesign of the Coenzyme Specificity in L-Lactate Dehydrogenase from Bacillus Stearothermophilus using Site-Directed Mutagenesis and Media Engineering. Protein Eng. 1999, 12, 851-856.
    • (1999) Protein Eng , vol.12 , pp. 851-856
    • Holmberg, N.1    Ryde, U.2    Bulow, L.3
  • 26
    • 33845365904 scopus 로고    scopus 로고
    • A 2.13 Angstrom Structure of E-coli Dihydrofolate Reductase Bound to a Novel Competitive Inhibitor Reveals a New Binding Surface Involving the M20 Loop Region
    • Summerfield, R. L.; Daigle, D. M.; Mayer, S.; Mallik, D.; Hughes, D. W.; Jackson, S. G.; Sulek, M.; Organ, M. G.; Brown, E. D.; Junop, M. S. A 2.13 Angstrom Structure of E-coli Dihydrofolate Reductase Bound to a Novel Competitive Inhibitor Reveals a New Binding Surface Involving the M20 Loop Region. J. Med. Chem. 2006, 49, 6977-6986.
    • (2006) J. Med. Chem , vol.49 , pp. 6977-6986
    • Summerfield, R.L.1    Daigle, D.M.2    Mayer, S.3    Mallik, D.4    Hughes, D.W.5    Jackson, S.G.6    Sulek, M.7    Organ, M.G.8    Brown, E.D.9    Junop, M.S.10
  • 28
    • 37249060128 scopus 로고    scopus 로고
    • Jorgensen, W. L. BOSS, Version 4.2; Yale University: New Haven, CT, 2000
    • Jorgensen, W. L. BOSS, Version 4.2; Yale University: New Haven, CT, 2000.
  • 29
    • 0029912748 scopus 로고    scopus 로고
    • Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 30
    • 33744807436 scopus 로고    scopus 로고
    • Gaussian-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures
    • Damm, K. L.; Carlson, H. A. Gaussian-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures. Biophys. J. 2006, 90, 4558-4573.
    • (2006) Biophys. J , vol.90 , pp. 4558-4573
    • Damm, K.L.1    Carlson, H.A.2
  • 31
    • 37249057288 scopus 로고    scopus 로고
    • Chemical Computing Group: Montreal, Canada
    • MOE, v2005.06; Chemical Computing Group: Montreal, Canada, 2005.
    • (2005) MOE, v2005.06
  • 32
    • 0004305176 scopus 로고    scopus 로고
    • MDL Information Systems Inc, San Leandro, CA
    • Comprehensive Medicinal Chemistry; MDL Information Systems Inc.: San Leandro, CA, 2005.
    • (2005) Comprehensive Medicinal Chemistry
  • 33
    • 37249089179 scopus 로고    scopus 로고
    • 1.8.b1; OpenEye Scientific Software, Inc, Santa Fe, NM
    • OMEGA, Version 1.8.b1; OpenEye Scientific Software, Inc.: Santa Fe, NM, 2004.
    • (2004) OMEGA, Version
  • 34
    • 0033056708 scopus 로고    scopus 로고
    • Folding Funnels, Binding Funnels, and Protein Function
    • Tsai, C. J.; Kumar, S.; Ma, B. Y.; Nussinov, R. Folding Funnels, Binding Funnels, and Protein Function. Protein Sci. 1999, 8, 1181-1190.
    • (1999) Protein Sci , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.Y.3    Nussinov, R.4
  • 35
    • 0037402655 scopus 로고    scopus 로고
    • Automated Generation of MCSS-Derived Pharmacophoric DOCK Site Points for Searching Multiconformation Databases
    • Joseph-McCarthy, D.; Alvarez, J. C. Automated Generation of MCSS-Derived Pharmacophoric DOCK Site Points for Searching Multiconformation Databases. Proteins: Struct., Funct., Bioinf. 2003, 51, 189-202.
    • (2003) Proteins: Struct., Funct., Bioinf , vol.51 , pp. 189-202
    • Joseph-McCarthy, D.1    Alvarez, J.C.2
  • 37
    • 0025916872 scopus 로고
    • Functionality Maps of Binding-Sites - a Multiple Copy Simultaneous Search Method
    • Miranker, A.; Karplus, M. Functionality Maps of Binding-Sites - a Multiple Copy Simultaneous Search Method. Proteins: Struct., Funct., Bioinf. 1991, 11, 29-34.
    • (1991) Proteins: Struct., Funct., Bioinf , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.