Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition

Journal of Physical Chemistry B

Volumn 119, Issue 35, 2015, Pages 11513-11526

  Kirmizialtin, Serdal ^a   Johnson, Kenneth A ^b   Elber, Ron ^c  

^a NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; ENZYMES; SUBSTRATES;

ATOMICALLY DETAILED SIMULATIONS; CLOSED TRANSITIONS; CONFORMATIONAL CHANGE; CONFORMATIONAL TRANSITIONS; ENERGY PARTITION; ENZYME CATALYSIS; HIV REVERSE TRANSCRIPTASE; REACTION COORDINATES;

FREE ENERGY;

DNA; RNA DIRECTED DNA POLYMERASE;

ALGORITHM; CATALYSIS; CHEMISTRY; KINETICS; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

ALGORITHMS; CATALYSIS; DNA; HIV REVERSE TRANSCRIPTASE; KINETICS; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION;

EID: 84941054457     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b05467     Document Type: Article

References (40)

1. Kirmizialtin, S.; Nguyen, V.; Johnson, K. A.; Elber, R. How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations Structure 2012, 20, 618-627 10.1016/j.str.2012.02.018
2. Johnson, K. A. Conformational Coupling in DNA Polymerase Fidelity Annu. Rev. Biochem. 1993, 62, 685-713 10.1146/annurev.bi.62.070193.003345
3. Prasad, B. R.; Kamerlin, S. C. L.; Florian, J.; Warshel, A. Prechemistry Barriers and Checkpoints do not Contribute to Fidelity and Catalysis as Long as They are not Rate Limiting Theor. Chem. Acc. 2012, 131, 1288 10.1007/s00214-012-1288-6
4. Briggs, G.; Haldane, J. B. S. A Note on The Kinetics of Enzyme Action Biochem. J. 1925, 19, 338-339
5. Elber, R.; Kirmizialtin, S. Molecular Machines Curr. Opin. Struct. Biol. 2013, 23, 206-211 10.1016/j.sbi.2012.12.002
6. Kirmizialtin, S.; Elber, R. Revisiting and Computing Reaction Coordinates with Directional Milestoning J. Phys. Chem. A 2011, 115, 6137-6148 10.1021/jp111093c
7. Bello-Rivas, J. M.; Elber, R. Exact Milestoning J. Chem. Phys. 2015, 142, 094102 10.1063/1.4913399
8. Boresch, S.; Archontis, G.; Karplus, M. Free-Energy Simulations-the Meaning of the Individual Contributions from a Component Analysis Proteins: Struct., Funct., Genet. 1994, 20, 25-33 10.1002/prot.340200105
9. E, W.; Ren, W. Q.; Vanden-Eijnden, E. String Method for the Study of Rare Events Phys. Rev. B: Condens. Matter Mater. Phys. 2002, 66, 052301 10.1103/PhysRevB.66.052301
10. Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces J. Chem. Phys. 2006, 125, 024106 10.1063/1.2212942
11. Ulitsky, A.; Elber, R. A New Technique to Calculate Steepest Descent Paths in Flexible Polyatomic Systems J. Chem. Phys. 1990, 92, 1510-1511 10.1063/1.458112
12. E, W.; Ren, W. Q.; Vanden-Eijnden, E. Finite Temperature String Method for the Study of Rare Events J. Phys. Chem. B 2005, 109, 6688-6693 10.1021/jp0455430
13. Elber, R.; Roitberg, A.; Simmerling, C.; Goldstein, R.; Li, H. Y.; Verkhivker, G.; Keasar, C.; Zhang, J.; Ulitsky, A. MOIL: A Program for Simulations of Macrmolecules Comput. Phys. Commun. 1995, 91, 159-189 10.1016/0010-4655(95)00047-J
14. West, A. M. A.; Elber, R.; Shalloway, D. Extending Molecular Dynamics Time Scales with Milestoning: Example of Complex Kinetics in a Solvated Peptide J. Chem. Phys. 2007, 126, 145104 10.1063/1.2716389
15. Majek, P.; Elber, R. Milestoning Without a Reaction Coordinate J. Chem. Theory Comput. 2010, 6, 1805-1817 10.1021/ct100114j
16. Kirmizialtin, S.; Elber, R. Revisiting and Computing Reaction Coordinate with Directional Milestoning J. Phys. Chem. A 2011, 115, 6137-6148 10.1021/jp111093c
17. Elber, R.; West, A. Atomically Detailed Simulation of the Recovery Stroke in Myosin by Milestoning Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 5001-5005 10.1073/pnas.0909636107
18. Elber, R. A Milestoning Study of the Kinetics of an Allosteric Transition: Atomically Detailed Simulations of Deoxy Scapharca Hemoglobin Biophys. J. 2007, 92, L85-L87 10.1529/biophysj.106.101899
19. Vanden-Eijnden, E.; Venturoli, M. Revisiting the Finite Temperature String Method for the Calculation of Reaction Tubes and Free Energies J. Chem. Phys. 2009, 130, 194103 10.1063/1.3130083
20. Czerminski, R.; Elber, R. Self-Avoiding Walk between Two Fixed End Points as a Tool to Calculate Reaction Paths in Large Molecular Systems Int. J. Quantum Chem. 1990, 38, 167-186 10.1002/qua.560382419
21. Elber, R.; Karplus, M. A Method for Determining Reaction Paths in Large Molecules-Application to Myoglobin Chem. Phys. Lett. 1987, 139, 375-380 10.1016/0009-2614(87)80576-6
22. Shalloway, D.; Faradjian, A. K. Efficient Computation of the First Passage Time Distribution of the Generalized Master Equation by Steady-State Relaxation J. Chem. Phys. 2006, 124, 054112 10.1063/1.2161211
23. Huang, H. F.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Structure of a Covalently Trapped Catalytic Complex of HIV-I Reverse Transcriptase: Implications for Drug Resistance Science 1998, 282, 1669-1675 10.1126/science.282.5394.1669
24. Sarafianos, S. G.; Das, K.; Clark, A. D.; Ding, J. P.; Boyer, P. L.; Hughes, S. H.; Arnold, E. Lamivudine (3TC) Resistance in HIV-1 Reverse Transcriptase Involves Steric Hindrance with Beta-Branched Amino Acids Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 10027-10032 10.1073/pnas.96.18.10027
25. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucl. Acid Res. 2000, 28, 235-242 10.1093/nar/28.1.235
26. Kaminski, G.; Friesner, R.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparameterization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides J. Phys. Chem. B 2001, 105, 6474-6487 10.1021/jp003919d
27. Pranata, J.; Wierschke, S. G.; Jorgensen, W. L. OPLS Potential Functions for Nucleotide Bases- Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform J. Am. Chem. Soc. 1991, 113, 2810-2819 10.1021/ja00008a002
28. Kirmizialtin, S.; Elber, R. Computational Exploration of Mobile Ion Distributions Around RNA Duplex J. Phys. Chem. B 2010, 114, 8207-8220 10.1021/jp911992t
29. Wang, J. M.; Cieplak, P.; Kollman, P. A. How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? J. Comput. Chem. 2000, 21, 1049-1074 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
30. Weinbach, Y.; Elber, R. Revisiting and Parallelizing SHAKE J. Comput. Phys. 2005, 209, 193-206 10.1016/j.jcp.2005.03.015
31. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald an N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092 10.1063/1.464397
32. Elber, R. Calculation of the Potential of Mean Force Using Molecular Dynamics with Linear Constraints -An Application to a Conformational Transition in a Solvated Dipeptide J. Chem. Phys. 1990, 93, 4312-4321 10.1063/1.458713
33. E, W. N.; Vanden-Eijnden, E. Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events Annu. Rev. Phys. Chem. 2010, 61, 391-420 10.1146/annurev.physchem.040808.090412
34. Donlin, M. J.; Patel, S. S.; Johnson, K. A. Kinetic Partitioning Between the Exonuclease and Polymerase Sites in DNA Error Correction Biochemistry 1991, 30, 538-546 10.1021/bi00216a031
35. Wong, I.; Patel, S. S.; Johnson, K. A. An Induced-Fit Kinetic Mechanism for DNA Replication Fidelity: Direct Measurement by Single-Turnover Kinetics Biochemistry 1991, 30, 526-537 10.1021/bi00216a030
36. Patel, S. S.; Wong, I.; Johnson, K. A. Pre-Steady-State Kinetic-Analysis of Processive DNA-Replication Including Complete Characterization of An Exonuclease-Deficient Mutant Biochemistry 1991, 30, 511-525 10.1021/bi00216a029
37. Kati, W. M.; Johnson, K. A.; Jerva, L. F.; Anderson, K. S. Mechanism and Fidelity of HIV Reverse Transcriptase J. Biol. Chem. 1992, 267, 25988-25997
38. Kellinger, M. W.; Johnson, K. A. Nucleotide-Dependent Conformational Change Governs Specificity and Analog Discrimination by HIV Reverse Transcriptase Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 7734-7739 10.1073/pnas.0913946107
39. Kellinger, M. W.; Johnson, K. A. Role of Induced Fit in Limiting Discrimination Against AZT by HIV Reverse Transcriptase Biochemistry 2011, 50, 5008-5015 10.1021/bi200204m
40. Johnson, K. A.; Benkovic, S. J. Analysis of Protein Function by Mutagenesis. In The Enzymes; Sigman, D. S.; Boyer, P. D., Eds.; Academic Press Inc.: San Diego, CA, 1990; Vol. XIX, pp 159-211.