Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Journal of Chemical Theory and Computation

Volumn 11, Issue 9, 2015, Pages 4086-4092

  Hostaš, Jiří ^a,b   Jakubec, Dávid ^a,b   Laskowski, Roman A ^c   Gnanasekaran, Ramachandran ^a   Řezáč, Jan ^a   Vondrášek, Jiří ^a   Hobza, Pavel ^a,d  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^d PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA; PROTEIN;

CHEMISTRY; COMPARATIVE STUDY; HYDROGEN BOND; QUANTUM THEORY;

AMINO ACIDS; DNA; HYDROGEN BONDING; PROTEINS; QUANTUM THEORY;

EID: 84941129427     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00398     Document Type: Article

References (44)

1. Laskowski, R. A.; Thornton, J. M. Understanding the molecular machinery of genetics through 3D structures Nat. Rev. Genet. 2008, 9, 141-151 10.1038/nrg2273
2. Gaj, T.; Gersbach, C. A.; Barbas, C. F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering Trends Biotechnol. 2013, 31, 397-405 10.1016/j.tibtech.2013.04.004
3. Jakubec, D.; Hostaš, J.; Laskowski, R. A.; Hobza, P.; Vondrášek, J. Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes J. Chem. Theory Comput. 2015, 11, 1939-1948 10.1021/ct501168n
4. Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level Nucleic Acids Res. 2001, 29, 2860-2874 10.1093/nar/29.13.2860
5. Černý, J.; Hobza, P. Non-covalent interactions in biomacromolecules Phys. Chem. Chem. Phys. 2007, 9, 5291-5303 10.1039/b704781a
6. Černý, J.; Pitoňák, M.; Riley, K. E.; Hobza, P. Complete basis set extrapolation and hybrid schemes for geometry gradients of noncovalent complexes J. Chem. Theory Comput. 2011, 7, 3924-3934 10.1021/ct200484e
7. Řezáč, J.; Hobza, P. Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the "Gold Standard," CCSD(T), at the Complete Basis Set Limit? J. Chem. Theory Comput. 2013, 9, 2151-2155 10.1021/ct400057w
8. Černý, J.; Pitoňák, M.; Riley, K. E.; Hobza, P. Complete basis set extrapolation and hybrid schemes for geometry gradients of noncovalent complexes J. Chem. Theory Comput. 2011, 7, 3924-3934 10.1021/ct200484e
9. Berka, K.; Laskowski, R. A.; Riley, K. E.; Hobza, P.; Vondrášek, J. Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures J. Chem. Theory Comput. 2009, 5, 982-992 10.1021/ct800508v
10. Singh, J.; Thornton, J. M. SIRIUS. An Automated Method for the Analysis of the Preferred Packing Arrangements between Protein Groups J. Mol. Biol. 1990, 211, 595-615 10.1016/0022-2836(90)90268-Q
11. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera-A visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25, 1605-12 10.1002/jcc.20084
12. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields J. Phys. Chem. 1994, 98, 11623-11627 10.1021/j100096a001
13. Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 1993, 98, 5648 10.1063/1.464913
14. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
15. Weigend, F.; Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy Phys. Chem. Chem. Phys. 2005, 7, 3297-3305 10.1039/b508541a
16. Halkier, A.; Helgaker, T.; Jørgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. Basis set convergence in correlated calculations on Ne, N2 and H2O Chem. Phys. Lett. 1998, 286, 243-252 10.1016/S0009-2614(98)00111-0
17. Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. Electron Affinities of the First-Row Atoms Revisited. Systematic Basis Sets and Wave Functions J. Chem. Phys. 1992, 96, 6796-6806 10.1063/1.462569
18. Pitoňák, M.; Riley, K. E.; Neogrády, P.; Hobza, P. Highly Accurate CCSD(T) and DFT-SAPT stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer ChemPhysChem 2008, 9, 1636-1644 10.1002/cphc.200800286
19. Sherrill, C. D.; Takatani, T.; Hohenstein, E. G. An Assessment of Theoretical Methods for Nonbonded Interactions: Comparison to Complete Basis Set Limit Coupled-Cluster Potential Energy Curves for the Benzene Dimer, the Methane Dimer, Benzene-Methane, and Benzene-H2S J. Phys. Chem. A 2009, 113, 10146-10159 10.1021/jp9034375
20. Řezáč, J.; Riley, K. E.; Hobza, P. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structure J. Chem. Theory Comput. 2011, 7, 2427-2438 10.1021/ct2002946
21. Řezáč, J.; Riley, K. E.; Hobza, P. Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules J. Chem. Theory Comput. 2012, 8, 4285-4292 10.1021/ct300647k
22. Boys, S. F.; Bernardi, F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors Mol. Phys. 1970, 19, 553-566 10.1080/00268977000101561
23. Feyereisen, M.; Fitzgerald, G.; Komornicki, A. Use of Approximate Integrals in Ab Initio Theory-An Application in Mp2 Energy Calculations Chem. Phys. Lett. 1993, 208, 359-363 10.1016/0009-2614(93)87156-W
24. Distasio, R. A., Jr.; Head-Gordon, M. Optimized spin-component scaled second-order Møller-Plesset perturbation theory for intermolecular interaction energies Mol. Phys. 2007, 105, 1073-1083 10.1080/00268970701283781
25. Sedlák, R.; Riley, K. E.; Řezáč, J.; Pitoňák, M.; Hobza, P. MP2.5 and MP2.X: Approaching CCSD(T) Quality Description of Noncovalent Interaction at the Cost of Single CCSD Iteration ChemPhysChem 2013, 14, 698-707 10.1002/cphc.201200850
26. Riley, K. E.; Řezáč, J.; Hobza, P. MP2.X: A generalized MP2.5 method that produces improved binding energies with smaller basis sets Phys. Chem. Chem. Phys. 2011, 13, 21121-21125 10.1039/c1cp22525a
27. Pitoňák, M.; Neogrády, P.; Černý, J.; Grimme, S.; Hobza, P. Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data ChemPhysChem 2009, 10, 282-289 10.1002/cphc.200800718
28. Peterson, K. A.; Adler, T. B.; Werner, H. J. Systematically convergent basis sets for explicitly correlated wavefunctions: The atoms H, He, B-Ne, and Al-Ar J. Chem. Phys. 2008, 128, 084102 10.1063/1.2831537
29. TURBOMOLE v6.5 2013, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com.
30. van Lenthe, J. H.; van Duijneveldt-van de Rijdt, J. G. C. M.; van Duijneveldt, F. B. Weakly Bonded Systems Adv. Chem. Phys. 1987, 69, 521-566 10.1002/9780470142943.ch9
31. Riley, K. E.; Pitoňák, M.; Jurečka, P.; Hobza, P. Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories Chem. Rev. 2010, 110, 5023-5063 10.1021/cr1000173
32. Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory J. Comput. Chem. 2011, 32, 1456-1465 10.1002/jcc.21759
33. Goerigk, L.; Kruse, H.; Grimme, S. Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions ChemPhysChem 2011, 12, 3421-3433 10.1002/cphc.201100826
34. Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic-behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
35. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
36. Tao, J. M.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the density functional ladder: Nonempirical meta-generalized gradient approximation designed for molecules and solids Phys. Rev. Lett. 2003, 91, 146401-146404 10.1103/PhysRevLett.91.146401
37. Miehlich, B.; Savin, A.; Stoll, H.; Preuss, H. Results obtained with the correlation-energy density functionals of Becke and Lee, Yang and Parr Chem. Phys. Lett. 1989, 157, 200-206 10.1016/0009-2614(89)87234-3
38. Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements J. Mol. Model. 2007, 13, 1173-1213 10.1007/s00894-007-0233-4
39. Řezáč, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods J. Chem. Theory Comput. 2012, 8, 141-151 10.1021/ct200751e
40. Stewart, J. J. P. MOPAC2012; Stewart Computational Chemistry: Colorado Springs, CO, USA, 2012, (http://OpenMOPAC.net).
41. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447 10.1021/ct700301q
42. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003, 24, 1999-2012 10.1002/jcc.10349
43. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197 10.1021/ja00124a002
44. Liakos, D. G.; Izsák, R.; Valeev, E. F.; Neese, F. What is the most efficient way to reach the canonical MP2 basis set limit? Mol. Phys. 2013, 111, 2653-2662 10.1080/00268976.2013.824624