QTAIM study of an α-helix hydrogen bond network

Journal of Physical Chemistry B

Volumn 113, Issue 31, 2009, Pages 10957-10964

  LaPointe, Shenna M ^a   Farrag, Sarah ^a   Bohórquez, Hugo J ^a   Boyd, Russell J ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; BINDING SITES; CARRIER CONCENTRATION; ELECTRON DENSITY MEASUREMENT; ELECTRONS; EQUATIONS OF STATE; HYDROGEN; HYDROGEN BONDS; ORGANIC ACIDS; PEPTIDES; QUANTUM THEORY;

ALANINE-BASED PEPTIDE; AMINO ACID SUBSTITUTION; ELECTRON DENSITIES; ENTROPIC EFFECTS; HYDROGEN BOND NETWORKS; QUANTUM THEORY OF ATOMS IN MOLECULES;

DENSITY FUNCTIONAL THEORY;

ALANINE; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; PROTEIN SECONDARY STRUCTURE; QUANTUM THEORY;

ALANINE; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; QUANTUM THEORY;

EID: 68149092131     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp903635h     Document Type: Article

References (71)

1. Anfinsen, C. B. Principles that Govern the Folding of Protein Chains. Science 1973, 181, 223-230.
2. Kabsch, W.; Sander, C. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 1983, 22, 2577-2637.
3. Bour, P.; Kubelka, J.; Keiderling, T. A. Ab Initio Quantum Mechanical Models of Peptide Helices and their Vibrational Spectra. Biopolymers 2002, 65, 45-59.
4. Baldwin, R. L. How does Protein Folding Get Started? Trends Biochem. Sci. 1989, 14, 291-294.
5. Levitt, M.; Gerstein, M.; Huang, E.; Subbiah, S.; Tsai, J. Protein Folding: The Endgame. Annu. Rev. Biochem. 1997, 66, 549-579.
6. Aurora, R.; Creamer, T. P.; Srinivasan, R.; Rose, G. D. Local Interactions in Protein Folding: Lessons from the Alpha-Helix. J. Biol. Chem. 1997, 272, 1413-1416.
7. Chandonia, J. M.; Karplus, M. New Methods for Accurate Prediction of Protein Secondary Structure. Proteins 1999, 35, 293-306.
8. Dyson, H. J.; Wright, P. E. Defining Solution Conformations of Small Linear Peptides. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 519-538.
9. Scholtz, J. M.; Baldwin, R. L. The Mechanism of Alpha-Helix Formation by Peptides. Annu. Rev. Biophys. Biomol. Struct. 1992, 21, 95-118.
10. Miick, S. M.; Casteel, K. M.; Millhauser, G. L. Experimental Molecular Dynamics of an Alanine-Based Helical Peptide Determined by Spin Label Electron Spin Resonance. Biochemistry 1993, 32, 8014-8021.
11. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Fast Events in Protein Folding: Helix Melting and Formation in a Small Peptide. Biochemistry 1996, 35, 691-697.
12. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Laser Temperature Jump Study of the Helixcoil Kinetics of an Alanine Peptide Interpreted with a 'Kinetic Zipper' Model. Biochemistry 1997, 36, 9200-9210.
13. Toniolo, C.; Benedetti, E. The Polypeptide 310-Helix. Trends Biochem. Sci. 1991, 16, 350-353.
14. Park, C.; Goddard, W. A. Stabilization of α-Helices by Dipole-Dipole Interactions within α-Helices. J. Phys. Chem. B 2000, 104, 7784-7789.
15. Parthasarathi, R.; Raman, S. S.; Subramanian, V.; Ramasami, T. Bader's Electron Density Analysis of Hydrogen Bonding in Secondary Structural Elements of Protein. J. Phys. Chem. A 2007, 111, 7141-7148.
16. Park, C.; Carlson, M. J.; Goddard, W. A. Solvent Effects on the Secondary Structures of Proteins. J. Phys. Chem. A 2000, 104, 2498-2503.
17. Ireta, J.; Neugebauer, J.; Scheffler, M.; Rojo, A.; Galvan, M. Density Functional Theory Study of the Cooperativity of Hydrogen Bonds in Finite and Infinite α-Helices. J. Phys. Chem. B 2003, 107, 1432-1437.
18. Vener, M. V.; Egorova, A. N.; Fomin, D. P.; Tsirelson, V. G. QTAIM Study of the Closed-Shell Interactions in Peptide Secondary Structures: A Cluster Treatment of Oligo- and Polyalanines. Chem. Phys. Lett. 2007, 440, 279-284.
19. Wang, Z.; Wu, C.; Lei, H.; Duan, Y. Accurate Ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures. J. Chem. Theory Comput. 2007, 3, 1527-1537.
20. Shi, Z.; Olson, C. A.; Bell, A. J., Jr.; Kallenbach, N. R. Stabilization of α-Helix Structure by Polar Side-Chain Interactions: Complex Salt Bridges, Cation-α Interactions, and C-H ··· O H-Bonds. Biopolymers 2001, 60, 366-380.
21. Guzzo, A. V. The Influence of Amino-Acid Sequence on Protein Structure. Biophys. J. 1965, 5, 809-822.
22. Prothero, J. W. Correlation between the Distribution of Amino Acids and Alpha Helices. Biophys. J. 1966, 6, 367-370.
23. Chou, P. Y.; Fasman, G. D. Conformational Parameters for Amino Acids in Helical, Beta-Sheet, and Random Coil Regions Calculated from Proteins. Biochemistry 1974, 13, 211-222.
24. Defay, T.; Cohen, F. E. Evaluation of Current Techniques for Ab Initio Protein Structure Prediction. Proteins 1995, 23, 431-445.
25. Frishman, D.; Argos, P. The Future of Protein Secondary Structure Prediction Accuracy. Fold. Des. 1997, 2, 159-162.
26. Branden, C.; Tooze, J. Introduction to protein structure; Garland: New York, 1991.
27. Lehninger, A. L.; Nelson, D. L.; Cox, M. M. Lehninger principles of biochemistry; W. H. Freeman: New York, 2005.
28. Wieczorek, R.; Dannenberg, J. J. Comparison of Fully Optimized α- and 310-Helices with Extended β-Strands. An ONIOM Density Functional Theory Study. J. Am. Chem. Soc. 2004, 126, 14198-14205.
29. Horvath, V.; Varga, Z.; Kovacs, A. Long-Range Effects in Oligopeptides. A Theoretical Study of the β-Sheet Structure of Glyn (n = 2-10). J. Phys. Chem. A 2004, 108, 6869-6873.
30. Koch, O.; Bocola, M.; Klebe, G. Cooperative Effects in Hydrogen-Bonding of Protein Secondary Structure Elements: A Systematic Analysis of Crystal Data using Secbase. Proteins 2005, 61, 310-317.
31. Lario, P. I.; Vrielink, A. Atomic Resolution Density Maps Reveal Secondary Structure Dependent Differences in Electronic Distribution. J. Am. Chem. Soc. 2003, 125, 12787-12794.
32. Wieczorek, R.; Dannenberg, J. J. Hydrogen-Bond Cooperativity, Vibrational Coupling, and Dependence of Helix Stability on Changes in Amino Acid Sequence in Small 310-Helical Peptides. A Density Functional Theory Study. J. Am. Chem. Soc. 2003, 125, 14065-14071.
33. Viswanathan, R.; Asensio, A.; Dannenberg, J. J. Cooperative Hydrogen-Bonding in Models of Antiparallel β-Sheets. J. Phys. Chem. A 2004, 108, 9205-9212.
34. Popelier, P. L. A.; Bader, R. F. W. Effect of Twisting a Polypeptide on its Geometry and Electron Distribution. J. Phys. Chem. 1994, 98, 4473-4481.
35. Chang, C.; Bader, R. F. W. Theoretical Construction of a Polypeptide. J. Phys. Chem. 1992, 96, 1654-1662.
36. Parthasarathi, R.; Subramanian, V. In Hydrogen Bonding: New Insights, Challenges and Advances in Computational Chemistry and Physics; Grabowski, S. J., Ed.; Springer: Dordrecht, 2006; Vol 3, p1.
37. Koch, U.; Popelier, P. L. A. Characterization of C-H-O Hydrogen Bonds on the Basis of the Charge Density. J. Phys. Chem. 1995, 99, 9747-9754.
38. Grabowski, S. J. Ab Initio Calculations on Conventional and Unconventional Hydrogen BondssStudy of the Hydrogen Bond Strength. J. Phys. Chem. A 2001, 105, 10739-10746.
39. Domagala, M.; Grabowski, S. J. C-H ··· N and C-H ··· S Hydrogen Bonds-Influence of Hybridization on their Strength. J. Phys. Chem. A 2005, 109, 5683-5688.
40. Domagala, M.; Grabowski, S.; Urbaniak, K.; Mloston, G. Role of C-H ··· S and C-H ··· N Hydrogen Bonds in Organic Crystal Structuressthe Crystal and Molecular Structure of 3-Methyl-2,4-Diphenyl-(1,3)-Thiazoli-dine-5-Spiro-2′-Adamantane and 3-Methyl-2,4,5,5-Tetraphenyl-(1,3)-Thia-zolidine. J. Phys. Chem. A 2003, 107, 2730-2736.
41. Grabowski, S. J.; Sokalski, W. A.; Leszczynski, J. How Short can the H ··· H Intermolecular Contact be? New Findings that Reveal the Covalent Nature of Extremely Strong Interactions. J. Phys. Chem. A 2005, 109, 4331-4341.
42. Carroll, M. T.; Bader, R. F. W. Mol. Phys. 1988, 65, 695-722.
43. Boyd, R. J.; Choi, S. C. Hydrogen Bonding between Nitriles and Hydrogen Halides and the Topological Properties of Molecular Charge Distributions. Chem. Phys. Lett. 1986, 129, 62-65.
44. Espinosa, E.; Molins, E.; Lecomte, C. Hydrogen Bond Strengths Revealed by Topological Analyses of Experimentally Observed Electron Densities. Chem. Phys. Lett. 1998, 285, 170-173.
45. Boyd, R. J.; Choi, S. C. A Bond-Length-Bond-Order Relationship for Intermolecular Interactions Based on the Topological Properties of Molecular Charge Distributions. Chem. Phys. Lett. 1985, 120, 80-85.
46. Bader, R. F. W. Atoms in Molecules: a Quantum Theory; International series of monographs on chemistry; Clarendon Press: Oxford, New York, 1994; Vol. 22.
47. Parthasarathi, R.; Amutha, R.; Subramanian, V.; Nair, B. U.; Ramasami, T. Bader's and Reactivity Descriptors' Analysis of DNA Base Pairs. J. Phys. Chem. A 2004, 108, 3817-3828.
48. Marqusee, S.; Robbins, V. H.; Baldwin, R. L. Unusually Stable Helix Formation in Short Alanine-Based Peptides. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5286-5290.
49. Presta, L. G.; Rose, G. D. Helix Signals in Proteins. Science 1988, 240, 1632-1641.
50. Schaftenaar, G.; Noordik, J. H. Molden: A Pre- and Post-Processing Program for Molecular and Electronic Structures. J. Comput.-Aided Mol. Des. 2000, 14, 123-134.
51. Dennington, R., II; Keith, T.; Millam, J.; Semichem, I. Gaussview, 4.1; 2007.
52. Hamprecht, F. A.; Cohen, A. J.; Tozer, D. J.; Handy, N. C. Development and Assessment of New Exchange-Correlation Functionals. J. Chem. Phys. 1998, 109, 6264-6271.
53. Becke, A. D. A New Mixing of Hartree-Fock and Local Density-Functional Theories. J. Chem. Phys. 1993, 98, 1372-1377.
54. 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 1988, 37, 785-789.
55. Johnson, E. R.; DiLabio, G. A. Structure and Binding Energies in Van Der Waals Dimers: Comparison between Density Functional Theory and Correlated Ab Initio Methods. Chem. Phys. Lett. 2006, 419, 333-339.
56. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B.05; Gaussian, Inc.: Wallingford, CT, 2004.
57. Biegler-Konig, F.; Schonbohm, J.; Bayles, D. AIM2000. J. Comput. Chem. 2001, 22, 545-559.
58. Tang, T.; Hu, W.; Yan, D.; Cui, Y. A Quantum Chemical Study on Selected α-Type Hydrogen-Bonded Systems. J. Mol. Struct. (THEOCHEM) 1990, 207, 319-326.
59. Jiménez, A. I.; Ballano, G.; Cativiela, C. First Observation of Two Consecutive Gamma Turns in a Crystalline Linear Dipeptide 13. Angew. Chem., Int. Ed. 2005, 44, 396-399.
60. Bolin, K. A.; Millhauser, G. L. A and 310: The Split Personality of Polypeptide Helices. Acc. Chem. Res. 1999, 32, 1027-1033.
61. Toniolo, C.; Benedetti, E. The Polypeptide 310-Helix. Trends Biochem. Sci. 1991, 16, 350-353.
62. Millhauser, G. L.; Stenland, C. J.; Hanson, P.; Bolin, K. A.; van de Ven, F. J. Estimating the Relative Populations of 3(10)-Helix and Alpha-Helix in Ala-Rich Peptides: A Hydrogen Exchange and High Field NMR Study. J. Mol. Biol. 1997, 267, 963-974.
63. Wieczorek, R.; Dannenberg, J. J. The Energetic and Structural Effects of Single Amino Acid Substitutions upon Capped Alpha-Helical Peptides Containing 17 Amino Acid Residues. An ONIOM DFT/AM1 Study. J. Am. Chem. Soc. 2005, 127, 17216-17223.
64. Blaber, M.; Zhang, X. J.; Matthews, B. W. Structural Basis of Amino Acid Alpha Helix Propensity. Science 1993, 260, 1637-1640.
65. Lyu, P. C.; Liff, M. I.; Marky, L. A.; Kallenbach, N. R. Side Chain Contributions to the Stability of Alpha-Helical Structure in Peptides. Science 1990, 250, 669-673.
66. Richardson, J. S.; Richardson, D. C. Amino Acid Preferences for Specific Locations at the Ends of Alpha Helices. Science 1988, 240, 1648-1652.
67. Pace, C. N.; Scholtz, J. M. A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins. Biophys. J. 1998, 75, 422-427.
68. Creamer, T. P.; Rose, G. D. Side-Chain Entropy Opposes Alpha-Helix Formation but Rationalizes Experimentally Determined Helix-Forming Propensities. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 5937-5941.
69. Kyte, J.; Doolittle, R. F. A Simple Method for Displaying the Hydropathic Character of a Protein. J. Mol. Biol. 1982, 157, 105-132.
70. Avbelj, F.; Moult, J. Role of Electrostatic Screening in Determining Protein Main Chain Conformational Preferences. Biochemistry (N. Y.) 1995, 34, 755-764.
71. Wang, J.; Purisima, E. O. Analysis of Thermodynamic Determinants in Helix Propensities of Nonpolar Amino Acids through a Novel Free Energy Calculation. J. Am. Chem. Soc. 1996, 118, 995-1001.