First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

Scientific Data

Volumn 3, Issue , 2016, Pages

  Ropo, Matti ^a,b,c   Schneider, Markus ^a   Baldauf, Carsten ^a   Blum, Volker ^a,d  

^a FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

^b TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^c AALTO UNIVERSITY   (Finland)

^d Duke University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DIPEPTIDE; DIVALENT CATION;

CONFORMATION;

AMINO ACIDS; CATIONS, DIVALENT; DIPEPTIDES; MOLECULAR CONFORMATION;

EID: 84961184519     PISSN: None     EISSN: 20524463     Source Type: Journal    
DOI: 10.1038/sdata.2016.9     Document Type: Article

References (112)

1. Yu, W. et al. Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers. J. Comput. Chem. 30, 2105-2121 (2009).
2. Kishor, S., Dhayal, S., Mathur, M. & Ramaniah, L. M. Structural and energetic properties of α-amino acids: A first principles density functional study. Mol. Phys. 106, 2289-2300 (2008).
3. Császár, A. G. & Perczel, A. Ab initio characterization of building units in peptides and proteins. Prog. Biophys. Mol. Biol. 71, 243-309 (1999).
4. Bouchoux, G. Gas phase basicities of polyfunctional molecules. Part 3: Amino acids. Mass Spectrom. Rev. 31, 391-435 (2012).
5. Matta, C. F. & Bader, R. F. W. Atoms-in-molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries. Proteins: Struct., Funct., Bioinf 48, 519-538 (2002).
6. Schlund, S., Muller, R., Grassmann, C. & Engels, B. Conformational analysis of arginine in gas phase - a strategy for scanning the potential energy surface effectively. J. Comput. Chem. 29, 407-415 (2008).
7. Császár, A. G. On the structures of free glycine and α-alanine. J. Mol. Struct. 346, 141-152 (1995).
8. Császár, A. G. Conformers of gaseous glycine. J. Am. Chem. Soc. 114, 9568-9575 (1992).
9. Riffet, V., Frison, G. & Bouchoux, G. Acid-base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met). Phys. Chem. Chem. Phys. 13, 18561-18580 (2011).
10. Kabelac, M., Hobza, P. & Spirko, V. The ab initio assigning of the vibrational probing modes of tryptophan: Linear shifting of approximate anharmonic frequencies vs. multiplicative scaling of harmonic frequencies. Phys. Chem. Chem. Phys. 11, 3921-3926 (2009).
11. Kaschner, R. & Hohl, D. Density functional theory and biomolecules: A study of glycine, alanine, and their oligopeptides. J. Phys. Chem. A 102, 5111-5116 (1998).
12. Maul, R., Ortmann, F., Preuss, M., Hannewald, K. & Bechstedt., F. DFT studies using supercells and projector-augmented waves for structure, energetics, and dynamics of glycine, alanine, and cysteine. J. Comput. Chem. 28, 1817-1833 (2007).
13. Selvarengan, P. & Kolandaivel, P. Potential energy surface study on glycine, alanine and their zwitterionic forms. J. Mol. Struct.: THEOCHEM 671, 77-86 (2004).
14. Cao, M., Newton, S. Q., Pranata, J. & Schafer, L. J. Mol. Struct. THEOCHEM 332, 251 (1995).
15. Jaeger, H. M., Schaefer, H. F., Demaison, J., Császár, A. G. & Allen, W. D. Lowest-lying conformers of alanine: Pushing theory to ascertain precise energetics and semiexperimental re structures. J. Chem. Theory Comput. 6, 3066-3078 (2010).
16. Beachy, M. D., Chasman, D., Murphy, R. B., Halgren, T. A. & Friesner, R. A. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. J. Am. Chem. Soc. 119, 5908-5920 (1997).
17. Baek, K. Y., Fujimura, Y., Hayashi, M., Lin, S. H. & Kim, S. K. Density functional theory study of conformation-dependent properties of neutral and radical cationic l-tyrosine and l-tryptophan. J. Phys. Chem. A 115, 9658-9668 (2011).
18. Chen, M. & Lin., Z. Ab initio studies of aspartic acid conformers in gas phase and in solution. J. Chem. Phys. 127, 154314 (2007).
19. Floris, F. M., Filippi, C. & Amovilli., C. A density functional and quantum monte carlo study of glutamic acid in vacuo and in a dielectric continuum medium. J. Chem. Phys. 137, 075102 (2012).
20. Heaton, A. L., Moision, R. M. & Armentrout, P. B. Experimental and theoretical studies of sodium cation interactions with the acidic amino acids and their amide derivatives. J. Phys. Chem. A 112, 3319-3327 (2008).
21. Armentrout, P.B., Gabriel, A. & Moision., R.M. An experimental and theoretical study of alkali metal cation/methionine interactions. Int. J. Mass Spectrom. 283, 56-68 (2009).
22. Nguyen, D. T. et al. A density functional study of the glycine molecule: Comparison with post-hartree-fock calculations and experiment. J. Comput. Chem. 18, 1609-1631 (1997).
23. Espinoza, C., Szczepanski, J., Vala, M. & Polfer, N. C. Glycine and its hydrated complexes: A matrix isolation infrared study. J. Phys. Chem. A 114, 5919-5927 (2010).
24. Boeckx, B., Nelissen, W. & Maes, G. Potential energy surface and matrix isolation ft-ir study of isoleucine. J. Phys. Chem. A 116, 3247-3258 (2012).
25. Close, D. M. Calculated vertical ionization energies of the common alpha-amino acids in the gas phase and in solution. J. Phys. Chem. A 115, 2900-2912 (2011).
26. Baek, K. Y., Hayashi, M., Fujimura, Y., Lin, S. H. & Kim, S. K. Investigation of conformation-dependent properties of l-phenylalanine in neutral and radical cations by using a density functional taking into account noncovalent interactions. J. Phys. Chem. A 114, 7583-7589 (2010).
27. Sahai, M. A. et al. First principle computational study on the full conformational space of l-proline diamides. J. Phys. Chem. A 109, 2660-2679 (2005).
28. Linder, R., Seefeld, K., Vavra, A. & Kleinermanns, K. Gas phase infrared spectra of nonaromatic amino acids. Chem. Phys. Lett. 453, 1-6 (2008).
29. Vyas, N. & Ojha, A. K. Investigation on transition states of [alanine+m2+] (m= ca, cu, and zn) complexes: A quantum chemical study. Int. J. Quant. Chem 112, 1526-1536 (2012).
30. Lavrich, R. J. et al. Experimental studies of peptide bonds: Identification of the c[sub 7][sup eq] conformation of the alanine dipeptide analog n-acetyl-alanine n[sup [prime]]-methylamide from torsion-rotation interactions. J. Chem. Phys. 118, 1253-1265 (2003).
31. Zhang, M., Huang, Z. & Lin, Z. Systematic ab initio studies of the conformers and conformational distribution of gas-phase tyrosine. J. Chem. Phys. 122, 134313 (2005).
32. Dokmaisrijan, S., Lee, V. S. & Nimmanpipug., P. The gas phase conformers and vibrational spectra of valine, leucine and isoleucine: An ab initio study. J. Mol. Struct.: THEOCHEM 953, 28-38 (2010).
33. Ceci, M. L. et al. Exploratory conformational analysis of n-acetyl-l-tryptophan-n-methylamide. an ab initio study. J. Mol. Struct.: THEOCHEM 631, 277-290 (2003).
34. Chen, M., Huang, Z. & Lin., Z. J. Mol. Struct. THEOCHEM 719, 153 (2005).
35. Rassolian, M., Chass, G. A., Setiadi, D. H. & Csizmadia., I. G. Asparagine-ab initio structural analyses. J. Mol. Struct.: {THEOCHEM} 666-667, 273-278 (2003).
36. Zamora, M. A. et al. An exploratory ab initio study of the full conformational space of n-acetyl-l-cysteine-n-methylamide. J. Mol. Struct.: {THEOCHEM} 540, 271-283 (2001).
37. Rai, A. K., Song, C. & Lin., Z. An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 73, 865-870 (2009).
38. von Helden, G., Compagnon, I., Blom, M. N., Frankowski, M., Erlekam, U., Oomens, J., Brauer, B., Gerber, R. B. & Meijer, G. Mid-ir spectra of different conformers of phenylalanine in the gas phase. Phys. Chem. Chem. Phys. 10, 1248-1256 (2008).
39. Riffet, V. & Bouchoux, G. Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base. Phys. Chem. Chem. Phys. 15, 6097-6106 (2013).
40. Shemesh, D., Sobolewski, A. L. & Domcke, W. Role of excited-state hydrogen detachment and hydrogen-transfer processes for the excited-state deactivation of an aromatic dipeptide: N-acetyl tryptophan methyl amide. Phys. Chem. Chem. Phys. 12, 4899-4905 (2010).
41. Gabor, P., Perczel, A., Vass, E., Magyarfalvi, G. & Tarczay., G. A matrix isolation study on ac-gly-nhme and ac-l-ala-nhme, the simplest chiral and achiral building blocks of peptides and proteins. Phys. Chem. Chem. Phys. 9, 4698-4708 (2007).
42. Bakker, J. M., Aleese, L. M., Meijer, G. & von Helden, G. Fingerprint ir spectroscopy to probe amino acid conformations in the gas phase. Phys. Rev. Lett. 91, 203003 (2003).
43. Blanco, S., Sanz, M. E., López, J. C. & Alonso, J. L. Revealing the multiple structures of serine. Proc. Natl. Acad. Sci. USA 104, 20183-20188 (2007).
44. Szidarovszky, T., Czakó, G. & Császár, A. Mol. Phys. 107, 761 (2009).
45. Boeckx, B. & Maes, G. Experimental and theoretical observation of different intramolecular h-bonds in lysine conformations. J. Phys. Chem. B 116, 12441-12449 (2012).
46. Meng, L. & Lin, Z. Comprehensive computational study of gas-phase conformations of neutral, protonated and deprotonated glutamic acids. Computational and Theoretical Chemistry 976, 42-50 (2011).
47. Shankar, R., Kolandaivel, P. & Senthilkumar, L. Interaction studies of cysteine with li+, na+, k+, be2+, mg2+, and ca2+ metal cation complexes. Journal of Physical Organic Chemistry 24, 553-567 (2011).
48. Fleming, G. J., McGill, P. R. & Idriss, H. Gas phase interaction of l-proline with be2+, mg2+ and ca2+ ions: a computational study. Journal of Physical Organic Chemistry 20, 1032-1042 (2007).
49. Hu, C.-H., Shen, M. & Schaefer., H. F. Glycine conformational analysis. J. Am. Chem. Soc. 115, 2923 (1993).
50. Barone, V., Biczysko, M., Bloino, J. & Puzzarini, C. Characterization of the elusive conformers of glycine from state-of-the-art structural, thermodynamic, and spectroscopic computations: Theory complements experiment. J. Chem. Theory Comput. 9, 1533-1547 (2013).
51. Ai, H. Q., Bu, Y. X., Li, P. & Zhang., C. The regulatory roles of metal ions (m+/2+ =li+, na+, k+, be2+, mg2+, and ca2+) and water molecules in stabilizing the zwitterionic form of glycine derivatives. New J. Chem. 29, 1540-1548 (2005).
52. Baldauf, C. & Hofmann., H.-J. Ab initio mo theory-an important tool in foldamer research: Prediction of helices in oligomers of ω-amino acids. Helvetica Chimica Acta 95, 2348-2383 (2012).
53. Ramek, M., Kelterer, A.-M. & Nikolić, S. Ab initio and molecular mechanics conformational analysis of neutral l-proline. Int. J. Quant. Chem 65, 1033-1045 (1997).
54. Czinki, E. & Császár, A. G. Conformers of gaseous proline. Chem. Eur. J 9, 1008-1019 (2003).
55. Kang., Y. K. Ab initio molecular orbital calculations on low-energy conformers of N-Acetyl-N'-methylprolineamide. J. Phys. Chem. 100, 11589 (1996).
56. Xu, S., Ke-Dong, W. & Peng-Fei, M. Conformation effects on the molecular orbitals of serine. Chinese Physics B 20, 33102 (2011).
57. Yuan, Y., Mills, M. J. L., Popelier, P. L. A. & Jensen, F. Comprehensive analysis of energy minima of the 20 natural amino acids. J. Phys. Chem. A 118, 7876-7891 (2014).
58. Karton, A., Yu, L.-J., Kesharwani, M. & Martin, J. M. L. Heats of formation of the amino acids re-examined by means of w1-f12 and w2-f12 theories. Theoretical Chemistry Accounts 133, 1483 (2014).
59. Kesharwani, M. K., Karton, A. & Martin, J. M. L. Benchmark ab initio conformational energies for the proteinogenic amino acids through explicitly correlated methods. assessment of density functional methods. J. Chem. Theory Comput. 12, 444-454 (2015).
60. Holm, R. H., Kennepohl, P. & Solomon, E. I. Structural and functional aspects of metal sites in biology. Chemical Reviews 96, 2239-2314 (1996).
61. Tainer, J. A., Roberts, V. A. & Getzoff, E. D. Protein metal-binding sites. Current Opinion in Biotechnology 3, 378-387 (1992).
62. Kirberger, M. & Yang, J. J. Structural differences between Pb2+-and Ca2+-binding sites in proteins: Implications with respect to toxicity. Journal of Inorganic Biochemistry 102, 1901-1909 (2008).
63. Zhou, M. et al. and Jianping Ding. A novel calcium-binding site of von Willebrand factor A2 domain regulates its cleavage by ADAMTS13. Blood 117, 4623-4631 (2011).
64. Cheng, R. & Zhorov, B. Docking of calcium ions in proteins with flexible side chains and deformable backbones. European Biophysics Journal 39, 825-838 (2010).
65. Sadiq, S., Ghazala, Z., Chowdhury, A. & Büsselberg, D. Metal toxicity at the synapse: Presynaptic, postsynaptic, and long-term effects. Journal of Toxicology 2012, 132671 (2012).
66. Sharma, S. K., Goloubinoff, P. & Christen, P. Heavy metal ions are potent inhibitors of protein folding. Biochemical and Biophysical Research Communications 372, 341-345 (2008).
67. Hohenberg, P. & Kohn, W. Inhomogeneous electron gas. Phys. Rev 136, B864-B871 (1964).
68. Kohn, W. & Sham, L. J. Self-consistent equations including exchange and correlation effects. Phys. Rev 140, A1133-A1138 (1965).
69. Perdew, J. P., Burke, K. & Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865-3868 (1996).
70. Tkatchenko, A. & Scheffler, M. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett. 102, 073005 (2009).
71. Rossi, M. et al. Secondary structure of Ac-Alan-LysH+ polyalanine peptides (n =5,10,15) in vacuo: Helical or not? J. Phys. Chem. Lett. 1, 3465-3470 (2010).
72. Tkatchenko, A., Rossi, M., Blum, V., Ireta, J. & Scheffler, M. Unraveling the stability of polypeptide helices: Critical role of van der Waals interactions. Phys. Rev. Lett. 106, 118102 (2011).
73. Baldauf, C. et al. How cations change peptide structure. Chemistry-A European Journal 19, 11224-11234 (2013).
74. Chutia, S., Rossi, M. & Blum, V. Water adsorption at two unsolvated peptides with a protonated lysine residue: From self-solvation to solvation. J. Phys. Chem. B 116, 14788-14804 (2012).
75. Rossi, M., Scheffler, M. & Blum, V. Impact of vibrational entropy on the stability of unsolvated peptide helices with increasing length. J. Phys. Chem. B 117, 5574-5584 (2013).
76. Rossi, M., Chutia, S., Scheffler, M. & Blum, V. Validation challenge of density-functional theory for peptides-example of Ac-Phe-Ala5-LysH+. J. Phys. Chem. A 118, 7349-7359 (2014).
77. Schubert, F. et al. Native like helices in a specially designed [small beta] peptide in the gas phase. Phys. Chem. Chem. Phys. 17, 5376-5385 (2015).
78. Schubert, F. et al. Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys+H+ vs. Ac-Lys-Ala19+H+ and the current reach of DFT. Phys. Chem. Chem. Phys. 17, 7375-7385 (2015).
79. 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. 118, 11225-11236 (1996).
80. Wales, D. J. & Doye, J. P. K. Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J. Phys. Chem. A 101, 5111-5116 (1997).
81. Wales, D. J. & Scheraga, H. A. Global optimization of clusters, crystals, and biomolecules. Science 285, 1368-1372 (1999).
82. Ponder, J. W. & Richards., F. M. An efficient Newton-like method for molecular mechanics energy minimization of large molecules. J. Comput. Chem. 8, 1016-1024 (1987).
83. Ren, P. & Ponder, J. W. Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B 107, 5933-5947 (2003).
84. Blum, V. et al. Ab initio molecular simulations with numeric atom-centered orbitals. Computer Physics Communications 180, 2175-2196 (2009).
85. Havu, V., Blum, V., Havu, P. & Scheffler, M. Efficient integration for all-electron electronic structure calculation using numeric basis functions. Journal of Computational Physics 228, 8367-8379 (2009).
86. Ren, X. et al. Resolution-of-identity approach to Hartree-Fock, hybrid density functionals, RPA, MP2 and GW with numeric atom-centered orbital basis functions. New Journal of Physics 14, 053020 (2012).
87. van Lenthe, J. H., Faas, S. & Snijders, J. G. Gradients in the ab initio scalar zeroth-order regular approximation (ZORA) approach. Chem. Phys. Lett. 328, 107-112 (2000).
88. van Wullen, C. Molecular density functional calculations in the regular relativistic approximation: Method, application to coinage metal diatomics, hydrides, fluorides and chlorides, and comparison with first-order relativistic calculations. J. Chem. Phys. 109, 392-399 (1998).
89. Swendsen, R. H. & Wang, J.-S. Replica Monte Carlo simulation of spin-glasses. Phys. Rev. Lett. 57, 2607-2609 (1986).
90. Sugita, Y. & Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141-151 (1999).
91. Earl, D. J. & Deem, M. W. Parallel tempering: Theory, applications, and new perspectives. Phys. Chem. Chem. Phys. 7, 3910 (2005).
92. Beret, E. C., Ghiringhelli, L. M. & Scheffler, M. Free gold clusters: beyond the static, monostructure description. Faraday Discuss. 152, 153-167 (2011).
93. Sindhikara, D., Meng, Y. & Roitberg, A. E. Exchange frequency in replica exchange molecular dynamics. J. Chem. Phys. 128, 024103 (2008).
94. Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).
95. Hartigan, J. A. & Wong, M. A. Algorithm as 136: A k-means clustering algorithm. Journal of the Royal Statistical Society. Series C (Applied Statistics) 28, 100-108 (1979).
96. Feig, M., Karanicolas, J. & Brooks III, C. L. MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics and Modelling 22, 377-395 (2004).
97. Humphrey, W., Dalke, A. & Schulten, K. VMD-Visual Molecular Dynamics. J. Molec. Graphics 14, 33-38 (1996).
98. Perdew., J. P. Unified Theory of Exchange and Correlation Beyond the Local Density Approximation. in Electronic Structure of Solids '91-Proceedings of the 75. WE-Heraeus-Seminar and 21st Annual International Symposium on Electronic Structure of Solids; Gaussig, Germany; 11-15 March 1991 (Akademie Verlag, Berlin, 1991).
99. Møller, C. & Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev 46, 618-622 (1934).
100. Head-Gordon, M., Poplei, J. A. & Frisch., M. J. MP2 energy evaluation by direct methods. Chem. Phys. Lett. 153, 503-506 (1988).
101. Neese., F. The ORCA program system. WIREs Comput. Mol. Sci. 2, 73-78 (2012).
102. Woon, D. E. & Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. V. Corevalence basis sets for boron through neon. J. Chem. Phys. 103, 4572-4585 (1995).
103. Karton, A. & Martin, J. M. L. Comment on: "Estimating the Hartree-Fock limit from finite basis set calculations" [Jensen F (2005) Theor Chem Acc 113:267]. Theor. Chem. Acc. 115, 330-333 (2006).
104. Truhlar, D.G. Basis-set extrapolation. Chem. Phys. Lett. 294, 45-48 (1998).
105. Ambrosetti, A., Reilly, A. M., DiStasio, R. A. & Tkatchenko, A. Long-range correlation energy calculated from coupled atomic response functions. J. Chem. Phys. 140, 18A508 (2014).
106. Adamo, C. & Barone., V. Toward reliable density functional methods without adjustable parameters: The PBE0 model. J. Chem. Phys. 110, 6158-6170 (1999).
107. Zhang, I. Y., Ren, X., Rinke, P., Blum, V. & Scheffler, M. Numeric atom-centered-orbital basis sets with valence-correlation consistency from h to ar. New Journal of Physics 15, 123033 (2013).
108. Jansen, H. B. & Ros, P. Non-empirical molecular orbital calculations on the protonation of carbon monoxide. Chem. Phys. Lett. 3, 140-143 (1969).
109. 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. 19, 553-566 (1970).
110. Ho, Y.-P., Yang, M.-W., Chen, L.-T. & Yang, Y.-C. Relative calcium-binding strengths of amino acids determined using the kinetic method. Rapid Communications in Mass Spectrometry 21, 1083-1089 (2007).
111. Liwo, A., Khalili, M. & Scheraga., H. A. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. USA 102, 2362-2367 (2005).
112. O'Boyle, N. et al. Open babel: An open chemical toolbox. Journal of Cheminformatics 3, 33 (2011).