공업화학 (Applied Chemistry for Engineering)

  • 제33권4호
  • /
  • Pages.425-430
  • /
  • 2022
  • /
  • 1225-0112(pISSN)
  • /
  • 2288-4505(eISSN)
한국공업화학회 (The Korean Society of Industrial and Engineering Chemistry)
권호 표지
DOI QR코드

DOI QR Code

Comparison of Structural Types of L-Alanine Pentamer by Quantum Chemical Calculation

  • Kobayashi, Minoru (Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology) ;
  • Sim, Jae Ho (Department of Advanced Materials & Chemical Engineering, Halla University)
  • 투고 : 2022.07.01
  • 심사 : 2022.07.21
  • 발행 : 2022.08.10
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

L-alanine (LA, as an amino acid residue) pentamer model was used to investigate changes in the dihedral angle, intramolecular hydrogen bonding and formation energies during structural optimization. LA pentamers having four conformation types [𝛽: 𝜑/𝜓=t-/t+, 𝛼: 𝜑/𝜓=g-/g-, PPII: 𝜑/𝜓=g-/t+ and P-like: 𝜑/𝜓= g-/g+] were carried out by quantum chemical calculations (QCC) [B3LYP/6-31G(d,p)]. In LA, 𝛽, 𝛼, and P-like types did not change by optimization, having an intra-molecular hydrogen bond: NH⋯OC (H-bond), and PPII types in the absence of H-bond were transformed into P-like at the designated 𝜓 of 140°, and to 𝛽 at that of 160° or 175°. P-like and 𝛼 were about 0.5 kcal/mol/mu more stable than 𝛽. In order to understand the processes of the transformations, the changes of 𝜑/𝜓, distances of NH-OC (dNH/CO) and formation energies (𝜟E, kcal/mol/mu) were examined.

키워드

과제정보

This research was supported by Halla University academic research fund, 2022.

참고문헌

  1. B. Yogeswari, R. Kanakaraju, S. Boopathi, and P. Kolandaivel, Combined theorentical studies on solvation and hydrogen bond interactions in glycine tripeptide, Mol. Simul., 40, 942-958 (2013). https://doi.org/10.1080/08927022.2013.828837
  2. V. Parchansky, J. Kapitan, J. Kaminsky, J. Sebestick, and P. Bour, Ramachandran plot for alanine dipeptide as determined from Raman optical activity. J. Phys. Chem. Lett., 4, 2763-2768 (2013). https://doi.org/10.1021/jz401366j
  3. S. Marqusee, V. H. Robbins, and R. L. Baldwin, Unusually stable helix formation in short alanine-based peptides, Proc. Natl. Acad. Sci., USA, 86, 5286-5290 (1989). https://doi.org/10.1073/pnas.86.14.5286
  4. F. Eker, X. Cao, L. Nafie, and R. Schweitzer-Stenner, Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study, J. Am. Chem. Soc., 124, 14330-14341 (2002). https://doi.org/10.1021/ja027381w
  5. F. Eker, K. Griebenow, and R. Schweitzer-Stenner, Stable conformation of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy, J. Am. Chem. Soc., 125, 8178-8185 (2003). https://doi.org/10.1021/ja034625j
  6. Z. Shi, C. A. Olson, G. D. Rose, R. L. Baldwin, and N. R. Kallenbach, Polyproline II structure in a sequence of seven alanine residues, Proc. Natl. Acad. Sci., USA, 99, 9190-9195 (2002). https://doi.org/10.1073/pnas.112193999
  7. S. Woutersen and P. Hamm, Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy, J. Phys. Chem. B, 104, 11316-11320 (2000). https://doi.org/10.1021/jp001546a
  8. S. Woutersen, R. Pfister, P. Hamm, Y. Mu, D. S. Kosov, and G. Stock, Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular-dynamics simulations, J. Chem. Phys., 117, 6833-6840 (2002). https://doi.org/10.1063/1.1506151
  9. J. Graf, P. H. Nguyen, G. Stock, and H. Schwalbe, Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study, J. Am. Chem. Soc., 129, 1179- 1189 (2007). https://doi.org/10.1021/ja0660406
  10. Y. Mu, D. S. Kosov, and G. Stock, Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments, J. Phys. Chem. B, 107, 5064-5073 (2003). https://doi.org/10.1021/jp022445a
  11. A. Kentsis, M. Mezei, T. Gindin, and R. Osman, Unfolded state of polyalanine is a segmented polyproline II helix, Proteins: Struct. Funct. Bioinf., 55, 493-501 (2004). https://doi.org/10.1002/prot.20051
  12. P. Bour, J. Kubelka, and T. A. Keiderling, Ab initio quantum mechanical models of peptide helices and their vibrational spectra, Biopolymers., 65, 45-49 (2002). https://doi.org/10.1002/bip.10224
  13. M. Kobayashi, J. H. SIM, and H. Sato, Conformational analyses for alanine oligomer during chain propagation by quantum chemical calculation, Polymer J., 47, 369-378 (2015). https://doi.org/10.1038/pj.2015.8
  14. J. Rigaudy and S. P. Klesney, Nomenclature of Organic Chemistry: Section E, 483, Oxford Pergamon Press (1979).
  15. M. J. Frish, G. W. Truck, H. B. Schlegel, and G. E. Scuseria, Gaussian 03 User's Reference, Manual version, Gaussian Inc., Carnegie, PA, 15106 USA, (2003).
  16. R. Ludwig, Water from cluster to the bulk, Angew. Chem. Int. Ed., 40, 1808-1827 (2001). https://doi.org/10.1002/1521-3773(20010518)40:10<1808::AID-ANIE1808>3.0.CO;2-1
  17. T. R. Dyke, K. M. Mack, and J. S. Muenter, The structure of water dimer from molecular beam electric resonance spectroscopy. J. Chem. Phys., 66, 498-510 (1977). https://doi.org/10.1063/1.433969
  18. J. A. Odutola and T. R. Dyke, Partially deuterated water dimers: Microwave spectra and structure, J. Chem. Phys., 72, 5062-5070 (1980). https://doi.org/10.1063/1.439795
  19. M. Kobayashi, J. H. Sim, and H. Sato, Conformational analyses for alanine oligomer during hydration by quantum chemical calculation (QCC), Polym. Bull., 74, 657-670 (2017). https://doi.org/10.1007/s00289-016-1736-x