dorsal/arxiv
View SchemaTertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm
| Authors | Ulrich H. E. Hansmann, Yuko Okamoto |
|---|---|
| Categories | |
| ArXiv ID | physics/9806017 |
| URL | https://arxiv.org/abs/physics/9806017 |
| Journal | J. Phys. Chem. B 102 (1998) 653-656 |
Abstract
We have performed multicanonical Monte Carlo simulations of C-peptide of ribonuclease A. It is known by CD and NMR experiments that this peptide has high alpha-helix content in aqueous solution and that the side-chain charges of residues Glu-2$^-$ and His-12$^+$ play an important role in the stability of the alpha-helix. In order to confirm these experimental implications, we have used two analogues of the peptide with charged and neutral side chains of Glu-2 and His-12. Two dielectric functions, distance-dependent and constant, are considered to study the effects of solvent contributions. All the simulations were started from random initial conformations. Various thermodynamic quantities such as average helicity as a function of residue number and average distance between two side chains as a function of temperature are calculated. The results are found to be in accord with the implications of CD and NMR experiments. The lowest-energy conformation obtained has an alpha-helix from Ala-4 to Gln-11 in complete agreement with the corresponding structure deduced from an X-ray crystallography experiment of ribonuclease A. It is shown that the salt bridge between the side chains of Glu-2$^-$ and Arg-10$^+$, which is known to exist from both NMR and X-ray experiments, is formed only when the side chains are properly charged. Its formation is greatly enhanced when the distance-dependent dielectric function is used.
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"abstract": "We have performed multicanonical Monte Carlo simulations of C-peptide of\nribonuclease A. It is known by CD and NMR experiments that this peptide has\nhigh alpha-helix content in aqueous solution and that the side-chain charges of\nresidues Glu-2$^-$ and His-12$^+$ play an important role in the stability of\nthe alpha-helix. In order to confirm these experimental implications, we have\nused two analogues of the peptide with charged and neutral side chains of Glu-2\nand His-12. Two dielectric functions, distance-dependent and constant, are\nconsidered to study the effects of solvent contributions. All the simulations\nwere started from random initial conformations. Various thermodynamic\nquantities such as average helicity as a function of residue number and average\ndistance between two side chains as a function of temperature are calculated.\nThe results are found to be in accord with the implications of CD and NMR\nexperiments. The lowest-energy conformation obtained has an alpha-helix from\nAla-4 to Gln-11 in complete agreement with the corresponding structure deduced\nfrom an X-ray crystallography experiment of ribonuclease A. It is shown that\nthe salt bridge between the side chains of Glu-2$^-$ and Arg-10$^+$, which is\nknown to exist from both NMR and X-ray experiments, is formed only when the\nside chains are properly charged. Its formation is greatly enhanced when the\ndistance-dependent dielectric function is used.",
"arxiv_id": "physics/9806017",
"authors": [
"Ulrich H. E. Hansmann",
"Yuko Okamoto"
],
"categories": [
"physics.chem-ph",
"physics.bio-ph",
"q-bio"
],
"journal_ref": "J. Phys. Chem. B 102 (1998) 653-656",
"title": "Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm",
"url": "https://arxiv.org/abs/physics/9806017"
},
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