Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm

Article Abstract:

A study using the multicanonical Monte Carlo simulation examined the alpha-helix stability of C-peptide of ribonuclease A as a result of the side-chain electrostatic interactions. Findings revealed that the lowest-energy conformation from the simulation possesses an alpha-helix from Ala-4 to Gln-11, which conforms with the equivalent structure obtained from an X-ray crystallographic experiment of the complete ribonuclease A. The distinctive salt bridge between Glu-2(-) and Arg-10(+) was found to develop with great probability only when the side chains are well charged and certain solvation effects are incorporated.

Electrostatics, C-peptide

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Effects of side-chain charges on alpha-helix stability in C-peptide of ribonuclease A studied by multicanonical algorithm

Article Abstract:

Multicanonical Monte Carlo simulations were used to examine the alpha-helix stability of C-peptide of ribonuclease A. Three analogues of the peptide with charged and neutral side chains were employed to observe the impact of these side-chains on the alpha-helix. The results provided good qualitative agreement with the implications of previous experiments done using circular dichroism, nuclear magnetic resonance and X-ray spectroscopy.

Nuclear magnetic resonance spectroscopy, X-ray spectroscopy, Circular dichroism

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Ab initio and molecular dynamics study of the active site of the reaction between ribonuclease A and cytidyl-3',5'-adenosine

Article Abstract:

The reaction mechanism of ribonuclease A and cytidyl-3',5'-adenosine and the geometry of the active site is optimized using the Hartree-Fock method and ab initio study. The refined conformations reveal an interesting hydrogen-bonding network that allows the prediction of the conformation of the active site in the initial step of the reaction mechanism.

Science & research, Analysis, Hydrogen bonding, Hydrogen bonds, Adenosine, Hartree-Fock approximation

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