Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2006-01-25
J. Comp. Chem. 27 (2006) 1733-1747
Biology
Quantitative Biology
Quantitative Methods
37 pages, 4 figures, LaTeX, BibTeX, AMSTeX
Scientific paper
10.1002/jcc.20467
If constraints are imposed on a macromolecule, two inequivalent classical models may be used: the stiff and the rigid one. This work studies the effects of such constraints on the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2 without any simplifying assumption. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of all the correcting terms to the naive CED based in the Potential Energy Surface (PES) that appear when the constraints are considered. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.
Alonso Jose L.
Calvo Ivan
Echenique Pablo
No associations
LandOfFree
Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-405412