Studies on the conformation of amino acids XII. Energy calculations on prolyl residue

Ramachandran, GN and Lakshminarayanan, AV and Balasubramanian, R and Tegoni, G (1970) Studies on the conformation of amino acids XII. Energy calculations on prolyl residue. In: Biochimica et Biophysica Acta (BBA) - Protein Structure, 221 (2). pp. 165-181.

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Abstract

The favoured conformations of the prolyl residue have been obtained by calculating their potential energies arising from bond-angle strain, torsion-angle strain, non-bonded and electrostatic interatomic energies. In addition to the five membered ring, the peptide unit at the amino end (with ω = 180°) and the C′ atom at the carboxyl end have been taken into account. It is found that there are two local minima in the configurational space of the parameters defining the conformation, as is actually observed-one (denoted by B) with Cγ displaced on the same side as C′, which is lower in energy than the other (denoted by A) with Cγ displaced on the opposite side of C′. The other four atoms Cδ, N, Cα, Cβ are nearly in a plane. The conformations of minimum energy (for both A and B) have bond angles very close to the mean observed values while the torsion angles are well within the range observed in various structures for each type. Taking into account the fact that the influence of neighbouring molecules in a crystal structure may make the conformation of a molecule different from the minimal one, the ranges of the conformational parameters for which the energy is within 0.6 kcal/mole above the minimum value (called the "most probable range") and within 1.2 kcal/mole (called the "probable range") have been determined. The ranges thus obtained, agree well with observation, and most of the observed data lie within the most probable ranges, although differing appreciably from the conformation of minimum energy. The study has been extended, in a limited way, to the conformation of the ring in the amino acid proline. Since the nitrogen is tetrahedral in this (as contrasted with being planar in the prolyl residue), it is found that any one of the five atoms can be out of plane (either way), with the other four lying nearly in a plane. These correspond to low energy conformations (up to 1.2 kcal/mole above the minimum). One such example, in which the Cα atom is out of plane is known for dl-proline · HCl. It is also shown that in these calculations energies due to bond length distortions can be neglected to a good degree of approximation, provided the 'best' values of the bond lengths for the particular compound are used in the theoretical calculations.

Item Type:	Journal Article
Publication:	Biochimica et Biophysica Acta (BBA) - Protein Structure
Publisher:	Elsevier Science
Additional Information:	Copyright of this article belongs to Elsevier Science.
Department/Centre:	Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited:	25 May 2010 05:48
Last Modified:	19 Sep 2010 06:07
URI:	http://eprints.iisc.ac.in/id/eprint/28090

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