Diresidue-monopeptide (DRMP) model for analysis of peptide and protein conformation

Geetha, V. ; Srinivasan, R. (1993) Diresidue-monopeptide (DRMP) model for analysis of peptide and protein conformation International Journal of Biological Macromolecules, 15 (3). pp. 169-175. ISSN 0141-8130

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Official URL: http://linkinghub.elsevier.com/retrieve/pii/014181...

Related URL: http://dx.doi.org/10.1016/0141-8130(93)90019-I


The paired torsional angle representation φi, ψi in protein conformational analysis is only one type of correlation with a focus on a given Cα residue and gives the relative orientation of a pair of peptide planes sandwiching a given residue (referred as mono-residue dipeptide model, MRDP). A shift of emphasis from a residue site to a given peptide plane (termed as diresidue monopeptide model, DRMP) leads to examination of pairs such as φi, ψi-1 and other parameters derived therefrom. General sum (αnii-n) and the difference (βnii-n) parameters are introduced, of which, n=0 and n=1 relate to MRDP models and DRMP models respectively. Apart from the helical regions, where 'α0' is found to be relatively stable, the sum parameters have been found to be more useful in the analysis of β-turns. The 'α0' at the second and third residue sites and 'α1' at the middle peptide plane of the four residue corner is found to offer a numerical triplet code for resolving various β-turn types. Besides these, an additional parameter introduced under the DRMP model is a virtual torsion angle 'σ1' involving Ci-1β··· C'i-1-Ni··· Ciβ, which is expected to reflect the effect of interaction of the side chain atoms. The σ1, α1 pair is found to play a role parallel to φ, ψ at a given residue site. Various combinations of the sum and difference parameters, as two dimensional plots, like the α0vsβ0, α0vsα1 and σ1vsα1 bring out the conformational features related to secondary structures of proteins.

Item Type:Article
Source:Copyright of this article belongs to Elsevier Science.
Keywords:Peptide Plane; DRMP Model; Derived Parameters; α-helices; β-turns
ID Code:36570
Deposited On:12 Apr 2011 10:32
Last Modified:12 Apr 2011 10:32

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