Influence of the Helical Backbone in the Behavior of a Simple Model for Dimeric Coiled-Coil Proteins

✍ Scribed by Lidia Prieto; Antonio Rey

• Publisher: John Wiley and Sons
• Year: 2003
• Tongue: English
• Weight: 367 KB
• Volume: 12
• Category: Article
• ISSN: 1022-1344
• DOI: 10.1002/mats.200350022

✦ Synopsis

Abstract

Using computer simulations as a tool for thought experiments, we investigate the influence of the helical backbone geometry in the association process and the final structures of a simple model which mimics parallel, two‐stranded coiled‐coil proteins. We define three types of helices: two of them have straight helical axes and 3.5 or 3.6 residues per helical turn; the third type presents a coiled helical axis, according to the canonical scheme defined by Crick. By using a Monte Carlo simulation algorithm, we observe that the three models exhibit different transition temperatures for the formation of the dimeric structure from two independent peptides, and a different behavior concerning the appearance of out‐of‐register structures. The energy minimized dimer structures present strong deviations from the correct association for straight helices with 3.6 residues/turn, especially for long peptides, deviations which are absent for the other two types when only the burial of hydrophobic residues is considered. A careful analysis of the energies for the out‐of‐register configurations and the contact maps reveals also differences between dimers resulting from the model with Crick parameterization and with 3.5 residues/turn. The results presented in this paper may be relevant for the design of simple models which use rigid α‐helices built from predicted elements of secondary structure.

Top views of the helical models used in this work.

imageTop views of the helical models used in this work.