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The European Physical Journal Special Topics

, Volume 225, Issue 8–9, pp 1463–1481 | Cite as

Representing environment-induced helix-coil transitions in a coarse grained peptide model

  • Cahit Dalgicdir
  • Christoph Globisch
  • Mehmet Sayar
  • Christine Peter
Regular Article Methodological Aspects of Coarse Graining
Part of the following topical collections:
  1. Modern Simulation Approaches in Soft Matter Science: From Fundamental Understanding to Industrial Applications

Abstract

Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that correctly represents the peptide's conformational response to different stimuli compared to atomistic reference simulations. The two types of auxiliary interactions lead to different kinetic behavior as well as to different structural properties for fully formed helices and folding intermediates, and we discuss the advantages and disadvantages of these approaches.

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Copyright information

© EDP Sciences and Springer 2016

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of KonstanzKonstanzGermany
  2. 2.Chemical and Biological Engineering Dept. & Mechanical Engineering Dept., College of Engineering, Koç UniversityIstanbulTurkey

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