Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations

We report results from multicanonical simulations of poly-alanine. Homopolymers of up to 30 amino acids were considered and various thermodynamic quantities as a function of temperature calculated. We study the nature of the observed helix-coil transition and present estimates for critical exponents.Comment: to appear in J.Chem.Phys. (Jan 99

On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase

Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas phase simulations. Introducing a charged Lys+ at the C terminal stabilizes the helix and leads to a higher transition temperature. On the other hand, adding the Lys+ at the N terminal inhibits helix formation. Instead, a more globular structure was found. These results are in agreement with recent experiments on alanine based polypeptides in gas phase. They indicate that present force fields describe accurately the intramolecular interactions in proteins

Structural transitions in biomolecules - a numerical comparison of two approaches for the study of phase transitions in small systems

We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.Comment: Accepted for publication in Int. J. Mol. Sci., to appear in a special issue devoted to R.S. Berr

Partition Function Zeros and Finite Size Scaling of Helix-Coil Transitions in a Polypeptide

We report on multicanonical simulations of the helix-coil transition of a polypeptide. The nature of this transition was studied by calculating partition function zeros and the finite-size scaling of various quantities. Estimates for critical exponents are presented.Comment: RevTex, 4 eps-files; to appear in Phys. Rev. Le

Generalized-ensemble Monte carlo method for systems with rough energy landscape

We present a novel Monte Carlo algorithm which enhances equilibrization of low-temperature simulations and allows sampling of configurations over a large range of energies. The method is based on a non-Boltzmann probability weight factor and is another version of the so-called generalized-ensemble techniques. The effectiveness of the new approach is demonstrated for the system of a small peptide, an example of the frustrated system with a rugged energy landscape.Comment: Latex; ps-files include

Side chain and backbone ordering in a polypeptide

We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed