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

Helix vs. Sheet Formation in a Small Peptide

Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both in gas phase and solvated EKAYLRT forms an $\alpha$-helix when not interacting with other molecules. However, in the vicinity of a $\beta$-strand, the peptide forms a $\beta$-strand. Because of this change in secondary structure our peptide may provide a simple model for the $\alpha \to \beta$ transition that is supposedly related to the outbreak of Prion diseases and similar illnesses.Comment: to appear in Physical Review

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

Is there a universality of the helix-coil transition in protein models?

The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-alanine chain, while the second model is a minimal helix-forming model that contains no system specifics. Key characteristics of the helix-coil transition, in particular, the effective critical exponents of these two models agree with each other, within a finite-size scaling analysis.Comment: Latex, to appear in Eur. Phys. J.

Bands, resonances, edge singularities and excitons in core level spectroscopy investigated within the dynamical mean field theory

Using a recently developed impurity solver we exemplify how dynamical mean field theory captures band excitations, resonances, edge singularities and excitons in core level x-ray absorption (XAS) and core level photo electron spectroscopy (cPES) on metals, correlated metals and Mott insulators. Comparing XAS at different values of the core-valence interaction shows how the quasiparticle peak in the absence of core-valence interactions evolves into a resonance of similar shape, but different origin. Whereas XAS is rather insensitive to the metal insulator transition, cPES can be used, due to nonlocal screening, to measure the amount of local charge fluctuation

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

Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations

We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300$K$. For the energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied. The simulations are compared with one another, with simulations with a distance dependent electrostatic permittivity $\epsilon (r)$, and with vacuum simulations ($\epsilon =2$). Parallel tempering and the biased Metropolis techniques RM$_1$ are employed and their performance is evaluated. The measured observables include energy and dihedral probability densities (pds), integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other systems selected configurations are minimized in search of the global energy minima, which are found for the vacuum and the $\epsilon(r)$ system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, we find three ASP sets for which the autocorrelations at 300$$K are considerably smaller than for vacuum simulations.Comment: 10 pages and 8 figure

Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002