Related papers: Tertiary structure prediction of C-peptide of ribo…
We study the relation between $\alpha$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into…
The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD)…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
We have performed exhaustive multicanonical Monte Carlo simulations of three 12-residue synthetic peptides in order to investigate the thermodynamic and structural properties as well as the characteristic helix-coil transitions. In these…
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…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…
Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former),…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the…
The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
In order to study the relation between backbone and side chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu10, Gln10, Asp10, Asn10, and Lys10 were selected to cover…
Helix-coil transitions in poly-alanine molecules of length 10 are studied by multicanonical Monte Carlo simulations. The solvation effects are included by either a distance-dependent dielectric permittivity or by a term that is proportional…
Salt bridges are known to be important for the stability of protein conformation, but up to now it has been difficult to study their geometry in solution. Here we characterize the spatial structure of a model salt bridge between guanidinium…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried…