Related papers: Helix vs. Sheet Formation in a Small Peptide
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
In this letter, we adopt a new approach combining theoretical modeling with silk stretching measurements to explore the mystery of the structures between silkworm and spider silks, leading to the differences in mechanical response against…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
We analyze, by means of an RPA calculation, the conditions under which a mixture of oppositely charged polyelectrolytes can micro-segregate in the neighborhood of a charged surface creating a layered structure. A number of stable layers can…
We consider nucleation of amyloid fibrils in the case when the process occurs by the mechanism of direct polymerization of practically fully extended protein segments, i.e. beta-strands, into beta-sheets. Applying the classical nucleation…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
We have performed multicanonical Monte Carlo simulations of C-peptide of ribonuclease A. It is known by CD and NMR experiments that this peptide has high alpha-helix content in aqueous solution and that the side-chain charges of residues…
We present a phenomenological theory for the phase behavior of ternary mixtures of cholesterol and saturated and unsaturated lipids, one which describes both liquid and gel phases, and illuminates the mechanism of the behavior. In a binary…
Therapeutic peptides have emerged as a pivotal modality in modern drug discovery, occupying a chemically and topologically rich space. While accurate prediction of their physicochemical properties is essential for accelerating peptide…
The 16-22 amino acid fragment of the beta-amyloid peptide associated with the Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we study the aggregation mechanism of Abeta(16-22) peptides by unbiased thermodynamic…
Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe…
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling…
The formation of coacervates through phase separation of oppositely charged polyelectrolytes (PEs) is critical for understanding biological condensates and developing responsive materials. Traditionally, coacervates are viewed as spherical…
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…
Experiments on supported lipid bilayers featuring liquid ordered/disordered domains have shown that the spatial arrangement of the lipid domains and their chemical composition are strongly affected by the curvature of the substrate.…
A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the…
Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Ab) (1 42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid…
The densities of states are evaluated for very short chain molecules made up of overlapping monomers, using a model which has previously been shown to produce helical structure. The results of numerical calculations are presented for…
It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference. The present observations with Quantum…