Related papers: Structural Stability and Immunogenicity of Peptide…
We classify the stability of flat-core $p$-elasticae in $\mathbf{R}^d$ subject to the pinned boundary condition. Together with previous work, this completes the classification of stable pinned $p$-elasticae in $\mathbf{R}^d$ for all…
Proteins are vital biological molecules found in every living organism, and their function is determined by what shape they fold into. Peptides are essentially subsets of proteins, and therefore ideal as model systems for protein folding.…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
The goal of quantitative elastography is to identify biomechanical parameters from interior displacement data, which are provided by other modalities, such as ultrasound or magnetic resonance imaging. In this paper, we analyze the stability…
We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Development of the new antimicrobial agents against antibiotic resistance pathogens is the nowadays challenge. Antimicrobial peptides (AMP) occur as important defence agents in many organisms and offer a viable alternative to conventional…
A theoretical approach has been undertaken in order to model the thermodynamic equilibrium of a vesicle adhering to a flat substrate. The vesicle is treated in a canonical description with a fixed number of sites. A finite number of these…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Assembly and stability of mitotic spindle is governed by the interplay of various intra-cellular forces, e.g. the forces generated by motor proteins by sliding overlapping anti-parallel microtubules (MTs) polymerized from the opposite…
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…
The linear stability of a lipid membrane under a DC electric field, applied perpendicularly to the interface, is investigated in the electrokinetic framework, taking into account the dynamics of the Debye layers formed near the membrane.…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
We introduce a simple theoretical approach for an equilibrium study of proteins with known native state structures. We test our approach with results on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and the alpha…