Related papers: Structural Stability and Immunogenicity of Peptide…
In this paper we propose an existence and uniqueness theory for the solutions of a system of non-linear hyperbolic conservation laws, structured in age and maturity variables, representing a tissue environment. In particular we are…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodelling cell membranes. However, the molecular driving forces behind these processes are not well…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We investigate the stability of electrodeposition at solid-solid interfaces for materials exhibiting an anisotropic mechanical response. The stability of electrodeposition or resistance to the formation of dendrites is studied within a…
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a…
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying…
The purpose of this paper is to study the shapes and stabilities of bio-membranes within the framework of exterior differential forms. After a brief review of the current status in theoretical and experimental studies on the shapes of…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A cell membrane can be simply regarded as composite material consisting of lipid bilayer, membrane cytoskeleton beneath lipid bilayer, and proteins embedded in lipid bilayer and linked with membrane cytoskeleton if one only concerns its…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each…