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The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
The density of synaptic receptors in front of presynaptic release sites is stabilized in the presence of scaffold proteins, but the receptors and scaffold molecules have local exchanges with characteristic times shorter than that of the…
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…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
Lipid phase heterogeneity in the plasma membrane is thought to be crucial for many aspects of cell signaling, but the physical basis of participating membrane domains such as "lipid rafts" remains controversial. Here we consider a lattice…
Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on…
We review the theoretical analyses and simulations of the interactions between curvature-inducing proteins and biomembranes. Laterally isotropic proteins induce spherical budding, whereas anisotropic proteins, such as Bin/Amphiphysin/Rvs…
Preliminary results are presented for the kinetics of phase separation in three distinct models of protein aggregation. The first is a model of the formation of spherical microcrystals of insulin via an initial formation of fractal clusters…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Integrin is an important transmembrane receptor protein which remodels the actin network and anchors the cell membrane towards the extracellular matrix via mechanochemical pathways. The clustering of specific lipids and lipid-anchored…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…