Related papers: Interrelationship Between Protein Electrostatics a…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
We study the effect of a coupling between two motor domains in highly-processive motor protein complexes. A simple stochastic discrete model, in which the two parts of the protein molecule interact through some energy potential, is…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
The host immune response can often efficiently suppress a virus infection, which may lead to selection for immune-resistant viral variants within the host. For example, during HIV infection, an array of CTL immune response populations…
The mitogen activated protein kinase (MAPK) family of proteins is involved in regulating cellular fate activities such as proliferation, differentiation and apoptosis. Their fundamental importance has attracted considerable attention on…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains"…
It has been reported in the literature that the survival probability $P(t)$ near an exceptional point where two eigenstates coalesce should generally exhibit an evolution $P(t) \sim t^2 e^{-\Gamma t}$, in which $\Gamma$ is the decay rate of…
We have studied the effect of amino acids on electron attachment properties of DNA nucleobases, taking cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the…
We analyze 14,651 HIV1 reverse transcriptase (HIV RT) sequences from the Stanford HIV Drug Resistance Database labeled with treatment regimen in order to study the evolution this enzyme under drug selection in the clinic. Our goal is to…
Epigenetic modifications of histones crucially affect the eukaryotic gene activity, while the epigenetic histone state is largely determined by the binding of specific factors such as the transcription factors (TFs) to DNA. Here, the way…
How typical elements that shape organisms, such as protein secondary structures, have evolved, or how evolutionarily susceptible/resistant they are to environmental changes, are significant issues in evolutionary biology, structural…
In this study, we introduced a new unit, named "protein token", as a dynamic protein structural unit for protein-protein interactions. Unlike the conventional structural units, protein token is not based on the sequential or spatial…
We will study a mathematical model of the human immunodeficiency virus (HIV) infection in the presence of combination therapy that includes within-host infectious dynamics. The deterministic model requires us to analyze asymptotic stability…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
RNA protein interactions control the fate of cellular RNAs and play an important role in gene regulation. An interdependency between such interactions allows for the implementation of logic functions in gene regulation. We investigate the…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…