Related papers: Novel structural features of CDK inhibition reveal…
Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
Composites of flexible and rigid polymers are ubiquitous in biology and industry alike, yet the physical principles determining their mechanical properties are far from understood. Here, we couple force spectroscopy with large-scale…
We study discrete solitons (kinks) accessible in state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-3D configurations, both theoretically and experimentally. We first extend the theoretical understanding of…
The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus…
The actin cortex of an animal cell is a thin polymeric layer attached to the inner side of the plasma membrane. It plays a key role in shape regulation and pattern formation on the cellular and tissue scale and, in particular, generates the…
Polymerization dynamics of single actin filaments is investigated theoretically using a stochastic model that takes into account the hydrolysis of ATP-actin subunits, the geometry of actin filament tips, the lateral interactions between the…
The viability of a new drug molecule is a time and resource intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibitor…
In nature interactions between biopolymers and motor proteins give rise to biologically essential emergent behaviours. Besides cytoskeleton mechanics, active nematics arise from such interactions. Here we present a study on 3D active…
A recent experimental study found that the binding affinity between the cellular receptor human angiotensin converting enzyme 2 (ACE2) and receptor-binding domain (RBD) in spike (S) protein of novel severe acute respiratory syndrome…
In Ti-intercalated self-doped $1T$-TiSe$_2$ crystals, the charge density wave (CDW) superstructure induces two nonequivalent sites for Ti dopants. Recently, it has been shown that increasing Ti doping dramatically influences the CDW by…
Objective: The reservoir of human immunodeficiency virus (HIV) latently infected cells is the major obstacle for eradication of acquired immunodeficiency syndrome (AIDS). Due to the noisy environment and multiple influencing factors in the…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
Two headed motor proteins, such as kinesin and dynein, hidrolyze environmental ATP in order to propel unidirectionally along cytoskeletal filaments such as microtubules. In the case of kinesin, protein heads bind primarily on the alpha…
As the glass (in molecular fluids\cite{Donth}) or the jamming (in colloids and grains\cite{LiuNature1998}) transitions are approached, the dynamics slow down dramatically with no marked structural changes. Dynamical heterogeneity (DH) plays…
We report here a molecular dynamics simulation study on water and aqueous LiCl solutions confined in 1.6 nm cylindrical pores of silica to investigate a dynamical cross-over, observed earlier experimentally, wherein LiCl slows down confined…
Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a folding molecular dynamics simulation of peptide T in a…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…
Immune cells recognize and discriminate antigens through immunological synapses - dynamic intercellular junctions exhibiting highly organized receptor-ligand patterns. While much work has focused on molecular kinetics and passive mechanisms…