Related papers: The atomic-level mechanism underlying the function…
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…
Exploring the protein-folding problem has been a long-standing challenge in molecular biology. Protein folding is highly dependent on folding of secondary structures as the way to pave a native folding pathway. Here, we demonstrate that a…
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…
The $\alpha$ and $\beta$ subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only $\beta$ subunits are…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Partitioning and transport of water and small solutes into and through nanopores is important to a variety of chemical and biological processes and applications. Here we study the partitioning of positive ions of increasing size into the…
The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the `Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine,…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++,…
The coffee-ring effect is a universal feature of evaporating sessile droplets with pinned contact line, wherein solutes or particles are advected to the droplet's edge due to evaporation-driven flows. While existing models have successfully…
The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the…
The long debated protein dynamical transition was recently found also in non-biological macromolecules, such as poly-N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description…
Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows…
Background: AQP1 belongs to aquaporins family, water-specific, membrane-channel proteins expressed in diverse tissues. Recent papers showed that during angiogenesis, AQP1 is expressed preferentially by microvessels, favoring angiogenesis…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
The interfacial behaviour of water remains a central question to fields as diverse as protein folding, friction and ice formation[1,2]. While the structural and dynamical properties of water at interfaces differ strongly from those in the…
The flow-driven transport of interacting micron-sized particles occurs in many soft matter systems spanning from the translocation of proteins to moving emulsions in microfluidic devices. Here we combine experiments and theory to…