Related papers: Nonlinear backbone torsional pair correlations in …
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…
The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…
The study of microscopic protein dynamics has historically presented significant challenges to researchers seeking to develop a comprehensive and detailed description of its diverse and intriguing features. Recent experimental and…
One of the key hallmarks of dense active matter in the liquid, supercooled, and solid phases is so-called equal-time velocity correlations. Crucially, these correlations can emerge spontaneously, i.e., they require no explicit alignment…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Planar cell polarity (PCP), the coherent in-plane polarization of a tissue on multicellular length scales, provides directional information that guides a multitude of developmental processes at cellular and tissue levels. While it is…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Run-and-Tumble Particles (RTPs) are a key model of active matter. They are characterized by alternating phases of linear travel and random direction reshuffling. By this dynamic behavior, they break time reversibility and energy…
Statistical mechanics is an important tool for understanding polymer electroelasticity because the elasticity of polymers is primarily due to entropy. However, a common approach for the statistical mechanics of polymer chains, the Gaussian…
We analyze theoretically the interplay between the torsional and the rotational motion of an aligned biphenyl-like molecule. To do so, we consider a transition between two electronic states with different internal torsional potentials,…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The transition from early long-term potentiation (E-LTP) to late LTP (L-LTP) involves protein synthesis and degradation. L-LTP is blocked by inhibiting either protein synthesis or proteasome-dependent degradation prior to and during a…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…