Related papers: Are proteins ultrametric?
We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields including protein structural modeling. Protein structural modeling, such as predicting…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
It is a common belief that metamorphic proteins challenge the Anfinsen thermodynamic hypothesis (or dogma). Here we argue against this view aims to show that metamorphic proteins not just fulfill the Anfinsen dogma but also exhibit marginal…
Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
We extend the Saffman theory of membrane hydrodynamics to account for the correlated motion of membrane proteins, along with the effect of protein concentration on that correlation and on the response of the membrane to stresses.…
The 200 K protein dynamical transition is observed for the first time in the teraherz dielectric response. The complex dielectric permittivity $\epsilon$ = $\epsilon$' + i$\epsilon$" is determined in the 0.2 - 2.0 THz and 80-294 K ranges.…
Proteinoids, or thermal proteins, are inorganic entities formed by heating amino acids to their melting point and commencing polymerisation to form polymeric chains. Typically, their diameters range from 10 to 100 micron. Some amino acids…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
Protein flexibility is crucial for understanding protein structures, functions, and dynamics, and it can be measured through experimental methods such as X-ray crystallography. Theoretical approaches have also been developed to predict…
Multisite protein modification is a ubiquitous mechanism utilized by cells to control protein functions. We have recently proposed a dynamical description of multisite protein modification which embodies all the essential features of the…