Related papers: Comparing proteins by their internal dynamics: exp…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Protein function prediction is currently achieved by encoding its sequence or structure, where the sequence-to-function transcendence and high-quality structural data scarcity lead to obvious performance bottlenecks. Protein domains are…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and…
While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Go model. The potential energies and vibrational free energies of inherent structures are…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…