Related papers: Simplified flexibility analysis of proteins
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Protein-nucleic acid complexes are important for many cellular processes including the most essential function such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…