Publications associées à Conformational entropy

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy

Sebastian James Davis

Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of glob ...

National Academy of Sciences2022

Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure

Diana Kornelia Morzy, Himanshu Joshi

DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improveme ...

AMER CHEMICAL SOC2021

Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry

Anne-Clémence Corminboeuf, Alberto Fabrizio, Benjamin André René Meyer, Raimon Fabregat I De Aguilar-Amat, Daniel Hollas

This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium-size organic molecules at high ab initio level. We offer a modular envir ...

AMER CHEMICAL SOC2020

Entropy as a tool for crystal discovery

Pablo Miguel Piaggi

The computational prediction of crystal structures has emerged as an useful alternative to expensive and often cumbersome experiments. We propose an approach to the prediction of crystal structures and polymorphism based on reproducing the crystallization ...

EPFL2019

Entropy production for coarse-grained dynamics

Daniel Maria Busiello, Amos Maritan

Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master equation (ME) that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We show that the ...

2019

Predicting polymorphism in molecular crystals using orientational entropy

Pablo Miguel Piaggi, Michele Parrinello

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This id ...

National Academy of Sciences2018

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Kai Johnsson, Alberto Schena

Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit bin ...

OXFORD UNIV PRESS2018

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

Giovanni Dietler, Paolo De Los Rios, Sandor Kasas, Giovanni Longo, Dusan Vobornik, Fabrizio Benedetti, Livan Bladimir Alonso Sarduy

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center ...

Public Library of Science2014

Active Conformation Control of Unfolded Proteins by Hyperthermal Collision with a Metal Surface

Klaus Kern, Stephan Rauschenbach, Gordon Rinke

The physical and chemical properties of macromolecules like proteins are strongly dependent on their conformation. The degrees of freedom of their chemical bonds generate a huge conformational space, of which, however, only a small fraction is accessible i ...

Amer Chemical Soc2014

The effect of crowding and confinement: a comparison of Yfh1 stability in different environments

Paolo De Los Rios

Crowding and confinement can affect protein stability, favouring the more compact species amongst the folded and unfolded conformations. An unbiased assessment of the relative efficacy of crowded and confined environments has been hampered so far by the pa ...

Institute of Physics2013

Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations

Jonathan Mitchell

DNA supercoiling plays a role in genetic control by imposing torsional stress. This can induce writhe, which changes the global shape of the DNA. We have used atomistic molecular dynamics simulations to partition the free energy changes driving the writhin ...

Amer Physical Soc2013

First-order coil-globule transition driven by vibrational entropy

Paolo De Los Rios, Francesco Piazza, Carlo Maffi

By shifting the balance between conformational entropy and internal energy, polymers modify their shape under external stimuli, such as changes in temperature. Prominent among such transformations is the coil-globule transition, whereby a polymer can switc ...

Nature Publishing Group2012

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

Public Library of Science2011

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

John Maddocks

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive ...

2010

Probing Mechanism and Transition State of RNA Refolding

Philipp Wenter

Kinetics and the atomic detail of RNA refolding are only poorly understood. It has been proposed that conformations with transient base pairing interaction are populated during RNA refolding, but a detailed description of those states is lacking. By NMR an ...

2010

Predicting conformational entropy of bond vectors in proteins by networks of coupled rotators

Geoffrey Bodenhausen, Daniel Abergel

In this article, a formal expression for the conformational entropy of a bond vector in a protein is derived using the networks of coupled rotators model for the description of internal dynamics. Analytical relationships between NMR order parameters and co ...

American Institute of Physics2008

Short range attractive colloids: Dynamics and energy landscape properties

Giuseppe Foffi

We discuss the static and dynamical properties of a model of short range attractive colloidal systems. Our model is a binary mixture of particles interacting with a modified Lennard-Jones potential that we simulated by molecular dynamics. As previously fou ...

2008

Solute energy based REMD : developments and applications to prion protein misfold predictions

Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...

EPFL2008