Publication

The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations

2001
Journal Articles

Abstract

The mechanism that allows proteins with the same fold to be different in their dynamic and stability properties is poorly understood. We report here the results of mol. dynamics (MD) simulations on rubredoxin (Rd) from hyperthermophilic and mesophilic bacteria that give new insights on this problem. In flexible proteins, the amino acid side chains can form multiple interchangeable non-bonded interaction networks, corresponding to iso-energetic min. in the energy landscape. Under these competing conditions, the system is said to be frustrated. A very stable fold instead, is poorly frustrated because it contains a well-defined and settled network of stabilizing non-bonded interactions. [on SciFinder (R)]

Official source

https://infoscience.epfl.ch/entities/publication/639047a3-aa0c-4c9f-9d85-66211d30456a

About this result

This page is automatically generated and may contain information that is not correct, complete, up-to-date, or relevant to your search query. The same applies to every other page on this website. Please make sure to verify the information with EPFL's official sources.

Graph Chat

Chat with Graph Search

Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.

DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.

2001
Journal Articles

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/639047a3-aa0c-4c9f-9d85-66211d30456a

About this result

Related concepts (32)

Protein dynamics

Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.

Protein structure

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.