Experiments and Simulations: A Pas de Deux to Unravel Biological Function

67.3K

views

62

authors

15

articles

Experiments and Simulations: A Pas de Deux to Unravel Biological Function

67.3K

views

62

authors

15

articles

Editorial

29 November 2021

Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function

Maya Topf

,

Edina Rosta

,

Gregory R. Bowman

and

Massimiliano Bonomi

2,286 views

0 citations

Editors

4

Massimiliano Bonomi

Institut Pasteur

Edina Rosta

King's College London

Maya Topf

Centre for Structural Systems Biology, Leibniz Institute of Experimental Biology and UKE

Gregory Bowman

School of Medicine, Washington University in St. Louis

Impact

About

Understanding the molecular mechanisms underlying biological functions is essential to rationally target health and disease. This goal is often easier to achieve if an accurate characterization of the structural and dynamical properties of biological systems is available. While both experimental and computational methods provide invaluable tools, limitations in each of the individual techniques can hamper their predictive capabilities. Experimental data, which often come from time- and ensemble-averaged observations over conformationally heterogeneous states, provide sparse and sometimes ambiguous information, and are always subject to random and systematic errors. On the other hand, computational approaches such as molecular dynamics simulations are limited by the inaccuracies of the simplified physicochemical models and/or force field used to predict structural and dynamical properties, as well as by the difficulty to exhaustively sample the conformational landscape of complex systems. A combined and integrative use of experiments and simulations has been proven to be a successful strategy to study the behavior of biological systems.

The goal of this Research Topic is to explore the different avenues for using experimental and computational approaches in synergy in order to accurately characterize structure, dynamics, and ultimately function of biological systems. A wide spatial spectrum of systems will be covered: from ordered and disordered proteins, small molecules interacting with proteins, protein complexes, RNA, DNA, up to entire cells. Molecular simulations at various degrees of resolution and accuracy of the physico-chemical description of the system will be considered: ab-initio, quantum mechanics/molecular mechanics, classical - at both atomistic and coarse-grained levels. The integration of molecular simulations with different types of experimental data will be investigated, including X-ray crystallography, Cryo-electron microscopy and tomography, Nuclear Magnetic Resonance spectroscopy, biochemical measurements, Small Angle X-ray Scattering, and single-molecule Fluorescence Resonance Energy Transfer data.

Computational and experimental approaches to characterize protein structure and dynamics can be used in several different synergistic ways. This Research Topic will explore the following four areas:

• How to use simulations to assist the interpretation of experimental data
• How to use simulations to design and propose novel experiments
• How to use experimental data to validate molecular simulations
• A tighter integration: how to use experimental data to drive and/or refine molecular simulations.

This Research Topic is open to different types of contributions such as Original Research articles in the fields of both method development and applications, Reviews, Perspectives, and all other article types supported by the publisher (please find a full list including descriptions here)

Download ebook

PDF

EPUB

Share

Editors

Massimiliano Bonomi

Institut Pasteur

Edina Rosta

King's College London

Maya Topf

Centre for Structural Systems Biology, Leibniz Institute of Experimental Biology and UKE

Gregory Bowman

School of Medicine, Washington University in St. Louis

Impact

67,307 Total views

51,377 Article views

14,548 Article downloads

1,382 Topic views

Published In

Frontiers in Molecular Biosciences

Biological Modeling and Simulation

Frontiers in Applied Mathematics and Statistics

Biological Modeling and Simulation

About Frontiers Research Topics

With their unique mixes of varied contributions from Original Research to Review Articles, Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author.

Suggest a topic