CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations.

Alessandro Marchetto,Carlo Alberto Rossi,Alejandro Giorgetti,Sergio Pantano,Rui Ribeiro,Zeineb Si Chaib,Giulia Rossetti

doi:10.3390/molecules25245934

Abstract

Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.

Highlights

Cellular processes lean on biological macromolecules and on interactions among them to serve as building blocks for large-scale functional complexes
These include: (i) the new version of Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID); (ii) the ‘water Martini’ web server dedicated to the simulation of soluble proteins using the Martini force field; (iii) a completely new web server for the preparation and running of coarse-grained molecular dynamics (CGMD) simulations using the SIRAH force field in explicit solvent; (iv) a server dedicated to the backmapping of Martini CG representation of the protein and/or some lipids to an atomistic-level description of the system
Understanding the mechanisms and dynamics underlying the function of big macromolecular complexes and membrane proteins embedded in their physiological lipidic environments has always been a challenge for researchers, as the time and space scales needed to gain a comprehensive understanding are very difficult to uncover

Summary

Introduction

Cellular processes lean on biological macromolecules and on interactions among them to serve as building blocks for large-scale functional complexes. These often contain many copies of the same or different biomolecules that aggregate through long-range interactions into functional suprastructures. These macromolecular complexes perform their function either in a soluble environment or embedded in the cell membrane. The availability of techniques that allow a systematic study of these lipids/membrane protein systems spanning large time- and space-scales is fundamental for the understanding of their functions. Molecular dynamics (MD) simulations have emerged as a powerful tool to study biological systems at varying lengths and timescales.

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