Molecular Modeling and Simulations of Biological Processes at Cell Membranes

About this Research Topic

Background

Membranes define the boundaries of cells and subcellular compartments and provide a venue for a vast variety of dynamic cellular processes, including the transfer of substances in and out of cells and the exchange of information that can determine the cell’s fate in response to environmental changes. Proteins penetrating a cell membrane or peripherally interacting with membranes are called integral or peripheral membrane proteins which encompass a significant portion of the whole proteome and represent one of the largest categories of drug targets. Alongside membrane proteins, small molecules or nanoparticles often join the interplay between proteins and cell membranes, directly or indirectly altering the physiological function of the molecular machines. Despite their relative abundance and essential roles in life processes, there is considerably less structural, dynamical, and functional information about membrane proteins and their functional partners in comparison to other biomolecular systems.



Studies of the structural dynamics of proteins in membrane environments used to be very challenging but has recently come of age. This is due to the recent progress in structural techniques investigating membrane proteins such as with the resolution revolution of single-particle cryo-electron microscopy, development of novel computational methods, and the exponential increase of computational power. It enables researchers to tackle membrane-associated events in biologically relevant time scales, including specific and non-specific interactions of membrane proteins with lipids and other molecules, dynamic conformational changes and oligomerization of membrane deforming proteins. To further aid this flourishing research field in molecular biosciences, this Research Topic aims to integrate computational approaches and models to study the dynamic nature of membranes and membrane proteins, providing the means to investigate complex interconnections among biomolecules at the cell membranes, as well as for comparative studies that derive general principles regarding membrane activities. Computational tools such as molecular dynamics simulations tied with multiscale approaches, enhanced sampling techniques and sophisticated free energy calculations have provided valuable molecular details for membrane systems of biologically relevant complexity.



In this Research Topics, we welcome both original research articles and reviews, offering exciting newest discoveries and overviews of the dynamic interplay among cell membranes, membrane proteins and their functional partners, with a particular focus on events revealed by molecular modelling and simulations. Areas to be covered may include, but are not limited to:

• Actions of peripheral membrane proteins on membrane surfaces

• Membrane protein dynamics and allostery induced by lipid binding and membrane composition changes

• Biomaterials and nanoparticles interacting with cell membranes

• Development of coarse-grained and multi-scale models for membrane proteins

• Experiment-guided simulation of membrane proteins

• Kinetic calculation of ligand binding and unbinding to membrane transporters

• Structure and function prediction of integral membrane proteins

• Enhanced sampling techniques and free energy calculation methods for membrane proteins

Keywords: Membranes, Membrane proteins, Protein-ligand interactions, Biomaterials, Molecular dynamics, Multi-scale modeling, Enhanced sampling, Free energy calculations

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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