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A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity

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Abstract

Specialized classes of proteins, working together in a tightly orchestrated manner, induce and maintain highly curved cellular and organelles membrane morphology. Due to the various experimental constraints, including the resolution limits of imaging techniques, it is non-trivial to accurately elucidate interactions among the various components involved in membrane deformation. The spatial and temporal scales of the systems also make it formidable to investigate them using simulations with molecular details. Interestingly, mechanics-based mesoscopic models have been used with great success in recapitulating the membrane deformations observed in experiments. In this review, we collate together and discuss the various mechanics-based mesoscopic models for protein-mediated membrane deformation studies. In particular, we provide an elaborate description of a mesoscopic model where the membrane is modeled as a triangulated sheet and proteins are represented as either nematics or filaments. This representation allows us to explore the various aspects of protein–protein and protein–membrane interactions as well as examine the underlying mechanistic pathways for emergent behavior such as curvature-mediated protein localization and membrane deformation. We also put forward current efforts in the field towards back-mapping these mesoscopic models to finer-grained particle-based models—a framework that could be used to explore how molecular interactions propagate to physical scales and vice-versa. We end the review with an integrative-modeling-based road map where experimental imaging micrograph and biochemical data are combined with mesoscopic and molecular simulations methods in a theoretically consistent manner to faithfully recapitulate the multiple length and time scales in the membrane remodeling processes.

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Acknowledgements

GK would like to acknowledge financial support from DST India, DBT-IISc, and SERB. High-performance computing facility “Beagle” setup from grants by a partnership between the Department of Biotechnology of India and the Indian Institute of Science (IISc-DBT partnership program) are greatly acknowledged. A.S. is thankful for the early career grant from DST, India. A.S. also thanks the DST for the National Supercomputing Mission grant. FIST program sponsored by the Department of Science and Technology and UGC, Centre for Advanced Studies and Ministry of Human Resource Development, India is gratefully acknowledged by the authors. This research was also supported in part by the National Science Foundation under Grant No. NSF PHY-1748958 (KITP e-visit).

Funding

This study is funded by the DST under the National Supercomputing Mission grant \(DST/NSM/RD-HPC-Applications/2021/03.10.\) This research was also supported in part by the National Science Foundation under Grant No. NSF PHY-1748958 (KITP e-visit). GK is supported as a National Postdoctoral fellow by SERB and SCD thanks the MoE for his financial support.

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  1. Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India

    Gaurav Kumar, Satya Chaithanya Duggisetty & Anand Srivastava

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AS created the blue prints for the review with the help of GK. GK wrote the paper with help from AS and SCD.

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Kumar, G., Duggisetty, S.C. & Srivastava, A. A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity. J Membrane Biol 255, 757–777 (2022). https://doi.org/10.1007/s00232-022-00268-4

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