Assembly and Analysis of Cell-Scale Membrane Envelopes

• Published in: Journal of chemical information and modeling Vol. 62; no. 3; pp. 602 - 617
• Main Authors: Vermaas, Josh V, Mayne, Christopher G, Shinn, Eric, Tajkhorshid, Emad
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 14.02.2022
• Subjects: Assembly; BASIC BIOLOGICAL SCIENCES; Beads; Best practice; Cell Membrane - metabolism; Cell membranes; cell proliferation; Complex systems; Computational Biochemistry; computer aided software engineering; Envelopes; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Membrane Proteins - chemistry; Membrane structures; Molecular dynamics; Molecular Dynamics Simulation; Nucleic acids; particle size analysis; Proteins; Scale models; Simulation; Software; Software development; Software development tools; Water - chemistry; Workflow
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.1c01050

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atomsa simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two “protocells” consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.