1
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Brueckner AC, Shields B, Kirubakaran P, Suponya A, Panda M, Posy SL, Johnson S, Lakkaraju SK. MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. J Comput Aided Mol Des 2024; 38:24. [PMID: 39014286 DOI: 10.1007/s10822-024-00564-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024]
Abstract
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and analyzing MD simulations continues to be a multi-step process making it cumbersome to assess a library of ligands in a protein binding pocket using MD. We present an automated workflow that streamlines setting up, running, and analyzing Desmond MD simulations for protein-ligand complexes using machine learning (ML) models. The workflow takes a library of pre-docked ligands and a prepared protein structure as input, sets up and runs MD with each protein-ligand complex, and generates simulation fingerprints for each ligand. Simulation fingerprints (SimFP) capture protein-ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization. SimFPs from a ligand library are used to build & deploy ML models that predict binding assay outcomes and automatically infer important interactions. Unlike relative free-energy methods that are constrained to assess ligands with high chemical similarity, ML models based on SimFPs can accommodate diverse ligand sets. We present two case studies on how SimFP helps delineate structure-activity relationship (SAR) trends and explain potency differences across matched-molecular pairs of (1) cyclic peptides targeting PD-L1 and (2) small molecule inhibitors targeting CDK9.
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Affiliation(s)
| | - Benjamin Shields
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Palani Kirubakaran
- Biocon Bristol Myers Squibb R&D Centre, Bangalore, 560099, Karnataka, India
| | - Alexander Suponya
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Manoranjan Panda
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Shana L Posy
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
| | - Stephen Johnson
- Molecular Structure & Design, Bristol Myers Squibb, Princeton, NJ, 08540, USA
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2
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Domanska M, Setny P. Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields. J Phys Chem B 2024. [PMID: 38990314 DOI: 10.1021/acs.jpcb.4c02310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Curvature emerges as a fundamental membrane characteristic crucial for diverse biological processes, including vesicle formation, cell signaling, and membrane trafficking. Increasingly valuable insights into atomistic details governing curvature-dependent membrane properties are provided by computer simulations. Nevertheless, the underlying force field models are conventionally calibrated and tested in relation to experimentally derived parameters of planar bilayers, thereby leaving uncertainties concerning their consistency in reproducing curved lipid systems. In this study we compare the depiction of buckled phosphatidylcholine (POPC) and POPC-cholesterol membranes by four popular force field models. Aside from agreement with respect to general trends in curvature dependence of a number of parameters, we observe a few qualitative differences. Among the most prominent ones is the difference between atomistic and coarse grained force fields in their representation of relative compressibility of the polar headgroup region and hydrophobic lipid core. Through a number of downstream effects, this discrepancy can influence the way in which curvature modulates the behavior of membrane bound proteins depending on the adopted simulation model.
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Affiliation(s)
- Maria Domanska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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3
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Kern NR, Lee J, Choi YK, Im W. CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems. Nat Commun 2024; 15:5459. [PMID: 38937468 PMCID: PMC11211406 DOI: 10.1038/s41467-024-49700-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.
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Affiliation(s)
- Nathan R Kern
- Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA
| | - Jumin Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Wonpil Im
- Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA.
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA.
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4
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Cornet J, Coulonges N, Pezeshkian W, Penissat-Mahaut M, Desgrez-Dautet H, Marrink SJ, Destainville N, Chavent M, Manghi M. There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. SOFT MATTER 2024; 20:4998-5013. [PMID: 38884641 DOI: 10.1039/d4sm00089g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Maël Penissat-Mahaut
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Hermes Desgrez-Dautet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
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5
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Allolio C, Fábián B, Dostalík M. OrganL: Dynamic triangulation of biomembranes using curved elements. Biophys J 2024; 123:1553-1562. [PMID: 38704638 PMCID: PMC11213972 DOI: 10.1016/j.bpj.2024.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/25/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi-tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations, at the cost of having only approximate tangent continuity away from the vertices. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid distributions as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL (https://zenodo.org/doi/10.5281/zenodo.11204709).
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Affiliation(s)
- Christoph Allolio
- Charles University, Faculty of Mathematics and Physics, Mathematical Institute, Prague, Czech Republic.
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mark Dostalík
- Charles University, Faculty of Mathematics and Physics, Mathematical Institute, Prague, Czech Republic
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6
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Mayorga LS, Masone D. The Secret Ballet Inside Multivesicular Bodies. ACS NANO 2024; 18:15651-15660. [PMID: 38830824 DOI: 10.1021/acsnano.4c01590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Lipid bilayers possess the capacity for self-assembly due to the amphipathic nature of lipid molecules, which have both hydrophobic and hydrophilic regions. When confined, lipid bilayers exhibit astonishing versatility in their forms, adopting diverse shapes that are challenging to observe through experimental means. Exploiting this adaptability, lipid structures motivate the development of bio-inspired mechanomaterials and integrated nanobio-interfaces that could seamlessly merge with biological entities, ultimately bridging the gap between synthetic and biological systems. In this work, we demonstrate how, in numerical simulations of multivesicular bodies, a fascinating evolution unfolds from an initial semblance of order toward states of higher entropy over time. We observe dynamic rearrangements in confined vesicles that reveal unexpected limit shapes of distinct geometric patterns. We identify five structures as the basic building blocks that systematically repeat under various conditions of size and composition. Moreover, we observe more complex and less frequent shapes that emerge in confined spaces. Our results provide insights into the dynamics of multivesicular systems, offering a richer understanding of how confined lipid bodies spontaneously self-organize.
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Affiliation(s)
- Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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7
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Brown CM, Marrink SJ. Modeling membranes in situ. Curr Opin Struct Biol 2024; 87:102837. [PMID: 38744147 DOI: 10.1016/j.sbi.2024.102837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, in situ, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.
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Affiliation(s)
- Chelsea M Brown
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. https://twitter.com/chelseabrowncg
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. s.j.marrinkrug.nl
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8
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Shivgan AT, Marzinek JK, Krah A, Matsudaira P, Verma CS, Bond PJ. Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations. J Chem Theory Comput 2024; 20:3308-3321. [PMID: 38358378 DOI: 10.1021/acs.jctc.3c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Proteoglycans contain glycosaminoglycans (GAGs) which are negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly in governing cellular communication and attachment. Depending on their sulfonation state, acetylation, and glycosidic linkages, GAGs belong to different families. The high molecular weight, heterogeneity, and flexibility of GAGs hamper their characterization at atomic resolution, but this may be circumvented via coarse-grained (CG) approaches. In this work, we report a CG model for a library of common GAG types in their isolated or proteoglycan-linked states compatible with version 2.2 (v2.2) of the widely popular CG Martini force field. The model reproduces conformational and thermodynamic properties for a wide variety of GAGs, as well as matching structural and binding data for selected proteoglycan test systems. The parameters developed here may thus be employed to study a range of GAG-containing biomolecular systems, thereby benefiting from the efficiency and broad applicability of the Martini framework.
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Affiliation(s)
- Aishwary T Shivgan
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Alexander Krah
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Paul Matsudaira
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
| | - Chandra S Verma
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Peter J Bond
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
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9
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Sadeghi M, Rosenberger D. Dynamic framework for large-scale modeling of membranes and peripheral proteins. Methods Enzymol 2024; 701:457-514. [PMID: 39025579 DOI: 10.1016/bs.mie.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In this chapter, we present a novel computational framework to study the dynamic behavior of extensive membrane systems, potentially in interaction with peripheral proteins, as an alternative to conventional simulation methods. The framework effectively describes the complex dynamics in protein-membrane systems in a mesoscopic particle-based setup. Furthermore, leveraging the hydrodynamic coupling between the membrane and its surrounding solvent, the coarse-grained model grounds its dynamics in macroscopic kinetic properties such as viscosity and diffusion coefficients, marrying the advantages of continuum- and particle-based approaches. We introduce the theoretical background and the parameter-space optimization method in a step-by-step fashion, present the hydrodynamic coupling method in detail, and demonstrate the application of the model at each stage through illuminating examples. We believe this modeling framework to hold great potential for simulating membrane and protein systems at biological spatiotemporal scales, and offer substantial flexibility for further development and parametrization.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
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10
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Crowley J, Hilpert C, Monticelli L. Predicting lipid sorting in curved membranes. Methods Enzymol 2024; 701:287-307. [PMID: 39025574 DOI: 10.1016/bs.mie.2024.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Most biological membranes are curved, and both lipids and proteins play a role in generating curvature. For any given membrane shape and composition, it is not trivial to determine whether lipids are laterally distributed in a homogeneous or inhomogeneous way, and whether the inter-leaflet distribution is symmetric or not. Here we present a simple computational tool that allows to predict the preference of any lipid type for membranes with positive vs. negative curvature, for any given value of curvature. The tool is based on molecular dynamics simulations of tubular membranes with hydrophilic pores. The pores allow spontaneous, barrierless flip-flop of most lipids, while also preventing differences in pressure between the inner and outer water compartments and minimizing membrane asymmetric stresses. Specifically, we provide scripts to build and analyze the simulations. We test the tool by performing simulations on simple binary lipid mixtures, and we show that, as expected, lipids with negative intrinsic curvature distribute to the tubule inner leaflet, the more so when the radius of the tubular membrane is small. Compared to other existing computational methods, relying on membrane buckles and tethers, our method is based on spontaneous inter-leaflet transport of lipids, and therefore allows to explore lipid distribution in asymmetric membranes. The method can easily be adapted to work with any molecular dynamics code and any force field.
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Affiliation(s)
- Jackson Crowley
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, Lyon, France
| | - Cécile Hilpert
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, Lyon, France
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, Lyon, France; Institut National de la Santé et de la Recherche Médicale, Lyon, France.
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11
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van der Pol RI, Brinkmann BW, Sevink GJA. Analyzing Lipid Membrane Defects via a Coarse-Grained to Triangulated Surface Map: The Role of Lipid Order and Local Curvature in Molecular Binding. J Chem Theory Comput 2024; 20:2888-2900. [PMID: 38537131 PMCID: PMC11008102 DOI: 10.1021/acs.jctc.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature. We have applied our protocol to investigate the role of local curvature and varying lipid packing on the defect constant π. We find that the defect size is greatly influenced by both factors, arguing strongly against the usual assignment of a single defect constant in the case of more realistic membrane conditions. An important discovery is that lipids in the gel phase produce larger defects, or a higher π, in domains of high (local) curvature than the same lipid in a liquid phase of any curvature. This finding suggests that membranes featuring very ordered lipid packing can bind proteins via large defects in curved regions. Finally, we propose a route for estimating defect constants directly from the standard membrane properties. Identifying the precise role of composition, lipid (tail) order, and (local) curvature in defects for the irregular lipid structures that are (temporally) present in many biological processes is instrumental for obtaining fundamental insight as well as for a rational design of membrane binding targets.
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Affiliation(s)
- Rianne
W. I. van der Pol
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bregje W. Brinkmann
- Institute
of Environmental Sciences, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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12
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Ozturk TN, König M, Carpenter TS, Pedersen KB, Wassenaar TA, Ingólfsson HI, Marrink SJ. Building complex membranes with Martini 3. Methods Enzymol 2024; 701:237-285. [PMID: 39025573 DOI: 10.1016/bs.mie.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.
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Affiliation(s)
- Tugba Nur Ozturk
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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13
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Fábián B, Javanainen M. Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD. J Phys Chem Lett 2024; 15:3214-3220. [PMID: 38483514 DOI: 10.1021/acs.jpclett.4c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Curved cellular membranes are both abundant and functionally relevant. While novel tomography approaches reveal the structural details of curved membranes, their dynamics pose an experimental challenge. Curvature especially affects the diffusion of lipids and macromolecules, yet neither experiments nor continuum models distinguish geometric effects from those caused by curvature-induced changes in membrane properties. Molecular simulations could excel here, yet despite community interest toward curved membranes, tools for their analysis are still lacking. Here, we satisfy this demand by introducing CurD, our novel and openly available implementation of the Vertex-oriented Triangle Propagation algorithm to the study of lipid diffusion along membranes with mean and/or Gaussian curvature. This approach, aided by our highly optimized implementation, computes geodetic distances significantly faster than conventional implementations of path-finding algorithms. Our tool, applied to coarse-grained simulations, allows for the first time the analysis of curvature effects on diffusion at size scales relevant to physiological processes such as endocytosis. Our analyses with different membrane geometries reveal that Gaussian curvature plays a surprisingly small role on lipid motion, whereas mean curvature; i.e., the packing of lipid headgroups largely dictates their mobility.
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Affiliation(s)
- Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
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14
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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15
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Hosseini AN, van der Spoel D. Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals? J Phys Chem Lett 2024; 15:1079-1088. [PMID: 38261634 PMCID: PMC10839907 DOI: 10.1021/acs.jpclett.4c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Computational chemistry is an important tool in numerous scientific disciplines, including drug discovery and structural biology. Coarse-grained models offer simple representations of molecular systems that enable simulations of large-scale systems. Because there has been an increase in the adoption of such models for simulations of biomolecular systems, critical evaluation is warranted. Here, the stability of the amyloid peptide and organic crystals is evaluated using the Martini 3 coarse-grained force field. The crystals change shape drastically during the simulations. Radial distribution functions show that the distance between backbone beads in β-sheets increases by ∼1 Å, breaking the crystals. The melting points of organic compounds are much too low in the Martini force field. This suggests that Martini 3 lacks the specific interactions needed to accurately simulate peptides or organic crystals without imposing artificial restraints. The problems may be exacerbated by the use of the 12-6 potential, suggesting that a softer potential could improve this model for crystal simulations.
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Affiliation(s)
- A. Najla Hosseini
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
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16
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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17
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Pezeshkian W, Ipsen JH. Mesoscale simulation of biomembranes with FreeDTS. Nat Commun 2024; 15:548. [PMID: 38228588 PMCID: PMC10792169 DOI: 10.1038/s41467-024-44819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024] Open
Abstract
We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.
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Affiliation(s)
- Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| | - John H Ipsen
- MEMPHYS/PhyLife, Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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18
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Chen LH, Hu JN. Development of nano-delivery systems for loaded bioactive compounds: using molecular dynamics simulations. Crit Rev Food Sci Nutr 2024:1-22. [PMID: 38206576 DOI: 10.1080/10408398.2023.2301427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Over the past decade, a remarkable surge in the development of functional nano-delivery systems loaded with bioactive compounds for healthcare has been witnessed. Notably, the demanding requirements of high solubility, prolonged circulation, high tissue penetration capability, and strong targeting ability of nanocarriers have posed interdisciplinary research challenges to the community. While extensive experimental studies have been conducted to understand the construction of nano-delivery systems and their metabolic behavior in vivo, less is known about these molecular mechanisms and kinetic pathways during their metabolic process in vivo, and lacking effective means for high-throughput screening. Molecular dynamics (MD) simulation techniques provide a reliable tool for investigating the design of nano-delivery carriers encapsulating these functional ingredients, elucidating the synthesis, translocation, and delivery of nanocarriers. This review introduces the basic MD principles, discusses how to apply MD simulation to design nanocarriers, evaluates the ability of nanocarriers to adhere to or cross gastrointestinal mucosa, and regulates plasma proteins in vivo. Moreover, we presented the critical role of MD simulation in developing delivery systems for precise nutrition and prospects for the future. This review aims to provide insights into the implications of MD simulation techniques for designing and optimizing nano-delivery systems in the healthcare food industry.
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Affiliation(s)
- Li-Hang Chen
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Jiang-Ning Hu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
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19
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van Tilburg MA, Marrink SJ, König M, Grünewald F. Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. J Chem Theory Comput 2024; 20:212-223. [PMID: 38109481 PMCID: PMC10782443 DOI: 10.1021/acs.jctc.3c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023]
Abstract
The process of osmosis, a fundamental phenomenon in life, drives water through a semipermeable membrane in response to a solute concentration gradient across this membrane. In vitro, osmotic shocks are often used to drive shape changes in lipid vesicles, for instance, to study fission events in the context of artificial cells. While experimental techniques provide a macroscopic picture of large-scale membrane remodeling processes, molecular dynamics (MD) simulations are a powerful tool to study membrane deformations at the molecular level. However, simulating an osmotic shock is a time-consuming process due to slow water diffusion across the membrane, making it practically impossible to examine its effects in classic MD simulations. In this article, we present Shocker, a Python-based MD tool for simulating the effects of an osmotic shock by selecting and relocating water particles across a membrane over the course of several pumping cycles. Although this method is primarily aimed at efficiently simulating volume changes in vesicles, it can also handle membrane tubes and double bilayer systems. Additionally, Shocker is force field-independent and compatible with both coarse-grained and all-atom systems. We demonstrate that our tool is applicable to simulate both hypertonic and hypotonic osmotic shocks for a range of vesicular and bilamellar setups, including complex multicomponent systems containing membrane proteins or crowded internal solutions.
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Affiliation(s)
- Marco
P. A. van Tilburg
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melanie König
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Fabian Grünewald
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
- Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
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20
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Mai TL, Derreumaux P, Nguyen PH. Structure and Elasticity of Mitochondrial Membranes: A Molecular Dynamics Simulation Study. J Phys Chem B 2023; 127:10778-10791. [PMID: 38084584 DOI: 10.1021/acs.jpcb.3c05112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Mitochondria are known as the powerhouse of the cell because they produce energy in the form of adenosine triphosphate. They also have other crucial functions such as regulating apoptosis, calcium homeostasis, and reactive oxygen species production. To perform these diverse functions, mitochondria adopt specific structures and frequently undergo dynamic shape changes, indicating that their mechanical properties play an essential role in their functions. To gain a detailed understanding at the molecular level of the structure and mechanical properties of mitochondria, we carry out atomistic molecular dynamics simulations for three inner mitochondrial membranes and three outer mitochondrial membrane models. These models take into account variations in cardiolipin and cholesterol concentrations as well as the symmetry/asymmetry between the two leaflets. Our simulations allow us to calculate various structural quantities and the bending, twisting, and tilting elastic moduli of the membrane models. Our results indicate that the structures of the inner and outer mitochondrial membranes are quite similar and do not depend much on the variation in lipid compositions. However, the bending modulus of the membranes increases with increasing concentrations of cardiolipin or cholesterol but decreases with a membrane asymmetry. Notably, we found that the dipole potential of the membrane increases with an increasing cardiolipin concentration. Finally, possible roles of cardiolipin in regulating ion and proton currents and maintaining the cristate are discussed in some details.
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Affiliation(s)
- Thi Ly Mai
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris 75005, France
- Institut Universitaire de France (IUF), Paris 75005, France
| | - Phuong H Nguyen
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris 75005, France
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21
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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22
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Kern NR, Lee J, Choi YK, Im W. CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555590. [PMID: 37693396 PMCID: PMC10491218 DOI: 10.1101/2023.08.30.555590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. We demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to facilitate innovative studies of complex interactions between small (organic and inorganic) molecules, biomacromolecules, polymers, and nanomaterials.
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Affiliation(s)
- Nathan R. Kern
- Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA
| | - Jumin Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA
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23
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Ugarte La Torre D, Takada S, Sugita Y. Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers. J Chem Phys 2023; 159:075101. [PMID: 37581417 DOI: 10.1063/5.0160417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
iSoLF is a coarse-grained (CG) model for lipid molecules with the implicit-solvent approximation used in molecular dynamics (MD) simulations of biological membranes. Using the original iSoLF (iSoLFv1), MD simulations of lipid bilayers consisting of either POPC or DPPC and these bilayers, including membrane proteins, can be performed. Here, we improve the original model, explicitly treating the electrostatic interactions between different lipid molecules and adding CG particle types. As a result, the available lipid types increase to 30. To parameterize the potential functions of the new model, we performed all-atom MD simulations of each lipid at three different temperatures using the CHARMM36 force field and the modified TIP3P model. Then, we parameterized both the bonded and non-bonded interactions to fit the area per lipid and the membrane thickness of each lipid bilayer by using the multistate Boltzmann Inversion method. The final model reproduces the area per lipid and the membrane thickness of each lipid bilayer at the three temperatures. We also examined the applicability of the new model, iSoLFv2, to simulate the phase behaviors of mixtures of DOPC and DPPC at different concentrations. The simulation results with iSoLFv2 are consistent with those using Dry Martini and Martini 3, although iSoLFv2 requires much fewer computations. iSoLFv2 has been implemented in the GENESIS MD software and is publicly available.
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Affiliation(s)
- Diego Ugarte La Torre
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
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24
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Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
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Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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25
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Álvarez D, Sapia J, Vanni S. Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity. Curr Opin Cell Biol 2023; 83:102205. [PMID: 37451175 DOI: 10.1016/j.ceb.2023.102205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
In the last decade, molecular dynamics (MD) simulations have become an essential tool to investigate the molecular properties of membrane trafficking processes, often in conjunction with experimental approaches. The combination of MD simulations with recent developments in structural biology, such as cryo-electron microscopy and artificial intelligence-based structure determination, opens new, exciting possibilities for future investigations. However, the full potential of MD simulations to provide a molecular view of the complex and dynamic processes involving membrane trafficking can only be realized if certain limitations are addressed, and especially those concerning the quality of coarse-grain models, which, despite recent successes in describing large-scale systems, still suffer from far-from-ideal chemical accuracy. In this review, we will highlight recent success stories of MD simulations in the investigation of membrane trafficking processes, their implications for future research, and the challenges that lie ahead in this specific research domain.
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Affiliation(s)
- Daniel Álvarez
- Department of Biology, University of Fribourg, Switzerland; Departamento de Química Física y Analítica, Universidad de Oviedo, Spain
| | - Jennifer Sapia
- Department of Biology, University of Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland; Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
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26
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Chaisson EH, Heberle FA, Doktorova M. Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One? MEMBRANES 2023; 13:629. [PMID: 37504995 PMCID: PMC10384462 DOI: 10.3390/membranes13070629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
The compositional asymmetry of biological membranes has attracted significant attention over the last decade. Harboring more differences from symmetric membranes than previously appreciated, asymmetric bilayers have proven quite challenging to study with familiar concepts and techniques, leaving many unanswered questions about the reach of the asymmetry effects. One particular area of active research is the computational investigation of composition- and number-asymmetric lipid bilayers with molecular dynamics (MD) simulations. Offering a high level of detail into the organization and properties of the simulated systems, MD has emerged as an indispensable tool in the study of membrane asymmetry. However, the realization that results depend heavily on the protocol used for constructing the asymmetric bilayer models has sparked an ongoing debate about how to choose the most appropriate approach. Here we discuss the underlying source of the discrepant results and review the existing methods for creating asymmetric bilayers for MD simulations. Considering the available data, we argue that each method is well suited for specific applications and hence there is no single best approach. Instead, the choice of a construction protocol-and consequently, its perceived accuracy-must be based primarily on the scientific question that the simulations are designed to address.
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Affiliation(s)
- Emily H. Chaisson
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37916, USA
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37916, USA
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
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27
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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28
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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29
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van Teijlingen A, Smith MC, Tuttle T. Short Peptide Self-Assembly in the Martini Coarse-Grain Force Field Family. Acc Chem Res 2023; 56:644-654. [PMID: 36866851 PMCID: PMC10035038 DOI: 10.1021/acs.accounts.2c00810] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
ConspectusPivotal to the success of any computational experiment is the ability to make reliable predictions about the system under study and the time required to yield these results. Biomolecular interactions is one area of research that sits in every camp of resolution vs the time required, from the quantum mechanical level to in vivo studies. At an approximate midpoint, there is coarse-grained molecular dynamics, for which the Martini force fields have become the most widely used, fast enough to simulate the entire membrane of a mitochondrion though lacking atom-specific precision. While many force fields have been parametrized to account for a specific system under study, the Martini force field has aimed at casting a wider net with more generalized bead types that have demonstrated suitability for broad use and reuse in applications from protein-graphene oxide coassembly to polysaccharides interactions.In this Account, the progressive (Martini versions 1 through 3) and peripheral (Sour Martini, constant pH, Martini Straight, Dry Martini, etc.) developmental trajectory of the Martini force field will be analyzed in terms of self-assembling systems with a focus on short (two to three amino acids) peptide self-assembly in aqueous environments. In particular, this will focus on the effects of the Martini solvent model and compare how changes in bead definitions and mapping have effects on different systems. Considerable effort in the development of Martini has been expended to reduce the "stickiness" of amino acids to better simulate proteins in bilayers. We have included in this Account a short study of dipeptide self-assembly in water, using all mainstream Martini force fields, to examine their ability to reproduce this behavior. The three most recently released versions of Martini and variations in their solvents are used to simulate in triplicate all 400 dipeptides of the 20 gene-encoded amino acids. The ability of the force fields to model the self-assembly of the dipeptides in aqueoues environments is determined by the measurement of the aggregation propensity, and additional descriptors are used to gain further insight into the dipeptide aggregates.
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Affiliation(s)
| | - Melissa C Smith
- Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Tell Tuttle
- Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
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30
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Lanrezac A, Baaden M. UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. MEMBRANES 2023; 13:362. [PMID: 36984749 PMCID: PMC10054542 DOI: 10.3390/membranes13030362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
The insertion of proteins into membranes is crucial for understanding their function in many biological processes. In this work, we present UNILIPID, a universal implicit lipid-protein description as a methodology for dealing with implicit membranes. UNILIPID is independent of the scale of representation and can be applied at the level of all atoms, coarse-grained particles down to the level of a single bead per amino acid. We provide example implementations for these scales and demonstrate the versatility of our approach by accurately reflecting the free energy of transfer for each amino acid. In addition to single membranes, we describe the analytical implementation of double membranes and show that UNILIPID is well suited for modeling at multiple scales. We generalize to membranes of arbitrary shape. With UNILIPID, we provide a methodological framework for a simple and general parameterization tuned to reproduce a selected reference hydrophobicity scale. The software we provide along with the methodological description is optimized for specific user features such as real-time response, live visual analysis, and virtual reality experiences.
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31
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Vo A, Murphy M, Phan P, Stone T, Prabhu R. Molecular Dynamics Simulation of Membrane Systems in the context of Traumatic Brain Injury. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023. [DOI: 10.1016/j.cobme.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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32
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Duncan AL, Pezeshkian W. Mesoscale simulations: An indispensable approach to understand biomembranes. Biophys J 2023:S0006-3495(23)00123-6. [PMID: 36809878 DOI: 10.1016/j.bpj.2023.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/10/2022] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
Computer simulation techniques form a versatile tool, a computational microscope, for exploring biological processes. This tool has been particularly effective in exploring different features of biological membranes. In recent years, thanks to elegant multiscale simulation schemes, some fundamental limitations of investigations by distinct simulation techniques have been resolved. As a result, we are now capable of exploring processes spanning multiple scales beyond the capacity of any single technique. In this perspective, we argue that mesoscale simulations require more attention and must be further developed to fill evident gaps in a quest toward simulating and modeling living cell membranes.
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Affiliation(s)
- Anna L Duncan
- Department of Chemistry, Aarhus University, Aarhus C, Denmark.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
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33
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Pezeshkian W, Grünewald F, Narykov O, Lu S, Arkhipova V, Solodovnikov A, Wassenaar TA, Marrink SJ, Korkin D. Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. Structure 2023; 31:492-503.e7. [PMID: 36870335 DOI: 10.1016/j.str.2023.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands; Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands
| | - Oleksandr Narykov
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Senbao Lu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | | | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, 9747AS Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands.
| | - Dmitry Korkin
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA 01609, USA; Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA.
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34
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Hilpert C, Beranger L, Souza PCT, Vainikka PA, Nieto V, Marrink SJ, Monticelli L, Launay G. Facilitating CG Simulations with MAD: The MArtini Database Server. J Chem Inf Model 2023; 63:702-710. [PMID: 36656159 DOI: 10.1021/acs.jcim.2c01375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.
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Affiliation(s)
- Cécile Hilpert
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Louis Beranger
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Paulo C T Souza
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Vincent Nieto
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Luca Monticelli
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Guillaume Launay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
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35
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Stevens JA, Grünewald F, van Tilburg PAM, König M, Gilbert BR, Brier TA, Thornburg ZR, Luthey-Schulten Z, Marrink SJ. Molecular dynamics simulation of an entire cell. Front Chem 2023; 11:1106495. [PMID: 36742032 PMCID: PMC9889929 DOI: 10.3389/fchem.2023.1106495] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell's spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future.
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Affiliation(s)
- Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - P. A. Marco van Tilburg
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Melanie König
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands,*Correspondence: Siewert J. Marrink,
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36
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Close, but not too close: a mesoscopic description of (a)symmetry and membrane shaping mechanisms. Emerg Top Life Sci 2023; 7:81-93. [PMID: 36645200 DOI: 10.1042/etls20220078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/17/2023]
Abstract
Biomembranes are fundamental to our understanding of the cell, the basic building block of all life. An intriguing aspect of membranes is their ability to assume a variety of shapes, which is crucial for cell function. Here, we review various membrane shaping mechanisms with special focus on the current understanding of how local curvature and local rigidity induced by membrane proteins leads to emerging forces and consequently large-scale membrane deformations. We also argue that describing the interaction of rigid proteins with membranes purely in terms of local membrane curvature is incomplete and that changes in the membrane rigidity moduli must also be considered.
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37
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Corey RA, Baaden M, Chavent M. A brief history of visualizing membrane systems in molecular dynamics simulations. FRONTIERS IN BIOINFORMATICS 2023; 3:1149744. [PMID: 37213533 PMCID: PMC10196259 DOI: 10.3389/fbinf.2023.1149744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/13/2023] [Indexed: 05/23/2023] Open
Abstract
Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
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Affiliation(s)
- R. A. Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - M. Baaden
- Centre Nationale de la Recherche Scientifique, Laboratoire de Biochimie Théorique, Université Paris Cité, Paris, France
| | - M. Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de Toulouse, Toulouse, France
- *Correspondence: M. Chavent,
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38
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Hadjidemetriou K, Kaur S, Cassidy CK, Zhang P. Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches. Biochem Soc Trans 2022; 50:1595-1605. [PMID: 36421737 PMCID: PMC9788364 DOI: 10.1042/bst20220191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Abstract
Chemotaxis signaling pathways enable bacteria to sense and respond to their chemical environment and, in some species, are critical for lifestyle processes such as biofilm formation and pathogenesis. The signal transduction underlying chemotaxis behavior is mediated by large, highly ordered protein complexes known as chemosensory arrays. For nearly two decades, cryo-electron tomography (cryoET) has been used to image chemosensory arrays, providing an increasingly detailed understanding of their structure and function. In this mini-review, we provide an overview of the use of cryoET to study chemosensory arrays, including imaging strategies, key results, and outstanding questions. We further discuss the application of molecular modeling and simulation techniques to complement structure determination efforts and provide insight into signaling mechanisms. We close the review with a brief outlook, highlighting promising future directions for the field.
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Affiliation(s)
| | - Satinder Kaur
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - C. Keith Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, U.K
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39
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Grünewald F, Punt MH, Jefferys EE, Vainikka PA, König M, Virtanen V, Meyer TA, Pezeshkian W, Gormley AJ, Karonen M, Sansom MSP, Souza PCT, Marrink SJ. Martini 3 Coarse-Grained Force Field for Carbohydrates. J Chem Theory Comput 2022; 18:7555-7569. [PMID: 36342474 DOI: 10.1021/acs.jctc.2c00757] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.
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Affiliation(s)
- Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Mats H Punt
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Elizabeth E Jefferys
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Valtteri Virtanen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Travis A Meyer
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.,The Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Adam J Gormley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Maarit Karonen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon 69367, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
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40
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Wang X, Danuser G. Remeshing flexible membranes under the control of free energy. PLoS Comput Biol 2022; 18:e1010766. [PMID: 36469547 PMCID: PMC9754615 DOI: 10.1371/journal.pcbi.1010766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/15/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Cell membranes are flexible and often undergo large-scale morphological changes during processes like mitosis, protrusion and retraction, or vesicle fusion. Mathematical modeling of cell membranes depends on a representation of the free-form surface by discrete meshes. During morphological changes, these meshes must be adjusted under the minimization of the total free energy. Current methodology for meshing is limited in one of two ways: 1) Free energy-dependent methods have no restriction on the mesh geometry. The resulting irregular meshes cause artifacts in follow-up models of morphodynamics. 2) Geometry-dependent methods maintain mesh quality but violate the physics of free energy minimization. To fill this gap, we regulate mesh geometries via a free-energy-determined remeshing process: adding and removing mesh elements upon morphological changes based on barrier crossings in a double-barrier potential between neighboring vertices in the meshes. We test the method's robustness by reproducing the morphodynamics of red blood cells and vesicle fusions; and we demonstrate the method's adaptability by simulating the formation of filopodia, lamellipodia and invaginations. Finally, we use the method to study a mechanical decoupling effect of two connected membrane tethers that has been recently observed experimentally, but has not been mechanistically explained in the context of a complete membrane surface. We propose a biophysical model that strengthens the decoupling effect and broadens the original interpretation of the experiment. The method is developed in C/Matlab and distributed via https://github.com/DanuserLab/biophysicsModels.
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Affiliation(s)
- Xinxin Wang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
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41
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Pantano S. Back and forth modeling through biological scales. Biochem Biophys Res Commun 2022; 633:39-41. [DOI: 10.1016/j.bbrc.2022.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/06/2022]
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42
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De Franceschi N, Pezeshkian W, Fragasso A, Bruininks BMH, Tsai S, Marrink SJ, Dekker C. Synthetic Membrane Shaper for Controlled Liposome Deformation. ACS NANO 2022; 17:966-978. [PMID: 36441529 PMCID: PMC9878720 DOI: 10.1021/acsnano.2c06125] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Shape defines the structure and function of cellular membranes. In cell division, the cell membrane deforms into a "dumbbell" shape, while organelles such as the autophagosome exhibit "stomatocyte" shapes. Bottom-up in vitro reconstitution of protein machineries that stabilize or resolve the membrane necks in such deformed liposome structures is of considerable interest to characterize their function. Here we develop a DNA-nanotechnology-based approach that we call the synthetic membrane shaper (SMS), where cholesterol-linked DNA structures attach to the liposome membrane to reproducibly generate high yields of stomatocytes and dumbbells. In silico simulations confirm the shape-stabilizing role of the SMS. We show that the SMS is fully compatible with protein reconstitution by assembling bacterial divisome proteins (DynaminA, FtsZ:ZipA) at the catenoidal neck of these membrane structures. The SMS approach provides a general tool for studying protein binding to complex membrane geometries that will greatly benefit synthetic cell research.
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Affiliation(s)
- Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Weria Pezeshkian
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
- The
Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, 17DK-2100Copenhagen, Denmark
| | - Alessio Fragasso
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Bart M. H. Bruininks
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
| | - Sean Tsai
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
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43
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Bottacchiari M, Gallo M, Bussoletti M, Casciola CM. Activation energy and force fields during topological transitions of fluid lipid vesicles. COMMUNICATIONS PHYSICS 2022; 5:283. [PMID: 36405503 PMCID: PMC9660165 DOI: 10.1038/s42005-022-01055-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Topological transitions of fluid lipid membranes are fundamental processes for cell life. For example, they are required for endo- and exocytosis or to enable neurotransmitters to cross the neural synapses. Here, inspired by the idea that fusion and fission proteins could have evolved in Nature in order to carry out a minimal work expenditure, we evaluate the minimal free energy pathway for the transition between two spherical large unilamellar vesicles and a dumbbell-shaped one. To address the problem, we propose and successfully use a Ginzburg-Landau type of free energy, which allows us to uniquely describe without interruption the whole, full-scale topological change. We also compute the force fields needed to overcome the involved energy barriers. The obtained forces are in excellent agreement, in terms of intensity, scale, and spatial localization with experimental data on typical fission protein systems, whereas they suggest the presence of additional features in fusion proteins.
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Affiliation(s)
- Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
- Present Address: School of Architecture, Technology and Engineering, University of Brighton, Brighton, United Kingdom
| | - Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
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44
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Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J Chem Theory Comput 2022; 18:5759-5791. [PMID: 36070494 PMCID: PMC9558379 DOI: 10.1021/acs.jctc.2c00643] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/14/2023]
Abstract
Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander J. Pak
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksander E. P. Durumeric
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy D. Loose
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
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45
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Schiaffarino O, Valdivieso González D, García-Pérez IM, Peñalva DA, Almendro-Vedia VG, Natale P, López-Montero I. Mitochondrial membrane models built from native lipid extracts: Interfacial and transport properties. Front Mol Biosci 2022; 9:910936. [PMID: 36213125 PMCID: PMC9538489 DOI: 10.3389/fmolb.2022.910936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
The mitochondrion is an essential organelle enclosed by two membranes whose functionalities depend on their very specific protein and lipid compositions. Proteins from the outer mitochondrial membrane (OMM) are specialized in mitochondrial dynamics and mitophagy, whereas proteins of the inner mitochondrial membrane (IMM) have dedicated functions in cellular respiration and apoptosis. As for lipids, the OMM is enriched in glycerophosphatidyl choline but cardiolipin is exclusively found within the IMM. Though the lipid topology and distribution of the OMM and IMM are known since more than four decades, little is known about the interfacial and dynamic properties of the IMM and OMM lipid extracts. Here we build monolayers, supported bilayers and giant unilamellar vesicles (GUVs) of native OMM and IMM lipids extracts from porcine heart. Additionally, we perform a comparative analysis on the interfacial, phase immiscibility and mechanical properties of both types of extract. Our results show that IMM lipids form more expanded and softer membranes than OMM lipids, allowing a better understanding of the physicochemical and biophysical properties of mitochondrial membranes.
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Affiliation(s)
- Olivia Schiaffarino
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
| | - David Valdivieso González
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
| | | | - Daniel A. Peñalva
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), ConsejoNacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Víctor G. Almendro-Vedia
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
- Departamento de Farmacia Galénica y Tecnología Alimentaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Paolo Natale
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
- *Correspondence: Iván López-Montero, ; Paolo Natale,
| | - Iván López-Montero
- Departamento Química Física, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Madrid, Spain
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Iván López-Montero, ; Paolo Natale,
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46
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Aho N, Buslaev P, Jansen A, Bauer P, Groenhof G, Hess B. Scalable Constant pH Molecular Dynamics in GROMACS. J Chem Theory Comput 2022; 18:6148-6160. [PMID: 36128977 PMCID: PMC9558312 DOI: 10.1021/acs.jctc.2c00516] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Noora Aho
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Anton Jansen
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Paul Bauer
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Berk Hess
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
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47
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Kieninger S, Keller BG. GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J Chem Theory Comput 2022; 18:5792-5798. [DOI: 10.1021/acs.jctc.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefanie Kieninger
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
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48
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Larsen AH. Molecular Dynamics Simulations of Curved Lipid Membranes. Int J Mol Sci 2022; 23:ijms23158098. [PMID: 35897670 PMCID: PMC9331392 DOI: 10.3390/ijms23158098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.
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49
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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50
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Patmanidis I, Souza PCT, Sami S, Havenith RWA, de Vries AH, Marrink SJ. Modelling structural properties of cyanine dye nanotubes at coarse-grained level. NANOSCALE ADVANCES 2022; 4:3033-3042. [PMID: 36133510 PMCID: PMC9419059 DOI: 10.1039/d2na00158f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/12/2022] [Indexed: 06/16/2023]
Abstract
Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. First, we optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we conducted random self-assembly simulations, and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials.
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Affiliation(s)
- Ilias Patmanidis
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen Nijenborgh 7 Groningen 9747 AG the Netherlands
- Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon Lyon France
| | - Selim Sami
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen Nijenborgh 7 Groningen 9747 AG the Netherlands
- Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Remco W A Havenith
- Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
- Ghent Quantum Chemistry Group, Department of Chemistry, Ghent University Krijgslaan 281 (S3) B-9000 Gent Belgium
| | - Alex H de Vries
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen Nijenborgh 7 Groningen 9747 AG the Netherlands
- Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen Nijenborgh 7 Groningen 9747 AG the Netherlands
- Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
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