Article
Chemistry, Physical
Anthony J. J. Cooper, Michael P. P. Howard, Sanket Kadulkar, David Zhao, Kris T. T. Delaney, Venkat Ganesan, Thomas M. M. Truskett, Glenn H. H. Fredrickson
Summary: We have developed a multiscale simulation model for predicting solute diffusion through porous triblock copolymer membranes. The model combines self-consistent field theory (SCFT) and on-lattice kinetic Monte Carlo (kMC) simulations. Solvation is simulated in SCFT by constraining the glassy membrane matrix while relaxing the brush-like membrane pore coating against the solvent. The kMC simulations capture the resulting solute spatial distribution and concentration-dependent local diffusivity in the polymer-coated pores.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Semen Yesylevskyy, Himanshu Khandelia
Summary: The EnCurv method is introduced for maintaining membrane curvature in molecular dynamics simulations, allowing for any desired curvature in a lipid membrane sector bent in a single plane. The method is simple, easy to implement, and scales linearly with system size, while being agnostic to force field, simulation parameters, and membrane composition. The proof of principle implementation is compatible with most modern simulation packages and yields consistent results on model systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Biochemistry & Molecular Biology
Andreas Haahr Larsen
Summary: Eukaryotic cells contain membranes with various curvatures, which are generated and sustained by specific proteins, peptides, and lipids. In addition, certain molecules can sense membrane curvature. Molecular dynamics simulations provide a valuable tool for investigating curved lipid membranes and their interactions with membrane-associated proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Polymer Science
Antonio Lamura
Summary: The dynamical response of a tethered semiflexible polymer with self-attractive interactions under an external force field was numerically investigated by varying stiffness and self-interaction strength. Different parameters led to various transitions and morphological changes in the polymer chain. The study showed that the external force had significant effects on the conformation and deformation of the polymer chain.
Article
Biophysics
Martin Girard, Tristan Bereau
Summary: The plasma membrane of eukaryotes exhibits lipid asymmetry, with different lipids primarily located in different leaflets. Using computational simulations, it has been found that saturation asymmetry arises as a result of phospholipid number asymmetry and sphingomyelin contents. This suggests that some asymmetries in lipid composition may naturally result from others and do not require external factors. The asymmetry of cholesterol, on the other hand, is fairly mild and influenced by all the other asymmetries.
BIOPHYSICAL JOURNAL
(2023)
Article
Multidisciplinary Sciences
Suvrajit Saha, Amit Das, Chandrima Patra, Anupama Ambika Anilkumar, Parijat Sil, Satyajit Mayor, Andmadan Rao
Summary: The spatiotemporal organization of proteins and lipids on the cell surface plays a crucial role in cellular functions. This study investigates the molecular interactions that drive the formation of nanoclusters of GPI-APs and transmembrane proteins, and proposes a theoretical model to explain the organization of membrane domains in living cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tamara C. Bidone, David J. Odde
Summary: Computational models have provided insights into how cells establish connections with the external environment, but how individual adhesion proteins regulate the dynamics of whole adhesion complexes remains unclear. This is due to the differences in time and length scales and limitations in accurately extracting key information from molecular simulation approaches. This review discusses the models of integrin-based adhesion complexes and highlights important findings related to conformational transitions and the molecular clutch mechanism.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Hiroshi Noguchi
Summary: The shapes of biomembrane in living cells are influenced by curvature-inducing proteins. However, the impact of membrane deformation on signal transductions, such as chemical waves, has not been adequately studied. This research demonstrates that membrane deformation can modify the propagation of excitable reaction-diffusion waves through advanced simulations. Reaction waves can induce significant shape transformations and affect wave propagation depending on curvature, feedback, and reaction-deformation time ratio. Furthermore, the occasional disappearance of waves can alter the pathway of wave propagation. These findings highlight the joint regulation of signal transductions by membrane deformation and reaction waves.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Physical
Min-Kang Hsieh, Jeffery B. Klauda
Summary: In this study, lipid composition asymmetry in Escherichia coli inner plasma membrane models at early-log and stationary stages was investigated using molecular dynamics simulations. The results showed differences in membrane properties between leaflets and whole membranes, as well as the effect of leaflet asymmetry on membrane properties. The stationary phase bilayer exhibited larger surface area per lipid, smaller thickness, larger tilt angle, smaller tilt modulus, and lower deuterium order parameters compared to the early-log stage, indicating a positive spontaneous curvature in the stationary phase.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Engineering, Chemical
Jianjun Jiang, Lei Fang, Zhijing Huang, Liang Chen, Yusong Tu, Zonglin Gu
Summary: The interlayer spacing of graphene oxide (GO) membranes can be controlled by cations, but the specific role of anions in treating GO membranes has not been reported. This study reveals that anions can also stabilize the interlayer spacing of GO membranes through the formation of ion bridges. The ion bridges greatly enhance the interaction between neighboring GO sheets, providing a new approach for the design of membrane materials.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Tomonori Tamura, Itaru Hamachi
Summary: Membrane biology studies have shown that organelle membranes play a crucial role in addition to providing structural support. Various chemical biology tools have been developed to understand the functions, properties, and dynamics of organelle membranes. This review focuses on the latest molecular probes for organelle membrane studies, highlighting chemical strategies for visualizing and quantitatively analyzing the dynamic properties of organelle membranes and lipids, and discussing the current limitations and future directions of this challenging research area.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sangmin Lee, Thi Vo, Sharon C. Glotzer
Summary: In this study, hard truncated triangular bipyramids self-assemble into seven different colloidal clathrate crystals, consisting of cages that are either empty or occupied by guest particles. Monte Carlo simulations reveal that the crystallization occurs through the compartmentalization of entropy between low- and high-entropy subsystems for the host and guest particles. The researchers also use entropic bonding theory to design host-guest colloidal clathrates with explicit interparticle attraction for experimental realization.
Article
Multidisciplinary Sciences
Helgi I. Ingolfsson, Chris Neale, Timothy S. Carpenter, Rebika Shrestha, Cesar A. Lopez, Timothy H. Tran, Tomas Oppelstrup, Harsh Bhatia, Liam G. Stanton, Xiaohua Zhang, Shiv Sundram, Francesco Di Natale, Animesh Agarwal, Gautham Dharuman, Sara I. L. Kokkila Schumacher, Thomas Turbyville, Gulcin Gulten, Que N. Van, Debanjan Goswami, Frantz Jean-Francois, Constance Agamasu, De Chen, Jeevapani J. Hettige, Timothy Travers, Sumantra Sarkar, Michael P. Surh, Yue Yang, Adam Moody, Shusen Liu, Brian C. Van Essen, Arthur F. Voter, Arvind Ramanathan, Nicolas W. Hengartner, Dhirendra K. Simanshu, Andrew G. Stephen, Peer-Timo Bremer, S. Gnanakaran, James N. Glosli, Felice C. Lightstone, Frank McCormick, Dwight Nissley, Frederick H. Streitz
Summary: In this study, a scale-bridging ensemble of over 100,000 simulations of RAS-membrane interactions was created using machine learning. The simulations revealed distinctive patterns of lipid composition that are correlated with RAS dynamics, potentially providing a mechanism for regulating cell signaling cascades.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biophysics
Henry J. Lessen, Kayla C. Sapp, Andrew H. Beaven, Rana Ashkar, Alexander J. Sodt
Summary: Membrane reshaping is crucial in biological processes, and the chemical composition of lipid membranes plays a significant role in determining their mechanical properties and shape. This study highlights the importance of specific chemical interactions between lipids in multicomponent bilayers and the impact of these interactions on bilayer stiffness. It also identifies two mechanisms of bilayer softening: diffusional softening and conformational softening.
BIOPHYSICAL JOURNAL
(2022)
Article
Engineering, Chemical
Javier Luque Di Salvo, Giorgio De Luca, Andrea Cipollina, Giorgio Micale
Summary: A novel full-atom multiscale method is presented to describe the diffusion of multiple ions in anion exchange membranes, particularly focusing on chloride and sodium ions in PSU-TMA membranes. The method combines Density Functional Theory and molecular dynamics simulations to evaluate diffusion behavior, with attention to co-ion diffusion and water content influence. Results show good agreement with literature values and experimental observations, emphasizing the importance of water content on ion diffusion.
JOURNAL OF MEMBRANE SCIENCE
(2021)
Review
Chemistry, Multidisciplinary
Siewert J. Marrink, Luca Monticelli, Manuel N. Melo, Riccardo Alessandri, D. Peter Tieleman, Paulo C. T. Souza
Summary: The Martini model is a coarse-grained force field for molecular dynamics simulations that has been developed and refined over nearly two decades. Its popularity stems from its systematic and intuitive building-block approach, as well as its open development and continuous validation. The model's easy implementation in the widely used Gromacs software suite has also contributed to its popularity.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
Maria Gabriella Chiariello, Fabian Grunewald, Rubi Zarmiento-Garcia, Siewert J. Marrink
Summary: The PsbS protein in photosystem II triggers the photoprotective mechanism in plants by sensing the acidification of the thylakoid lumen. Research shows that pH-induced structural changes in the lumen-exposed helices of the PsbS dimer provide an effective switch between its inactive and active forms, contributing to its dimerization propensity and the photoprotective mechanism.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Jan A. A. Stevens, Fabian Grunewald, P. A. Marco van Tilburg, Melanie Koenig, Benjamin R. Gilbert, Troy A. A. Brier, Zane R. R. Thornburg, Zaida Luthey-Schulten, Siewert J. J. Marrink
Summary: Computational microscopes are on the verge of achieving the ultimate goal of revealing the dynamics of a cell's components with atomic resolution. In this perspective, the integrative approach used to model the minimal cell, JCVI-syn3A, showcases the potential of molecular dynamics simulations to study the spatio-temporal evolution of cells, extending its applicability to other cell types in the near future.
FRONTIERS IN CHEMISTRY
(2023)
Article
Gastroenterology & Hepatology
Barbora Waclawikova, Paulo Cesar Telles de Souza, Markus Schwalbe, Constantinos G. Neochoritis, Warner Hoornenborg, Sieger A. Nelemans, Siewert J. Marrink, Sahar El Aidy
Summary: The gut-bacterial metabolite 5-hydroxyindole has been found to stimulate intestinal motility and can serve as a potential therapeutic for gastrointestinal motility disorders such as constipation. Oral administration of 5-hydroxyindole has minimal effects on the rat cecal microbiota. Molecular dynamics simulations suggest potential-binding pockets of 5-hydroxyindole in the L-type voltage-gated calcium channels, which have been associated with gastrointestinal motility disorders.
Review
Biochemistry & Molecular Biology
Victoria Thusgaard Ruhoff, Poul Martin Bendix, Weria Pezeshkian
Summary: Biomembranes are crucial for our understanding of the basic building blocks of life – cells. A key characteristic of membranes is their ability to adopt various shapes that are essential for cellular function. In this article, we review different mechanisms by which membranes can change shape, with a special focus on how membrane proteins induce local curvature and rigidity, resulting in emerging forces and large-scale membrane deformations. We also argue that considering changes in membrane rigidity moduli is necessary to fully understand the interaction between rigid proteins and biomembranes.
EMERGING TOPICS IN LIFE SCIENCES
(2023)
Article
Biophysics
Meina Ren, Lina Zhao, Ziyi Ma, Hailong An, Siewert Jan Marrink, Fude Sun
Summary: The association between CD44 and the N-terminal (FERM) domain of cytoskeleton adaptors is crucial for cell proliferation, migration, and signaling. Phosphorylation of the cytoplasmic domain (CTD) of CD44 regulates this association, with phosphorylation at S291 inhibiting complexation and phosphorylation at S325 promoting the CD44-FERM linkage. This phosphorylation-driven transformation is PIP2-dependent, with PIP2 affecting the stability of the closed and open conformation, and its replacement by POPS greatly reducing this effect.
BIOPHYSICAL JOURNAL
(2023)
Article
Biophysics
Anna L. Duncan, Weria Pezeshkian
Summary: Computer simulation techniques are a versatile tool for exploring biological processes, especially the features of biological membranes. Recent advances in multiscale simulation schemes have overcome the limitations of traditional simulation techniques, allowing us to study processes that span multiple scales beyond the capacity of any single technique. Therefore, we argue that mesoscale simulations require more attention and further development to bridge the evident gaps in simulating and modeling living cell membranes.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Medicinal
Charly Empereur-mot, Kasper B. Pedersen, Riccardo Capelli, Martina Crippa, Cristina Caruso, Mattia Perrone, Paulo C. T. Souza, Siewert J. Marrink, Giovanni M. Pavan
Summary: By using the SwarmCG automatic multiobjective optimization approach, we have successfully refined the bonded interaction parameters in the Martini coarse-grained force field (CG FF) lipid models. Through experimental observables and all-atom molecular dynamics simulations, we optimized 80 model parameters and obtained improved and transferable Martini lipid models.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Carlos Ramirez-Palacios, Siewert J. Marrink
Summary: A Graph Convolutional Neural Network (GCN) can accurately predict the binding energy of enzyme variants using only sequence information, and can score an enzyme variant in under 1 ms using a pre-trained language module.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Weria Pezeshkian, Fabian Grunewald, Oleksandr Narykov, Senbao Lu, Valeria Arkhipova, Alexey Solodovnikov, Tsjerk A. Wassenaar, Siewert J. Marrink, Dmitry Korkin
Summary: Despite efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains unknown. This study developed a computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail and focused on the understudied M protein. Molecular dynamics simulations revealed the agglomeration of M dimers into large macromolecular assemblies with distinct patterns, in agreement with experimental data, demonstrating a versatile approach for de novo virus structure modeling.
Review
Chemistry, Physical
Luis Borges-Araujo, Ilias Patmanidis, Akhil P. Singh, Lucianna H. S. Santos, Adam K. Sieradzan, Stefano Vanni, Cezary Czaplewski, Sergio Pantano, Wataru Shinoda, Luca Monticelli, Adam Liwo, Siewert J. Marrink, Paulo C. T. Souza
Summary: In this review, the authors provide an overview of pragmatic coarse-grained (CG) protein models, which combine physics-based implementation and top-down experimental approaches for parameterization. These CG models, with most protein residues represented by at least two beads, allow for some degree of chemical specificity. The review includes discussions on recent applications and future perspectives in the field.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Luis Borges-Araujo, Ana C. Borges-Araujo, Tugba Nur Ozturk, Daniel P. Ramirez-Echemendia, Balazs Fabian, Timothy S. Carpenter, Sebastian Thallmair, Jonathan Barnoud, Helgi I. Ingolfsson, Gerhard Hummer, D. Peter Tieleman, Siewert J. Marrink, Paulo C. T. Souza, Manuel N. Melo
Summary: Cholesterol plays a crucial role in biomembranes by regulating various properties of lipid bilayers. Martini 3 model offers significant improvements in interaction balance and molecular packing, and includes a new cholesterol model that mitigates some limitations of its predecessor.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Alexandre Blanco-Gonzalez, Siewert J. Marrink, Angel Pineiro, Rebeca Garcia-Fandino
Summary: Administration of focused ultrasounds is a promising therapy for various diseases due to its non-invasive nature, targeted delivery, easy dosage control, and low risks. However, its direct interaction with cell membranes at the molecular level is still not well understood.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Cell Biology
Benjamin R. Gilbert, Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grunewald, John E. Stone, Siewert J. Marrink, Zaida Luthey-Schulten
Summary: To model the replication and inheritance of genetic material in cells, researchers created a computational framework that simulates the replication of bacterial chromosomes and applied it to a genetically minimal bacterium. By modeling the chromosome as a self-avoiding polymer and studying its interaction with ribosomes, they found that the mechanisms of loop extrusion and protein complexes are sufficient for chromosome segregation. Additionally, they developed a methodology to validate their cell state predictions by mapping the polymer model to a coarse-grained representation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Engineering, Biomedical
Aida Nonn, Balint Kiss, Weria Pezeshkian, Thomas Tancogne-Dejean, Albert Cerrone, Miklos Kellermayer, Yuanli Bai, Wei Li, Tomasz Wierzbicki
Summary: A methodology combining experimental and simulation techniques was proposed to investigate the internal structure and mechanical properties of SARS-CoV-2. The elastic properties and fracture strength of the viral membrane were estimated, and the results showed a close association between membrane proteins and ribonucleoproteins. These findings provide valuable knowledge for the development of novel prevention and treatment methods.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2023)
