A5010416659- Protein Structure and Dynamics
- Lipid Membrane Structure and Behavior
- Nanopore and Nanochannel Transport Studies
- Enzyme Structure and Function
- Machine Learning in Materials Science
- Fullerene Chemistry and Applications
- Scientific Computing and Data Management
- Cell Image Analysis Techniques
- Mass Spectrometry Techniques and Applications
- Advanced Image and Video Retrieval Techniques
- Computational Drug Discovery Methods
- Organic Electronics and Photovoltaics
- Molecular Junctions and Nanostructures
- Erythrocyte Function and Pathophysiology
- Spectroscopy and Quantum Chemical Studies
- Receptor Mechanisms and Signaling
- 3D Surveying and Cultural Heritage
- Virtual Reality Applications and Impacts
- Single-cell and spatial transcriptomics
- 3D Modeling in Geospatial Applications
- Surfactants and Colloidal Systems
- ATP Synthase and ATPases Research
- Conducting polymers and applications
- Distributed and Parallel Computing Systems
- Evolution and Paleontology Studies
University of Groningen
2016-2024
Université Claude Bernard Lyon 1
2014-2024
Biotechnology Institute
2016-2023
University of Bristol
2020-2023
Universidade de Santiago de Compostela
2022-2023
Center for Research in Molecular Medicine and Chronic Diseases
2023
Ghent University
2020
University of Pennsylvania
2020
Délégation Paris 7
2012-2017
Sorbonne Paris Cité
2012-2017
MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories individual protein structures. MD simulations biological molecules have become an important tool to elucidate the relationship between structure physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output in their own formats so that development new trajectory algorithms confined...
Polystyrene is abundant in marine debris. Like most synthetic polymers, it degrades very slowly, producing smaller and particles easily ingested by wildlife. The presence of plastic microscopic fish wildlife massive well documented, but its impact on cellular activity not understood. Biological generally requires interaction with biological membranes, this difficult to study at the molecular scale vivo. Here we use coarse-grained simulations determine effect nanosized polystyrene (PS)...
Abstract The recent re‐parametrization of the Martini coarse‐grained force field, 3, improved accuracy model in predicting molecular packing and interactions dynamics simulations. Here, we describe how small molecules can be accurately parametrized within 3 framework present a database validated molecule models. We pay particular attention to description aliphatic aromatic ring‐like structures, which are ubiquitous such as solvents drugs or building blocks constituting macromolecules...
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with ultimate goal reaching cellular complexity. At same time, rational design by high-throughput (HT) simulations is another forefront MD. In these areas, Martini coarse-grained field, especially latest version ( i.e. v3), being actively explored because it offers enhanced spatial-temporal resolution. However, automation tools for preparing...
The MARTINI coarse-grained model is used to gain insight into the association of WALP23 helices in three different lipid membranes: DMPC, DPPC and DOPC. Potentials mean force describing two embedded bilayers indicate no barrier a stabilization more than 20 kJ mol(-1) associated state relative fully dissociated state. Association strongest followed by Helix-helix appears be enthalpically favorable all bilayers, while entropic contribution only presence significant positive hydrophobic...
In this work, we deliver a proof of concept for fast method that introduces pH effects into classical coarse-grained (CG) molecular dynamics simulations. Our approach is based upon the latest version popular Martini CG model to which explicit proton mimicking particles are added. We verify our against experimental data involving several different molecules and environmental conditions. particular, compute titration curves, dependent free energies transfer, lipid bilayer membrane affinities...
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version the Martini model, 3, offers significant improvements interaction balance, molecular packing, inclusion new bead types sizes. However, release model resulted need to reparameterize many core molecules, including cholesterol. Here, we describe development validation 3 cholesterol addressing issues related its bonded...
Nonionic surfactants are used for the isolation and purification of membrane proteins, as well study fundamental aspects protein diffusion in membranes. Here we present a new coarse-grained model polyethylene glycol (PEG) family polyoxyethylene alkyl ether (C(i)E(j)) surfactants. The is compatible with MARTINI force-field lipids proteins. We validate by comparing molecular dynamics simulations experimental data. In particular, show that reproduces phase behavior water-surfactant mixtures...
Cell membranes have a complex lateral organization featuring domains with distinct composition, also known as rafts, which play an essential role in cellular processes such signal transduction and protein trafficking. In vivo, perturbations of membrane (e.g., by drugs or lipophilic compounds) major effects on the activity raft-associated proteins signaling pathways, but they are difficult to characterize because small size domains, typically below optical resolution. Model membranes,...
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with ultimate goal reaching cellular complexity. At same time, rational design by high-throughput (HT) simulations is another forefront MD. In these areas, Martini coarse-grained field, especially latest version ( i.e. v3), being actively explored because it offers enhanced spatial-temporal resolution. However, automation tools for preparing...
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with ultimate goal reaching cellular complexity. At same time, rational design by high-throughput (HT) simulations is another forefront MD. In these areas, Martini coarse-grained field, especially latest version ( i.e. v3), being actively explored because it offers enhanced spatial-temporal resolution. However, automation tools for preparing...
Fullerene is scarcely soluble in most solvents, including alkanes. Yet, it has been shown that ${\mathrm{C}}_{60}$ dissolves lipid bilayers, whose interior chemically identical to Here, we use molecular simulations explain why bilayers are better than alkanes at dissolving fullerene clusters. aggregation driven by entropy, but enthalpic contributions determine the difference between and bilayers. Surprisingly, confinement chain alignment bilayer do not affect aggregation, while solvent...
Cation-π interactions play an important role in biomolecular recognition, including between membrane phosphatidylcholine lipids and aromatic amino acids of peripheral proteins. While molecular mechanics coarse grain (CG) force fields are particularly well suited to simulate proteins general, they not parameterized explicitly reproduce cation-π interactions. We here propose a modification the polarizable MARTINI model enabling it binding events whose acid with choline headgroups crucial for...
Given the need for modern researchers to produce open, reproducible scientific output, lack of standards and best practices sharing data workflows used analyze molecular dynamics (MD) simulations has become an important issue in field. There are now multiple well-established packages perform simulations, often highly tuned exploiting specific classes hardware, each with strong communities surrounding them, but very limited interoperability/transferability options. Thus, choice software...
The main protease (Mpro) of the SARS-CoV-2 virus is one focus drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) a useful and effective tool creating Mpro complexes. We make these tools models freely available. iMD-VR provides an immersive environment which users can interact with MD simulations so build protein complexes physically rigorous flexible way. Recently, have demonstrated method interactive, docking small molecule...
Abstract Organic semiconductors consisting of molecules bearing polar side chains have been proposed as potential candidates to overcome the limitations organic photovoltaics owing their enhanced dielectric constant. However, introducing such in photovoltaic devices has not yet resulted higher efficiencies. A microscopic understanding impact on electronic and structural properties is paramount rationalize effect. Here, bulk heterojunction overall morphology, molecular configurations at...
Introduction The potential of virtual reality (VR) to contribute drug design and development has been recognized for many years. A recent advance is use VR not only visualize interact with molecules, but also molecular dynamics simulations 'on the fly' (interactive in VR, IMD-VR), which useful flexible docking examining binding processes conformational changes.Areas Covered authors term 'interactive VR' refer software where interactivity an inherent part user experience e.g. making...
All-atomistic (AA) and coarse-grain (CG) simulations have been successfully applied to investigate a broad range of biomolecular processes. However, the accessible time length scales AA simulation are limited specific molecular details CG simplified. Here, we propose virtual site (VS) based hybrid scheme that can concurrently couple resolutions in single membrane simulation, mitigating shortcomings either representation. With some adjustments make force fields compatible, demonstrate lipid...
Airborne nanometre-sized pollutants are responsible for various respiratory diseases. Such can reach the gas-exchange surface in alveoli, which is lined with a monolayer of lung surfactant. The relationship between physiological effects and molecular-level interactions largely unknown. Here, we determine carbon nanoparticles on properties model using molecular simulations. We simulate phase-separated lipid monolayers presence pollutant nanoparticle, C₆₀ fullerene. In absence nanoparticles,...
We investigate the structural changes to lipid membrane that ensue from addition of aliphatic alcohols with various alkyl tail lengths. Small angle neutron diffraction flat bilayers are hydrated through water vapor has been employed eliminate possible artefacts curvature and alcohol's membrane-water partitioning. have observed clear structure in both transversal lateral directions. Most importantly, our results suggest alteration interface. The encroachment shifted way alcohol loaded...
This paper describes the development and application of a suite tools, called PBxplore, to analyze dynamics deformability protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, classical way their inherent flexibility is perform molecular simulations. The advantage small structural prototypes such as PBs give good approximation local structure backbone. More importantly, by reducing conformational complexity structures, allow analysis which cannot be done...