A5028135857- Lipid Membrane Structure and Behavior
- Antimicrobial Peptides and Activities
- Protein Structure and Dynamics
- ATP Synthase and ATPases Research
- Cellular transport and secretion
- Spectroscopy and Quantum Chemical Studies
- Nanopore and Nanochannel Transport Studies
- Force Microscopy Techniques and Applications
- Mitochondrial Function and Pathology
- Receptor Mechanisms and Signaling
- Biochemical and Structural Characterization
- RNA Interference and Gene Delivery
- Enzyme Structure and Function
- Immune Response and Inflammation
- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- Virology and Viral Diseases
- Influenza Virus Research Studies
- DNA and Nucleic Acid Chemistry
- Material Dynamics and Properties
- Photoreceptor and optogenetics research
- Block Copolymer Self-Assembly
- Theoretical and Computational Physics
Universidade Nova de Lisboa
2016-2025
Instituto de Tecnología Química
2022-2025
Hospital Nacional Dos de Mayo
2025
University of Lisbon
2006-2022
Instituto de Biologia Experimental e Tecnológica
2020
University of Groningen
2011-2019
National Institute of Chemistry
2014
University of Ljubljana
2014
Noble (United States)
2010
Instituto de Medicina Molecular João Lobo Antunes
2009
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...
The detailed organization of cellular membranes remains rather elusive. Based on large-scale molecular dynamics simulations, we provide a high-resolution view the lipid plasma membrane at an unprecedented level complexity. Our model consists 63 different species, combining 14 types headgroups and 11 tails asymmetrically distributed across two leaflets, closely mimicking idealized mammalian membrane. We observe enrichment cholesterol in outer leaflet general non-ideal lateral mixing species....
Cell membranes contain hundreds of different proteins and lipids in an asymmetric arrangement. Our current understanding the detailed organization cell remains rather elusive, because challenge to study fluctuating nanoscale assemblies with required spatiotemporal resolution. Here, we use molecular dynamics simulations characterize lipid environment 10 membrane proteins. To provide a realistic environment, are embedded model plasma membrane, where more than 60 species represented,...
Coarse-grained (CG) models allow simulation of larger systems for longer times by decreasing the number degrees freedom compared with all-atom models. Here we introduce an implicit-solvent version popular CG Martini model, nicknamed "Dry" Martini. To account omitted solvent freedom, nonbonded interaction matrix underlying force field was reparametrized. The Dry reproduces relatively well a variety lipid membrane properties such as area per lipid, bilayer thickness, bending modulus, and...
Abstract Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b 6 f complex. To understand how PLQ enters leaves PSII, here we show results of coarse grained molecular dynamics simulations PSII embedded in thylakoid membrane, covering a total simulation time more than 0.5 ms. The long scale allows observation many spontaneous entries into unbinding plastoquinol (PLQol) from In addition to two known channels, observe third channel for PLQ/PLQol...
Ceramides draw wide attention as tumor suppressor lipids that act directly on mitochondria to trigger apoptotic cell death. However, molecular details of the underlying mechanism are largely unknown. Using a photoactivatable ceramide probe, we here identify voltage-dependent anion channels VDAC1 and VDAC2 mitochondrial binding proteins. Coarse-grain dynamics simulations reveal both harbor site one side barrel wall. This includes membrane-buried glutamate mediates direct contact with head...
The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current modeling landscape. Building block based CG models, such as Martini model, possess key advantage of allowing for broad range applications without need to reparametrize force field each time. However, there are certain inherent limitations this approach, which we investigate detail work. We first study consequences absence specific cross Lennard-Jones parameters...
Abstract The Martini model, a coarse‐grained force field for molecular dynamics simulations, has been around nearly two decades. Originally developed lipid‐based systems by the groups of Marrink and Tieleman, model over years extended as community effort to current level general‐purpose field. Apart from obvious benefit reduction in computational cost, popularity is largely due systematic yet intuitive building‐block approach that underlies well open nature development its continuous...
ABSTRACT Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency accurate representation of protein dynamics with the capabilities studying proteins in different biological environments. This paper introduces enhanced model, which a virtual-site implementation Gō...
Abstract BAX and BAK are proapoptotic members of the BCL2 family that directly mediate mitochondrial outer membrane permeabilition (MOMP), a central step in apoptosis execution. However, molecular architecture apoptotic pore remains key open question especially little is known about contribution lipids to MOMP. By performing comparative lipidomics analysis proximal environment isolated lipid nanodiscs, we find significant enrichment unsaturated species nearby conditions. We then demonstrate...
The potential of antimicrobial peptides (AMPs) as an alternative to conventional therapies is well recognized. Insights into the biological and biophysical properties AMPs are thus key understanding their mode action. In this study, mechanisms adopted by two in disrupting gram-negative Escherichia coli bacterial envelope were explored. BP100 a short cecropin A-melittin hybrid peptide known inhibit growth phytopathogenic bacteria. pepR, on other hand, novel AMP derived from dengue virus...
Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol related molecules are available the Martini force field have been successfully used multiple lipid studies. In this work, we focus on use of virtual sites as a means increasing stability cholesterol-like structures. We improve extend parameterization sterols four different ways: 1—the were adapted to make interaction sites, which markedly improves...
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...
The Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of 2 and protein interactions two types systems: coiled coil peptide dimers water transmembrane peptides. Coiled form incorrectly under not at all 3. With peptides, represents better membrane thickness–peptide tilt relationship, but shorter peptides do remain transmembranar. We discuss related observations, describe...
We present an adaptive resolution simulation of protein G in multiscale water. couple atomistic water around the with mesoscopic water, where four molecules are represented one coarse-grained bead, farther away. circumvent difficulties that arise from coupling to model via a 4-to-1 molecule coarse-grain mapping by using bundled models, i.e., we restrict relative movement mapped same bead employing harmonic springs. The change their particle and vice versa adaptively on-the-fly. Having...
Phosphoinositides are a family of membrane phospholipids that play crucial roles in regulatory events. As such, these lipids often key part molecular dynamics simulation studies biological membranes, particular those employing coarse-grain models because the potential long times and sizes involved processes. Version 3 widely used Martini force field has been recently published, greatly refining many aspects biomolecular interactions. In order to properly use it for lipid simulations with...
Many cellular phenomena occur on the biomembranes. There are plenty of molecules (natural or xenobiotics) that interact directly partially with cell membrane. Biomolecules, such as several peptides (e.g., antimicrobial peptides) and proteins, exert their effects at membrane level. This feature makes necessary investigating interactions lipids to clarify mechanisms action side necessary. The determination molecular lipid/water partition constants (K ( p )) is frequently used quantify...
The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case severe osmotic downshock. Sensing bilayer tension, MscL sensitive to changes the environment and are, therefore, an ideal test for exploring protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations characterize gating kinetics different environments under influence alcohols. We performed over five hundred...
The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed direct interactions between and lipid bilayers possible net charge bilayer as well presence divalent ions in buffer play an important role. vivo, colocalization suppressed, cells rely on linker proteins to connect plasma membrane network. Little is known, however, about why this case what microscopic important. A deeper understanding highly...
We performed coarse-grained simulations of the antimicrobial peptides Magainin-2, BP100, MSI-103, and MSI-78 on a phase-separated membrane to study their preference for different domains. All displayed clear liquid-disordered (Ld) phase over liquid-ordered (Lo) one. For there was further domain interface. The peptides' toward disordered shown reflect penalization lipid-lipid interaction enthalpy in Lo phase, when vicinity peptides. Similar results were observed at two studied concentrations,...