Author
Maria Maddalena Sperotto
Bio: Maria Maddalena Sperotto is an academic researcher from Technical University of Denmark. The author has contributed to research in topics: Lipid bilayer & Biological membrane. The author has an hindex of 20, co-authored 33 publications receiving 1755 citations.
Papers
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TL;DR: In this article, the authors compare various strategies to coarse-grained simulation of a biological membrane and conclude that the results obtained by the various mesoscopic models are surprisingly consistent. But they do not discuss the effect of transmembrane peptides on the local structure of a membrane and the mechanism of vesicle fusion and fission.
307 citations
TL;DR: A mesoscopic model for lipid bilayers with embedded proteins, which has been studied with the help of the dissipative particle dynamics simulation technique, suggests that, when the embedded protein has a small size, the main mechanism to compensate for a large hydrophobic mismatch is the tilt, whereas large proteins react to negative mismatch by causing an increase of theHydrophobic thickness of the nearby bilayer.
243 citations
TL;DR: Phenomena discussed include lipid sorting and selectivity at protein surfaces, protein-lipid phase equilibria, lipid-mediated protein-protein interactions, wetting and capillary condensation as means of protein organization, mechanisms of two-dimensional protein crystallization, as well as non-equilibrium organization of active proteins in membranes.
221 citations
Technical University of Denmark1, Pasteur Institute2, University of Bergen3, University of Copenhagen4, University of Manchester5, Palacký University, Olomouc6, European Bioinformatics Institute7, French Institute for Research in Computer Science and Automation8, Institut national de la recherche agronomique9, Masaryk University10, University of Bologna11, University of Rome Tor Vergata12, Ghent University13, University of Milano-Bicocca14, Swiss Institute of Bioinformatics15, Bielefeld University16, Institut Français17, University of Freiburg18, University of Ljubljana19, The Chinese University of Hong Kong20, University of Padua21, University of Lausanne22, Daresbury Laboratory23, University of Lübeck24, University of Rostock25, University of Tartu26, Imperial College London27, University of Southern Denmark28, Central European Institute of Technology29, University of Milan30, Radboud University Nijmegen31
TL;DR: A community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources is presented.
Abstract: Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
111 citations
TL;DR: It is shown that the non-ideal mixing of lipid species due to mismatch in the hydrophobic lengths leads to a progressively increasing local ordering as the chain-length difference is increased and a pronounced local structure is found to persist deep inside the fluid phase of the mixture.
102 citations
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TL;DR: The latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability are described.
Abstract: The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.
3,529 citations
TL;DR: A new CG model for proteins as an extension of the MARTINI force field is developed and effectively reproduces peptide-lipid interactions and the partitioning of amino acids and peptides in lipid bilayers.
Abstract: Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. We developed a new CG model for proteins as an extension of the MARTINI force field. Here, we validate the model for its use in peptide-bilayer systems. In order to validate the model, we calculated the potential of mean force for each amino acid as a function of its distance from the center of a dioleoylphosphatidylcholine (DOPC) lipid bilayer. We then compared amino acid association constants, the partitioning of a series of model pentapeptides, the partitioning and orientation of WALP23 in DOPC lipid bilayers and a series of KALP peptides in dimyris...
2,173 citations
TL;DR: The simplest cell-like structure, the lipid bilayer vesicle, can respond to mechanical deformation by elastic membrane dilation/thinning and curvature changes and changes in local membrane curvature may shift the equilibrium between channel conformations.
Abstract: The simplest cell-like structure, the lipid bilayer vesicle, can respond to mechanical deformation by elastic membrane dilation/thinning and curvature changes. When a protein is inserted in the lip...
1,085 citations
TL;DR: The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago and is described as a building block principle model that combines speed and versatility while maintaining chemical specificity.
Abstract: The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model.
1,022 citations
TL;DR: It is proposed that various transmembrane proteins anchored to the actin-based membrane skeleton meshwork act as rows of pickets that temporarily confine phospholipids.
Abstract: The diffusion rate of lipids in the cell membrane is reduced by a factor of 5-100 from that in artificial bilayers. This slowing mechanism has puzzled cell biologists for the last 25 yr. Here we address this issue by studying the movement of unsaturated phospholipids in rat kidney fibroblasts at the single molecule level at the temporal resolution of 25 micros. The cell membrane was found to be compartmentalized: phospholipids are confined within 230-nm-diameter (phi) compartments for 11 ms on average before hopping to adjacent compartments. These 230-nm compartments exist within greater 750-nm-phi compartments where these phospholipids are confined for 0.33 s on average. The diffusion rate within 230-nm compartments is 5.4 microm2/s, which is nearly as fast as that in large unilamellar vesicles, indicating that the diffusion in the cell membrane is reduced not because diffusion per se is slow, but because the cell membrane is compartmentalized with regard to lateral diffusion of phospholipids. Such compartmentalization depends on the actin-based membrane skeleton, but not on the extracellular matrix, extracellular domains of membrane proteins, or cholesterol-enriched rafts. We propose that various transmembrane proteins anchored to the actin-based membrane skeleton meshwork act as rows of pickets that temporarily confine phospholipids.
910 citations