Meyer, Tim

[["dc.bibliographiccitation.firstpage","88"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Structure"],["dc.bibliographiccitation.lastpage","95"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","de la Cruz, Xavier"],["dc.contributor.author","Orozco, Modesto"],["dc.date.accessioned","2022-06-08T11:11:36Z"],["dc.date.available","2022-06-08T11:11:36Z"],["dc.date.issued","2009-01-14"],["dc.description.abstract","Extended all-atom molecular dynamics simulations on all protein metafolds have been performed to obtain a complete picture of the gas phase proteome. The structural atlas of the gas phase proteome obtained here shows an unexpected maintenance of the global and local structure and of the general deformability pattern upon transfer to the gas phase under electrospray conditions. Despite a general compression, the solution structure can be easily very well recognized from the gas phase one, and most structural details, such as secondary structure, are well preserved upon vaporization. Rehydration of the gas phase protein leads in most cases to a very fast transition from gas phase to solution structure. Overall, our massive analysis (over 4 micros in solution and over 12 micros in the gas phase) demonstrates that solution-like structures can be determined by using mass spectroscopy and related techniques to obtain fast approximations to the solution structure."],["dc.identifier.doi","10.1016/j.str.2008.11.006"],["dc.identifier.pmid","19141285"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/111137"],["dc.language.iso","en"],["dc.relation.issn","0969-2126"],["dc.title","An atomistic view to the gas phase proteome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1399-409"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","Structure"],["dc.bibliographiccitation.lastpage","1409"],["dc.bibliographiccitation.volume","18"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","D'Abramo, Marco"],["dc.contributor.author","Hospital, Adam"],["dc.contributor.author","Rueda, Manuel"],["dc.contributor.author","Ferrer-Costa, Carles"],["dc.contributor.author","Pérez, Alberto"],["dc.contributor.author","Carrillo, Oliver"],["dc.contributor.author","Camps, Jordi"],["dc.contributor.author","Fenollosa, Carles"],["dc.contributor.author","Repchevsky, Dmitry"],["dc.contributor.author","Gelpí, Josep Lluis"],["dc.contributor.author","Orozco, Modesto"],["dc.date.accessioned","2022-06-08T11:11:22Z"],["dc.date.available","2022-06-08T11:11:22Z"],["dc.date.issued","2010-11-10"],["dc.description.abstract","More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. The trajectories and analyses are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. Here, we describe the project and the structure and contents of our database, and provide examples of how it can be used to describe the global flexibility properties of proteins. Basic analyses and trajectories stripped of solvent molecules at a reduced resolution level are available from our web server."],["dc.identifier.doi","10.1016/j.str.2010.07.013"],["dc.identifier.pmid","21070939"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/111135"],["dc.language.iso","en"],["dc.relation.eissn","1878-4186"],["dc.relation.issn","0969-2126"],["dc.title","MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","408"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Wiley Interdisciplinary Reviews: Computational Molecular Science"],["dc.bibliographiccitation.lastpage","425"],["dc.bibliographiccitation.volume","3"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","Gabelica, Valérie"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Orozco, Modesto"],["dc.date.accessioned","2018-02-12T11:19:28Z"],["dc.date.available","2018-02-12T11:19:28Z"],["dc.date.issued","2013"],["dc.description.abstract","Proteins are complex macromolecules that evolved over billions of years to be active in aqueous solution. Water is a key element that stabilizes their structure, and most structural studies on proteins have thus been carried out in aqueous environment. However, recent experimental approaches have opened the possibility to gain structural information on proteins from gas-phase measurements. The obtained results revealed significant structural memory in proteins when transferred from water to the gas phase. However, after several years of experimental and theoretical research, the nature of the structural changes induced by vaporization, the exact characteristics of proteins in the gas phase, and the physicochemical forces stabilizing dehydrated proteins are still unclear. We will review here these issues using both experimental and theoretical sources of information."],["dc.identifier.doi","10.1002/wcms.1130"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12161"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1759-0884"],["dc.relation.issn","1759-0876"],["dc.title","Proteins in the gas phase"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e0119978"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","PLoS One"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Barbany, Montserrat"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","Hospital, Adam"],["dc.contributor.author","Faustino, Ignacio"],["dc.contributor.author","D'Abramo, Marco"],["dc.contributor.author","Morata, Jordi"],["dc.contributor.author","Orozco, Modesto"],["dc.contributor.author","de la Cruz, Xavier"],["dc.date.accessioned","2022-06-08T11:11:17Z"],["dc.date.available","2022-06-08T11:11:17Z"],["dc.date.issued","2015"],["dc.description.abstract","Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results."],["dc.identifier.doi","10.1371/journal.pone.0119978"],["dc.identifier.pmid","25816327"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/111134"],["dc.language.iso","en"],["dc.relation.issn","1932-6203"],["dc.title","Molecular dynamics study of naturally existing cavity couplings in proteins"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","83"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Proteins"],["dc.bibliographiccitation.lastpage","94"],["dc.bibliographiccitation.volume","78"],["dc.contributor.author","Emperador, Agustí"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","Orozco, Modesto"],["dc.date.accessioned","2022-06-08T11:11:27Z"],["dc.date.available","2022-06-08T11:11:27Z"],["dc.date.issued","2010-01"],["dc.description.abstract","We have applied all atoms discrete molecular dynamics (DMD) based on a quasi-physical potential to study the flexibility of an extended set of proteins for which atomistic MD simulations are available. The method uses pure physical potentials supplemented by information on secondary structure and despite its simplicity is able to reproduce with good accuracy the dynamics of proteins in solution. The method presents a clear improvement with respect to coarse-grained methods based on structure potentials and opens the possibility to explore dynamics of proteins out from the equilibrium and to trace conformational changes induced by interaction of proteins with both small and macromolecular ligands."],["dc.identifier.doi","10.1002/prot.22563"],["dc.identifier.pmid","19816993"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/111136"],["dc.language.iso","en"],["dc.relation.eissn","1097-0134"],["dc.relation.issn","0887-3585"],["dc.title","Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","796"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences of the United States of America"],["dc.bibliographiccitation.lastpage","801"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Rueda, Manuel"],["dc.contributor.author","Ferrer-Costa, Carles"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","Pérez, Alberto"],["dc.contributor.author","Camps, Jordi"],["dc.contributor.author","Hospital, Adam"],["dc.contributor.author","Gelpí, Josep Lluis"],["dc.contributor.author","Orozco, Modesto"],["dc.date.accessioned","2022-06-08T11:11:31Z"],["dc.date.available","2022-06-08T11:11:31Z"],["dc.date.issued","2007-01-16"],["dc.description.abstract","The dynamics of proteins in aqueous solution has been investigated through a massive approach based on \"state of the art\" molecular dynamics simulations performed for all protein metafolds using the four most popular force fields (OPLS, CHARMM, AMBER, and GROMOS). A detailed analysis of the massive database of trajectories (>1.5 terabytes of data obtained using approximately 50 years of CPU) allowed us to obtain a robust-consensus picture of protein dynamics in aqueous solution."],["dc.identifier.doi","10.1073/pnas.0605534104"],["dc.identifier.pmid","17215349"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/111138"],["dc.language.iso","en"],["dc.relation.issn","0027-8424"],["dc.title","A consensus view of protein dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2001"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Journal of Chemical Theory and Computation"],["dc.bibliographiccitation.lastpage","2010"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Emperador, Agustí"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","Orozco, Modesto"],["dc.date.accessioned","2022-06-08T11:11:41Z"],["dc.date.available","2022-06-08T11:11:41Z"],["dc.date.issued","2008-12-09"],["dc.description.abstract","We present a method for the efficient simulation of the equilibrium dynamics of proteins based on the well established discrete molecular dynamics algorithm, which avoids integration of Newton equations of motion at short time steps, allowing then the derivation of very large trajectories for proteins with a reduced computational cost. In the presented implementation we used an all heavy-atoms description of proteins, with simple potentials describing the conformational region around the experimental structure based on local physical interactions (covalent structure, hydrogen bonds, hydrophobic contacts, solvation, steric hindrance, and bulk dispersion interactions). The method shows a good ability to describe the flexibility of 33 diverse proteins in water as determined by atomistic molecular dynamics simulation and can be useful for massive simulation of proteins in crowded environments or for refinement of protein structure in large complexes."],["dc.identifier.doi","10.1021/ct8003832"],["dc.identifier.pmid","26620473"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/111139"],["dc.language.iso","en"],["dc.relation.issn","1549-9618"],["dc.title","United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]