Briones, Rodolfo

[["dc.bibliographiccitation.firstpage","1396"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","1405"],["dc.bibliographiccitation.volume","112"],["dc.contributor.author","Machtens, Jan-Philipp"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Alleva, Claudia"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Fahlke, Christoph"],["dc.date.accessioned","2021-03-05T08:58:02Z"],["dc.date.available","2021-03-05T08:58:02Z"],["dc.date.issued","2017"],["dc.identifier.doi","10.1016/j.bpj.2017.02.016"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79978"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Gating Charge Calculations by Computational Electrophysiology Simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Frontiers in Physiology"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Aponte-Santamaría, Camilo"],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:59:16Z"],["dc.date.available","2021-03-05T08:59:16Z"],["dc.date.issued","2017"],["dc.identifier.doi","10.3389/fphys.2017.00124"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80416"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1664-042X"],["dc.title","Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","12390"],["dc.bibliographiccitation.issue","40"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences of the United States of America"],["dc.bibliographiccitation.lastpage","12395"],["dc.bibliographiccitation.volume","112"],["dc.contributor.author","Linser, Rasmus"],["dc.contributor.author","Salvi, Nicola"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Rovó, Petra"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Wagner, Gerhard"],["dc.date.accessioned","2021-03-05T08:58:46Z"],["dc.date.available","2021-03-05T08:58:46Z"],["dc.date.issued","2015"],["dc.identifier.doi","10.1073/pnas.1513782112"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80239"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.title","The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1540"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Structure"],["dc.bibliographiccitation.lastpage","1549"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Zachariae, Ulrich"],["dc.contributor.author","Schneider, Robert"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Gattin, Zrinka"],["dc.contributor.author","Demers, Jean-Philippe"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Maier, Elke"],["dc.contributor.author","Zweckstetter, Markus"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Benz, Roland"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Lange, Adam"],["dc.date.accessioned","2017-09-07T11:48:25Z"],["dc.date.available","2017-09-07T11:48:25Z"],["dc.date.issued","2012"],["dc.description.abstract","The voltage-dependent anion channel (VDAC) is the major protein in the outer mitochondrial membrane, where it mediates transport of ATP and ADP. Changes in its permeability, induced by voltage or apoptosis-related proteins, have been implicated in apoptotic pathways. The three-dimensional structure of VDAC has recently been determined as a 19-stranded beta-barrel with an in-lying N-terminal helix. However, its gating mechanism is still unclear. Using solid-state NMR spectroscopy, molecular dynamics simulations, and electrophysiology, we show that deletion of the rigid N-terminal helix sharply increases overall motion in VDAC's beta-barrel, resulting in elliptic, semicollapsed barrel shapes. These states quantitatively reproduce conductance and selectivity of the closed VDAC conformation. Mutation of the N-terminal helix leads to a phenotype intermediate to the open and closed states. These data suggest that the N-terminal helix controls entry into elliptic beta-barrel states which underlie VDAC closure. Our results also indicate that beta-barrel channels are intrinsically flexible."],["dc.identifier.doi","10.1016/j.str.2012.06.015"],["dc.identifier.gro","3142466"],["dc.identifier.isi","000308682700013"],["dc.identifier.pmid","22841291"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/8596"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Cell Press"],["dc.relation.eissn","1878-4186"],["dc.relation.issn","0969-2126"],["dc.title","beta-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1223"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","1234"],["dc.bibliographiccitation.volume","111"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Weichbrodt, Conrad"],["dc.contributor.author","Paltrinieri, Licia"],["dc.contributor.author","Mey, Ingo"],["dc.contributor.author","Villinger, Saskia"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Lange, Adam"],["dc.contributor.author","Zweckstetter, Markus"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Steinem, Claudia"],["dc.contributor.author","De Groot, Bert L."],["dc.date.accessioned","2017-09-07T11:44:37Z"],["dc.date.available","2017-09-07T11:44:37Z"],["dc.date.issued","2016"],["dc.description.abstract","The voltage-dependent anion channel 1 (VDAC-1) is an important protein of the outer mitochondria! membrane that transports energy metabolites and is involved in apoptosis. The available structures of VDAC proteins show a wide beta-stranded barrel pore, with its N-terminal alpha-helix (N-alpha) bound to its interior. Electrophysiology experiments revealed that voltage, its polarity, and membrane composition modulate VDAC currents. Experiments with VDAC-1 mutants identified amino acids that regulate the gating process. However, the mechanisms for how these factors regulate VDAC-1, and which changes they trigger in the channel, are still unknown. In this study, molecular dynamics simulations and single-channel experiments of VDAC-1 show agreement for the current-voltage relationships of an \"open\" channel and they also show several subconducting transient states that are more cation selective in the simulations. We observed voltage-dependent asymmetric distortions of the VDAC-1 barrel and the displacement of particular charged amino acids. We constructed conformational models of the protein voltage response and the pore changes that consistently explain the protein conformations observed at opposite voltage polarities, either in phosphatidylethanolamine or phosphatidylcholine membranes. The submicrosecond VDAC-1 voltage response shows intrinsic structural changes that explain the role of key gating amino acids and support some of the current gating hypotheses. These voltage-dependent protein changes include asymmetric barrel distortion, its interaction with the membrane, and significant displacement of N-alpha amino acids."],["dc.identifier.doi","10.1016/j.bpj.2016.08.007"],["dc.identifier.gro","3141619"],["dc.identifier.isi","000383925700015"],["dc.identifier.pmid","27653481"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13769"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1900"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1542-0086"],["dc.relation.issn","0006-3495"],["dc.rights","CC BY-NC-ND 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc-nd/4.0"],["dc.title","Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","9887"],["dc.bibliographiccitation.issue","25"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences of the United States of America"],["dc.bibliographiccitation.lastpage","9892"],["dc.bibliographiccitation.volume","109"],["dc.contributor.author","Aponte-Santamaria, C."],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Schenk, A. D."],["dc.contributor.author","Walz, T."],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:58:45Z"],["dc.date.available","2021-03-05T08:58:45Z"],["dc.date.issued","2012"],["dc.identifier.doi","10.1073/pnas.1121054109"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80236"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.title","Molecular driving forces defining lipid positions around aquaporin-0"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","22546"],["dc.bibliographiccitation.issue","52"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","22551"],["dc.bibliographiccitation.volume","107"],["dc.contributor.author","Villinger, Saskia"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Zachariae, Ulrich"],["dc.contributor.author","Lange, Adam"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Zweckstetter, Markus"],["dc.date.accessioned","2017-09-07T11:45:10Z"],["dc.date.available","2017-09-07T11:45:10Z"],["dc.date.issued","2010"],["dc.description.abstract","The voltage-dependent anion channel (VDAC), located in the outer mitochondrial membrane, acts as a gatekeeper for the entry and exit of mitochondrial metabolites. Here we reveal functional dynamics of isoform one of VDAC (VDAC1) by a combination of solution NMR spectroscopy, Gaussian network model analysis, and molecular dynamics simulation. Micro-to millisecond dynamics are significantly increased for the N-terminal six beta-strands of VDAC1 in micellar solution, in agreement with increased B-factors observed in the same region in the bicellar crystal structure of VDAC1. Molecular dynamics simulations reveal that a charge on the membrane-facing glutamic acid 73 (E73) accounts for the elevation of N-terminal protein dynamics as well as a thinning of the nearby membrane. Mutation or chemical modification of E73 strongly reduces the micro-to millisecond dynamics in solution. Because E73 is necessary for hexokinase-I-induced VDAC channel closure and inhibition of apoptosis, our results imply that micro- to millisecond dynamics in the N-terminal part of the barrel are essential for VDAC interaction and gating."],["dc.identifier.doi","10.1073/pnas.1012310108"],["dc.identifier.gro","3142815"],["dc.identifier.isi","000285684200039"],["dc.identifier.pmid","21148773"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/261"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Natl Acad Sciences"],["dc.relation.issn","0027-8424"],["dc.title","Functional dynamics in the voltage-dependent anion channel"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","11"],["dc.bibliographiccitation.volume","116"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Aponte-Santamaría, Camilo"],["dc.date.accessioned","2021-03-05T08:58:03Z"],["dc.date.available","2021-03-05T08:58:03Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1016/j.bpj.2018.11.3126"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79991"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","786"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","796"],["dc.bibliographiccitation.volume","103"],["dc.contributor.author","Krivobokova, Tatyana"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Munk, Axel"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:48:27Z"],["dc.date.available","2017-09-07T11:48:27Z"],["dc.date.issued","2012"],["dc.description.abstract","We introduce an approach based on the recently introduced functional mode analysis to identify collective modes of internal dynamics that maximally correlate to an external order parameter of functional interest. Input structural data can be either experimentally determined structure ensembles or simulated ensembles, such as molecular dynamics trajectories. Partial least-squares regression is shown to yield a robust solution to the multidimensional optimization problem, with a minimal and controllable risk of overfitting, as shown by extensive cross-validation. Several examples illustrate that the partial least-squares-based functional mode analysis successfully reveals the collective dynamics underlying the fluctuations in selected functional order parameters. Applications to T4 lysozyme, the Trp-cage, the aquaporin channels Aqy1 and hAQP1, and the CLC-ec1 chloride antiporter are presented in which the active site geometry, the hydrophobic solvent-accessible surface, channel gating dynamics, water permeability (p(f)), and a dihedral angle are defined as functional order parameters. The Aqy1 case reveals a gating mechanism that connects the inner channel gating residues with the protein surface, thereby providing an explanation of how the membrane may affect the channel. hAQP1 shows how the p(f) correlates with structural changes around the aromatic/arginine region of the pore. The CLC-ec1 application shows how local motions of the gating Glu(148) couple to a collective motion that affects ion affinity in the pore."],["dc.identifier.doi","10.1016/j.bpj.2012.07.022"],["dc.identifier.gro","3142477"],["dc.identifier.isi","000307799100018"],["dc.identifier.pmid","22947940"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/10646"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/8718"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0006-3495"],["dc.relation.orgunit","Fakultät für Mathematik und Informatik"],["dc.rights","CC BY-NC 2.0"],["dc.rights.uri","http://creativecommons.org/licenses/by-nc/2.0/"],["dc.title","Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","845"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Journal of Computer-Aided Molecular Design"],["dc.bibliographiccitation.lastpage","858"],["dc.bibliographiccitation.volume","27"],["dc.contributor.author","Gapsys, Vytautas"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Briones, Rodolfo"],["dc.date.accessioned","2021-03-05T09:05:21Z"],["dc.date.available","2021-03-05T09:05:21Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1007/s10822-013-9684-0"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80446"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1573-4951"],["dc.relation.issn","0920-654X"],["dc.title","Computational analysis of local membrane properties"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]