Hub, Jochen S.

[["dc.bibliographiccitation.firstpage","e1000480"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","PLoS Computational Biology"],["dc.bibliographiccitation.volume","5"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.editor","Nussinov, Ruth"],["dc.date.accessioned","2021-03-05T08:59:11Z"],["dc.date.available","2021-03-05T08:59:11Z"],["dc.date.issued","2009"],["dc.identifier.doi","10.1371/journal.pcbi.1000480"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80388"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1553-7358"],["dc.title","Detection of Functional Modes in Protein Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","10246"],["dc.bibliographiccitation.issue","35"],["dc.bibliographiccitation.journal","Physical Chemistry, Chemical Physics"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Aponte-Santamaría, Camilo"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:58:34Z"],["dc.date.available","2021-03-05T08:58:34Z"],["dc.date.issued","2010"],["dc.identifier.doi","10.1039/c004384m"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80185"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1463-9084"],["dc.relation.issn","1463-9076"],["dc.title","Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","8364"],["dc.bibliographiccitation.issue","25"],["dc.bibliographiccitation.journal","The Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical"],["dc.bibliographiccitation.lastpage","8366"],["dc.bibliographiccitation.volume","115"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:58:25Z"],["dc.date.available","2021-03-05T08:58:25Z"],["dc.date.issued","2011"],["dc.identifier.doi","10.1021/jp2022242"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80129"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1520-5207"],["dc.relation.issn","1520-6106"],["dc.title","Comment on “Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory”"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","455"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Computer Physics Communications"],["dc.bibliographiccitation.lastpage","458"],["dc.bibliographiccitation.volume","180"],["dc.contributor.author","Reinhard, F."],["dc.contributor.author","Lange, O. F."],["dc.contributor.author","Hub, J. S."],["dc.contributor.author","Haas, J."],["dc.contributor.author","Grubmüller, H."],["dc.date.accessioned","2018-02-13T12:25:56Z"],["dc.date.available","2018-02-13T12:25:56Z"],["dc.date.issued","2009"],["dc.description.abstract","Biomolecular processes are governed by free energy changes and thus depend on a fine-tuned interplay between entropy and enthalpy. To calculate accurate values for entropies from simulations is particularly challenging for the solvation shell of proteins, which contributes crucially to the total entropy of solvated proteins, due to the diffusive motion of the solvent molecules. Accordingly, for each frame of a Molecular dynamics (MD) trajectory, our software relabels the solvent molecules, such that the resulting configuration space volume is reduced by a factor of N! with N being the number of solvent molecules. The combinatorial explosion of a naive implementation is here overcome by transforming the task into a linear assignment problem, for which algorithms with complexity exist. We have shown in previous research that the solvent entropy can be estimated from such a compacted trajectory by established entropy estimation methods. In this paper, we describe the software implementation which also allows applications beyond entropy estimation, such as the permutation of lipids in membrane bilayers."],["dc.identifier.doi","10.1016/j.cpc.2008.10.018"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12222"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.issn","0010-4655"],["dc.title","g_permute: Permutation-reduced phase space density compaction"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","663"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Pflügers Archiv European Journal of Physiology"],["dc.bibliographiccitation.lastpage","669"],["dc.bibliographiccitation.volume","456"],["dc.contributor.author","Mueller, E. Matthias"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:48:16Z"],["dc.date.available","2017-09-07T11:48:16Z"],["dc.date.issued","2008"],["dc.description.abstract","Excessive water uptake through aquaporins can be life threatening, and disregulation of water permeability causes many diseases. Therefore, reversible aquaporin inhibitors are highly desired. In this paper, we identified the binding site for tetraethylammonium (TEA) of the membrane water channel aquaporin-1 by a combined molecular docking and molecular dynamics simulation approach. The binding site identified from docking studies was independently confirmed with an unbiased molecular dynamics simulation of an aquaporin tetramer embedded in a lipid membrane, surrounded by a 100-mM tetraethylammonium solution in water. A third independent assessment of the binding site was obtained by umbrella sampling simulations. These simulations, in addition, revealed a binding affinity of more than 17kJ/mol, corresponding to an IC50 value of << 3mM. Finally, we observed in our simulations a 50% reduction of the water flux in the presence of TEA, in agreement with water permeability measurements on aquaporin expressed in oocytes. These results confirm TEA as a putative lead for an aquaporin-1 inhibitor."],["dc.identifier.doi","10.1007/s00424-007-0422-0"],["dc.identifier.gro","3143275"],["dc.identifier.isi","000255866800003"],["dc.identifier.pmid","18196268"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/771"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1432-2013"],["dc.relation.issn","0031-6768"],["dc.title","Is TEA an inhibitor for human aquaporin-1?"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","104108"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","The Journal of Chemical Physics"],["dc.bibliographiccitation.volume","143"],["dc.contributor.author","Brinkmann, Levin U. L."],["dc.contributor.author","Hub, Jochen S."],["dc.date.accessioned","2018-11-07T09:51:40Z"],["dc.date.available","2018-11-07T09:51:40Z"],["dc.date.issued","2015"],["dc.description.abstract","Time-resolved wide-angle X-ray scattering (TR-WAXS) is an emerging experimental technique used to track chemical reactions and conformational transitions of proteins in real time. Thanks to increased time resolution of the method, anisotropic TR-WAXS patterns were recently reported, which contain more structural information than isotropic patterns. So far, however, no method has been available to compute anisotropic WAXS patterns of biomolecules, thus limiting the structural interpretation. Here, we present a method to compute anisotropic TR-WAXS patterns from molecular dynamics simulations. The calculations accurately account for scattering of the hydration layer and for thermal fluctuations. For many photo-excitable proteins, given a low intensity of the excitation laser, the anisotropic pattern is described by two independent components: (i) an isotropic component, corresponding to common isotropic WAXS experiments and (ii) an anisotropic component depending on the orientation of the excitation dipole of the solute. We present a set of relations for the calculation of these two components from experimental scattering patterns. Notably, the isotropic component is not obtained by a uniform azimuthal average on the detector. The calculations are illustrated and validated by computing anisotropic WAXS patterns of a spheroidal protein model and of photoactive yellow protein. Effects due to saturated excitation at high intensities of the excitation laser are discussed, including opportunities to extract additional structural information by modulating the laser intensity. (C) 2015 AIP Publishing LLC."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [HU 1971/1-1]"],["dc.identifier.doi","10.1063/1.4930013"],["dc.identifier.isi","000361572900031"],["dc.identifier.pmid","26374019"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35960"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Inst Physics"],["dc.relation.issn","1089-7690"],["dc.relation.issn","0021-9606"],["dc.title","Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","566a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","98"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Van der Spoel, David"],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:57:49Z"],["dc.date.available","2021-03-05T08:57:49Z"],["dc.date.issued","2010"],["dc.identifier.doi","10.1016/j.bpj.2009.12.3071"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79898"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Detection of Functional Modes in Protein Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4799"],["dc.bibliographiccitation.issue","23"],["dc.bibliographiccitation.journal","The Journal of Physical Chemistry Letters"],["dc.bibliographiccitation.lastpage","4803"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Diaz-Tejada, Celsa"],["dc.contributor.author","Ariz-Extreme, Igor"],["dc.contributor.author","Awasthi, Neha"],["dc.contributor.author","Hub, Jochen S."],["dc.date.accessioned","2018-11-07T09:47:50Z"],["dc.date.available","2018-11-07T09:47:50Z"],["dc.date.issued","2015"],["dc.description.abstract","Lateral inhomogeneity plays a critical role for many properties of cholesterol-containing membranes, yet the thermodynamic forces involved in inhomogeneity remain poorly understood. Based on coarse-grained simulations of cholesterol in four increasingly unsaturated phospholipids, we computed lateral density fluctuations and free energies of domain formation, and we quantitatively relate those to variations in the chemical potential of cholesterol. Our simulations suggest that the lateral organization is dominated by weak repulsive cholesterol interactions, leading to a significantly more homogeneous distribution as compared to a two-dimensional ideal gas. Hence, phospholipids provide a \"good\" solvent for cholesterol. Unexpectedly, the degree of unsaturation of the phospholipid has only a minor effect on the lateral inhomogeneity of cholesterol in binary lipid mixtures. These results provide a link between functional properties and thermal fluctuations in lipid membranes."],["dc.identifier.doi","10.1021/acs.jpclett.5b02414"],["dc.identifier.isi","000366008500021"],["dc.identifier.pmid","26575955"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35181"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Chemical Soc"],["dc.relation.issn","1948-7185"],["dc.title","Quantifying Lateral lnhomogeneity of Cholesterol-Containing Membranes"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Scientific Reports"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Anselmi, Massimiliano"],["dc.contributor.author","Hub, Jochen S."],["dc.date.accessioned","2021-04-14T08:31:46Z"],["dc.date.available","2021-04-14T08:31:46Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1038/s41598-020-75409-7"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83709"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","2045-2322"],["dc.title","An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5635"],["dc.bibliographiccitation.issue","20"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","5639"],["dc.bibliographiccitation.volume","57"],["dc.contributor.author","Ivanović, Miloš T."],["dc.contributor.author","Bruetzel, Linda K."],["dc.contributor.author","Lipfert, Jan"],["dc.contributor.author","Hub, Jochen S."],["dc.date.accessioned","2020-12-10T14:05:30Z"],["dc.date.available","2020-12-10T14:05:30Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1002/anie.201713303"],["dc.identifier.issn","1433-7851"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/69562"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Temperature-Dependent Atomic Models of Detergent Micelles Refined against Small-Angle X-Ray Scattering Data"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]