Hub, Jochen S.

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[["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","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.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","381"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Chemical Theory and Computation"],["dc.bibliographiccitation.lastpage","390"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groenhof, Gerrit"],["dc.date.accessioned","2017-09-07T11:46:56Z"],["dc.date.available","2017-09-07T11:46:56Z"],["dc.date.issued","2014"],["dc.description.abstract","Ewald summation, which has become the de facto standard for computing electrostatic interactions in biomolecular simulations, formally requires that the simulation box is neutral. For non-neutral systems, the Ewald algorithm implicitly introduces a uniform background charge distribution that effectively neutralizes the simulation box. Because a uniform distribution of counter charges typically deviates from the spatial distribution of counterions in real systems, artifacts may arise, in particular in systems with an inhomogeneous dielectric constant. Here, we derive an analytical expression for the effect of using an implicit background charge instead of explicit counterions, on the chemical potential of ions in heterogeneous systems, which (i) provides a quantitative criterium for deciding if the background charge offers an acceptable trade-off between artifacts arising from sampling problems and artifacts arising from the homogeneous background charge distribution, and (ii) can be used to correct this artifact in certain cases. Our model quantifies the artifact in terms of the difference in charge density between the non-neutral system with a uniform neutralizing background charge and the real neutral system with a physically correct distribution of explicit counterions. We show that for inhomogeneous systems, such as proteins and membranes in water, the artifact manifests itself by an overstabilization of ions inside the lower dielectric by tens to even hundreds kilojoules per mole. We have tested the accuracy of our model in molecular dynamics simulations and found that the error in the calculated free energy for moving a test charge from water into hexadecane, at different net charges of the system and different simulation box sizes, is correctly predicted by the model. The calculations further confirm that the incorrect distribution of counter charges in the simulation box is solely responsible for the errors in the PMFs."],["dc.identifier.doi","10.1021/ct400626b"],["dc.identifier.gro","3142219"],["dc.identifier.isi","000330142400036"],["dc.identifier.pmid","26579917"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5854"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1549-9626"],["dc.relation.issn","1549-9618"],["dc.title","Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","57"],["dc.bibliographiccitation.lastpage","76"],["dc.bibliographiccitation.seriesnr","190"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.editor","Beitz, E."],["dc.date.accessioned","2017-09-07T11:52:29Z"],["dc.date.available","2017-09-07T11:52:29Z"],["dc.date.issued","2008"],["dc.description.abstract","Aquaporins (AQPs) are a family of integral membrane proteins, which facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Molecular dynamics (MD) simulations contributed substantially to the understanding of the molecular mechanisms that underlie this remarkable efficiency and selectivity of aquaporin channels. This chapter reviews the current state of MD simulations of aquaporins and related aquaglyceroporins as well as the insights these simulations have provided. The mechanism of water permeation through AQPs and methods to determine channel permeabilities from simulations are described. Protons are strictly excluded from AQPs by a large electrostatic barrier and not by an interruption of the Grotthuss mechanism inside the pore. Both the protein's electric field and desolvation effects contribute to this barrier. Permeation of apolar gas molecules such as CO2 through AQPs is accompanied by a large energetic barrier and thus can only be expected in membranes with a low intrinsic gas permeability. Additionally, the insights from simulations into the mechanism of glycerol permeation through the glycerol facilitator GlpF from E. coli are summarized. Finally, MD simulations are discussed that revealed that the aro-matic/arginine constriction region is generally the filter for uncharged solutes, and that AQP selectivity is controlled by a hydrophobic effect and steric restraints."],["dc.identifier.doi","10.1007/978-3-540-79885-9_3"],["dc.identifier.gro","3144943"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2623"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.publisher","Springer Nature"],["dc.publisher.place","Heidelberg"],["dc.relation.crisseries","Handbook of Experimental Pharmacology"],["dc.relation.isbn","978-3-540-79885-9"],["dc.relation.isbn","978-3-540-79884-2"],["dc.relation.ispartof","Aquaporins"],["dc.relation.ispartofseries","Handbook of Experimental Pharmacology; 190"],["dc.relation.issn","0171-2004"],["dc.title","Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations?"],["dc.type","book_chapter"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

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