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.artnumber","e0196751"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","PLOS ONE"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Ariz-Extreme, Igor"],["dc.contributor.author","Hub, Jochen S."],["dc.date.accessioned","2019-07-09T11:45:49Z"],["dc.date.available","2019-07-09T11:45:49Z"],["dc.date.issued","2018"],["dc.description.abstract","Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative binding affinities, for instance between an ion and water, (ii) absolute binding free energies, i.e., free energies for transferring a solute from bulk solvent to a binding site, and (iii) stability assessments during equilibrium simulations may reveal the most plausible assignments. We illustrate this strategy using the crystal structure of the fluoride specific channel (Fluc), which contains five disconnected electron densities previously interpreted as four fluoride and one sodium ion. The simulations support the assignment of the sodium ion. In contrast, calculations of relative and absolute binding free energies as well as stability assessments during free MD simulations suggest that four of the densities represent water molecules instead of fluoride. The assignment of water is compatible with the loss of these densities in the non-conductive F82I/F85I mutant of Fluc. We critically discuss the role of the ion force fields for the calculations presented here. Overall, these findings indicate that MD simulations and free energy calculations are helpful tools for modeling water and ions into crystallographic density maps."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2018"],["dc.identifier.doi","10.1371/journal.pone.0196751"],["dc.identifier.pmid","29771936"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15319"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59312"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1932-6203"],["dc.relation.orgunit","Fakultät für Physik"],["dc.rights","CC BY 4.0"],["dc.rights.uri","http://creativecommons.org/licenses/by/4.0/"],["dc.subject.ddc","530"],["dc.subject.mesh","Binding Sites"],["dc.subject.mesh","Crystallography, X-Ray"],["dc.subject.mesh","Databases, Protein"],["dc.subject.mesh","Electrons"],["dc.subject.mesh","Entropy"],["dc.subject.mesh","Fluorides"],["dc.subject.mesh","Ions"],["dc.subject.mesh","Ligands"],["dc.subject.mesh","Molecular Dynamics Simulation"],["dc.subject.mesh","Protein Binding"],["dc.subject.mesh","Proteins"],["dc.subject.mesh","Thermodynamics"],["dc.subject.mesh","Water"],["dc.title","Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","496"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Acta Crystallographica Section D Structural Biology"],["dc.bibliographiccitation.lastpage","509"],["dc.bibliographiccitation.volume","77"],["dc.contributor.affiliation","Hamann, Florian; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Zimmerningkat, Lars C.; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Becker, Robert A.; 3Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany"],["dc.contributor.affiliation","Garbers, Tim B.; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Neumann, Piotr; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Hub, Jochen S.; 3Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany"],["dc.contributor.author","Hamann, Florian"],["dc.contributor.author","Zimmerningkat, Lars C."],["dc.contributor.author","Becker, Robert A."],["dc.contributor.author","Garbers, Tim B."],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Ficner, Ralf"],["dc.date.accessioned","2021-06-01T09:41:58Z"],["dc.date.available","2021-06-01T09:41:58Z"],["dc.date.issued","2021"],["dc.date.updated","2022-02-09T13:20:58Z"],["dc.description.abstract","Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excised via the spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct of Chaetomium thermophilum Prp2 was crystallized in the presence of ADP-BeF 3 − and a poly-U 12 RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF 3 − - and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures."],["dc.identifier.doi","10.1107/S2059798321001194"],["dc.identifier.pmid","33825710"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85096"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/249"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.publisher","International Union of Crystallography"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.issn","2059-7983"],["dc.relation.workinggroup","RG Ficner (Molecular Structural Biology)"],["dc.rights","This is an open access article under the terms of the Creative Commons Attribution License, which permits use,\r\n distribution and reproduction in any medium, provided the original work is properly cited."],["dc.title","The structure of Prp2 bound to RNA and ADP-BeF 3 − reveals structural features important for RNA unwinding by DEAH-box ATPases"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["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"]]