Grubmüller, Helmut

[["dc.bibliographiccitation.firstpage","258a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Schroeder, Gunnar F."],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-03-01T11:44:56Z"],["dc.date.available","2022-03-01T11:44:56Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.1447"],["dc.identifier.pii","S0006349512026938"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103165"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","0006-3495"],["dc.title","Modulation of Intersubunit Interactions during tRNA Translocation through the Ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","171a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Volkhardt, Andreas"],["dc.contributor.author","Meyer, Tim"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:56Z"],["dc.date.available","2021-03-05T08:57:56Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.963"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79936"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Exploring Protein Energy Landscapes with Time-Dependent Principal Component Analysis"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","133"],["dc.bibliographiccitation.issue","3-4"],["dc.bibliographiccitation.journal","Molecular Simulation"],["dc.bibliographiccitation.lastpage","165"],["dc.bibliographiccitation.volume","5"],["dc.contributor.author","Heller, H."],["dc.contributor.author","Grubmüller, H."],["dc.contributor.author","Schulten, K."],["dc.date.accessioned","2018-04-23T11:47:56Z"],["dc.date.available","2018-04-23T11:47:56Z"],["dc.date.issued","1990"],["dc.description.abstract","For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer with a systolic loop architecture, based on Transputers as computational units, and have programmed it in occam II. The computational nodes of the computer are linked together in a systolic ring. The program based on this topology for large biopolymers increases its computational throughput nearly linearly with the number of computational nodes. The program developed is closely related to the simulation programs CHARMM and XPLOR, the input files required (force field, protein structure file, coordinates) and output files generated (sets of atomic coordinates representing dynamic trajectories and energies) are compatible with the corresponding files of these programs. Benchmark results of simulations of biopolymers comprising 66, 568, 3 634, 5 797 and 12 637 atoms are compared with XPLOR simulations on conventional computers (Cray, Convex, Vax). These results demonstrate that the software and hardware developed provide extremely cost effective biopolymer simulations. We present also a simulation (equilibrium of X-ray structure) of the complete photosynthetic reaction center of Rhodopseudomonas viridis (12 637 atoms). The simulation accounts for the Coulomb forces exactly, i.e. no cut-off had been assumed."],["dc.identifier.doi","10.1080/08927029008022127"],["dc.identifier.gro","3142310"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13442"],["dc.language.iso","en"],["dc.notes.intern","lifescience updates Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","0892-7022"],["dc.title","Molecular Dynamics Simulation on a Parallel Computer"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","960"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","965"],["dc.bibliographiccitation.volume","110"],["dc.contributor.author","Monecke, Thomas"],["dc.contributor.author","Haselbach, David"],["dc.contributor.author","Voss, Bela"],["dc.contributor.author","Russek, Andreas"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Thomson, Emma"],["dc.contributor.author","Hurt, Ed"],["dc.contributor.author","Zachariae, Ulrich"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Dickmanns, Achim"],["dc.contributor.author","Ficner, Ralf"],["dc.date.accessioned","2017-09-07T11:48:18Z"],["dc.date.available","2017-09-07T11:48:18Z"],["dc.date.issued","2013"],["dc.description.abstract","In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-beta superfamily termed importins and exportins. The highly versatile exportin chromosome region maintenance 1 (CRM1) is essential for nuclear depletion of numerous structurally and functionally unrelated protein and ribonucleoprotein cargoes. CRM1 has been shown to adopt a toroidal structure in several functional transport complexes and was thought to maintain this conformation throughout the entire nucleocytoplasmic transport cycle. We solved crystal structures of free CRM1 from the thermophilic eukaryote Chaetomium thermophilum. Surprisingly, unbound CRM1 exhibits an overall extended and pitched superhelical conformation. The two regulatory regions, namely the acidic loop and the C-terminal a-helix, are dramatically repositioned in free CRM1 in comparison with the ternary CRM1-Ran-Snurportin1 export complex. Single-particle EM analysis demonstrates that, in a noncrystalline environment, free CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations. Molecular dynamics simulations show that the C-terminal helix plays an important role in regulating the transition from an extended to a compact conformation and reveal how the binding site for nuclear export signals of cargoes is modulated by different CRM1 conformations. Combining these results, we propose a model for the cooperativity of CRM1 export complex assembly involving the long-range allosteric communication between the distant binding sites of GTP-bound Ran and cargo."],["dc.identifier.doi","10.1073/pnas.1215214110"],["dc.identifier.gro","3142406"],["dc.identifier.isi","000313909100042"],["dc.identifier.pmid","23277578"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/7930"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0027-8424"],["dc.title","Structural basis for cooperativity of CRM1 export complex formation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","415a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Herrmann, Andreas"],["dc.contributor.author","Sieben, Christian"],["dc.contributor.author","Kappel, Christian"],["dc.contributor.author","Zhu, Rong"],["dc.contributor.author","Rankl, Christian"],["dc.contributor.author","Wozniak, Anna"],["dc.contributor.author","Hinterdorfer, Peter"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:52:30Z"],["dc.date.available","2017-09-07T11:52:30Z"],["dc.date.issued","2013"],["dc.description.abstract","Influenza virus belongs to a wide range of enveloped viruses. The major spike protein hemagglutinin binds sialic acid residues of glycoproteins and glycolipids with dissociation constants in the millimolar range [Sauter NK, et al. (1992) Biochemistry 31:9609–9621], indicating a multivalent binding mode. Here, we characterized the attachment of influenza virus to host cell receptors using three independent approaches. Optical tweezers and atomic force microscopy-based single-molecule force spectroscopy revealed very low interaction forces. Further, the observation of sequential unbinding events strongly suggests a multivalent binding mode between virus and cell membrane. Molecular dynamics simulations reveal a variety of unbinding pathways that indicate a highly dynamic interaction between HA and its receptor, allowing rationalization of influenza virus–cell binding quantitatively at the molecular level."],["dc.identifier.doi","10.1016/j.bpj.2012.11.2312"],["dc.identifier.gro","3144941"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2620"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","0006-3495"],["dc.title","Influenza Virus Binds its Host Cell using Multiple Dynamic Interactions Revealed by Single Virus Force Spectroscopy and Force Probe Molecular Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","1709"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-05-02T08:02:06Z"],["dc.date.available","2022-05-02T08:02:06Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft"],["dc.identifier.doi","10.1038/s41467-022-29332-2"],["dc.identifier.pii","29332"],["dc.identifier.pmid","35361752"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/107232"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/503"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-561"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","2041-1723"],["dc.relation.workinggroup","RG Grubmüller"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Effects of cryo-EM cooling on structural ensembles"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","acs.jcim.2c00044"],["dc.bibliographiccitation.journal","Journal of Chemical Information and Modeling"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Kniep, Christian"],["dc.contributor.author","Cherian, Austin"],["dc.contributor.author","Nordstrom, Ludvig"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Gapsys, Vytautas"],["dc.date.accessioned","2022-04-01T10:01:40Z"],["dc.date.available","2022-04-01T10:01:40Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1021/acs.jcim.2c00044"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/105722"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation.eissn","1549-960X"],["dc.relation.issn","1549-9596"],["dc.title","GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","234a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","110"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Arenz, Stefan"],["dc.contributor.author","Wilson, Daniel N."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Vaiana, Andrea C."],["dc.date.accessioned","2021-03-05T08:57:59Z"],["dc.date.available","2021-03-05T08:57:59Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1016/j.bpj.2015.11.1291"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79959"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","ErmBL Translation on the Ribosome in the Presence of Erythromycin is Stalled by Inhibition of Peptide Bond Formation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","666a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Buelens, Floris"],["dc.contributor.author","Grininger, Martin"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:55Z"],["dc.date.available","2021-03-05T08:57:55Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.3675"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79934"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Reaction Control in Fungal Fatty Acid Synthase"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2583"],["dc.bibliographiccitation.issue","15"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","2585"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Kumar, Rajendra"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2018-02-09T08:03:14Z"],["dc.date.available","2018-02-09T08:03:14Z"],["dc.date.issued","2015-08-01"],["dc.description.abstract","The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize statistical analyses of complex data obtained from the trajectories."],["dc.identifier.doi","10.1093/bioinformatics/btv190"],["dc.identifier.pmid","25838463"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12082"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1367-4811"],["dc.title","do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]