Schulten, Klaus

[["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","443"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Journal of Structural Biology"],["dc.bibliographiccitation.lastpage","443"],["dc.bibliographiccitation.volume","157"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Schulten, Klaus"],["dc.date.accessioned","2018-04-19T07:15:19Z"],["dc.date.available","2018-04-19T07:15:19Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1016/j.jsb.2007.02.002"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13239"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.title","Editorial: Special issue: Advances in molecular dynamics simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","editorial_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","121"],["dc.bibliographiccitation.issue","1-3"],["dc.bibliographiccitation.journal","Molecular Simulation"],["dc.bibliographiccitation.lastpage","142"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Grubmüller, H."],["dc.contributor.author","Heller, H."],["dc.contributor.author","Windemuth, A."],["dc.contributor.author","Schulten, K."],["dc.date.accessioned","2018-04-23T11:47:55Z"],["dc.date.available","2018-04-23T11:47:55Z"],["dc.date.issued","1991"],["dc.description.abstract","For the purpose of molecular dynamics simulations of large biopolymers we have developed a new method to accelerate the calculation of long-range pair interactions (e.g. Coulomb interaction). The algorithm introduces distance classes to schedule updates of non-bonding interactions and to avoid unnecessary computations of interactions between particles which are far apart. To minimize the error caused by the updating schedule, the Verlet integration scheme has been modified. The results of the method are compared to those of other approximation schemes as well as to results obtained by numerical integration without approximation. For simulation of a protein with 12 637 atoms our approximation scheme yields a reduction of computer time by a factor of seven. The approximation suggested can be implemented on sequential as well as on parallel computers. We describe an implementation on a (Transputer-based) MIMD machine with a systolic ring architecture."],["dc.identifier.doi","10.1080/08927029108022142"],["dc.identifier.gro","3142309"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13441"],["dc.language.iso","en"],["dc.notes.intern","lifescience updates Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","0892-7022"],["dc.title","Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","7816"],["dc.bibliographiccitation.issue","28"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","7821"],["dc.bibliographiccitation.volume","113"],["dc.contributor.author","Schweitzer, Andreas"],["dc.contributor.author","Aufderheide, Antje"],["dc.contributor.author","Rudack, Till"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Pfeifer, Günter"],["dc.contributor.author","Plitzko, Jürgen M."],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Schulten, Klaus"],["dc.contributor.author","Förster, Friedrich"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.date.accessioned","2022-03-01T11:46:23Z"],["dc.date.available","2022-03-01T11:46:23Z"],["dc.date.issued","2016"],["dc.description.abstract","Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing."],["dc.description.abstract","Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing."],["dc.identifier.doi","10.1073/pnas.1608050113"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103654"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.rights.uri","http://www.pnas.org/preview_site/misc/userlicense.xhtml"],["dc.title","Structure of the human 26S proteasome at a resolution of 3.9 Å"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","255"],["dc.bibliographiccitation.lastpage","280"],["dc.contributor.author","Changeux, J.-P."],["dc.contributor.author","Moffat, K."],["dc.contributor.author","Grubmüller, H."],["dc.contributor.author","Crothers, D. M."],["dc.contributor.author","Palma, M. U."],["dc.contributor.author","Nienhaus, G. U."],["dc.contributor.author","Schulten, K."],["dc.contributor.author","Parak, F. G."],["dc.contributor.author","Warshel, A."],["dc.contributor.editor","Deisenhofer, J."],["dc.contributor.editor","Frauenfelder, H."],["dc.contributor.editor","Wolynes, P."],["dc.date.accessioned","2018-04-23T17:02:31Z"],["dc.date.available","2018-04-23T17:02:31Z"],["dc.date.issued","1999"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13756"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.publisher","Dahlem University Press"],["dc.publisher.place","Berlin"],["dc.relation.crisseries","Dahlem Workshop Reports"],["dc.relation.ispartof","Simplicity and Complexity in Proteins and Nucleic Acids"],["dc.relation.ispartofseries","Dahlem Workshop Reports"],["dc.title","How does complexity lead to apparently simple function?"],["dc.type","book_chapter"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","eLife"],["dc.bibliographiccitation.volume","3"],["dc.contributor.author","Wickles, Stephan"],["dc.contributor.author","Singharoy, Abhishek"],["dc.contributor.author","Andreani, Jessica"],["dc.contributor.author","Seemayer, Stefan"],["dc.contributor.author","Bischoff, Lukas"],["dc.contributor.author","Berninghausen, Otto"],["dc.contributor.author","Soeding, Johannes"],["dc.contributor.author","Schulten, Klaus"],["dc.contributor.author","van der Sluis, Eli O"],["dc.contributor.author","Beckmann, Roland"],["dc.date.accessioned","2022-03-01T11:44:31Z"],["dc.date.available","2022-03-01T11:44:31Z"],["dc.date.issued","2014"],["dc.description.abstract","The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion."],["dc.description.abstract","Cells are surrounded by a plasma membrane that acts like a barrier to help to keep the cell intact. Proteins are embedded in this plasma membrane; and some of these membrane proteins act as channels that allow molecules to enter and leave the cell, while others allow the cell to communicate with its surroundings. Like all proteins, membrane proteins are chains of amino acids that are joined together by a molecular machine called a ribosome. Most membrane proteins are inserted into the membrane as they are being built. All bacteria contain a protein called YidC that inserts proteins into the plasma membrane of bacterial cells. However, the mechanism behind this activity and the parts of the YidC protein that interact with the ribosome and plasma membrane are unknown. Wickles et al. have now used data from a range of sources to predict the three-dimensional structure of the YidC protein taken from a bacterium called E. coli. The model shows how the YidC protein is threaded back-and-forth through the membrane, a total of five times. Some of the protein also extends into the inside of the bacterial cell. Wickles et al. then used a technique called cyro-electron microscopy to look at the structure of a YidC protein bound to a ribosome that is building a new protein. Fitting the more detailed model of YidC into this overall structure of the whole complex revealed how a single YidC protein might interact with the ribosome to insert a newly built protein into a membrane. Wickles et al. then used a combination of theoretical modeling and other experiments to identify the amino acids in the YidC protein that bind to the ribosome: as expected, the binding takes place where the newly formed protein chain exits the ribosome. Further experiments also identified the amino acids in the YidC protein that interact with the newly built membrane protein, thus revealing where it might leave the YidC protein and be inserted into the membrane. The next challenge will be to investigate how the YidC protein assists the folding of new membrane proteins into their own highly specific three-dimensional structure."],["dc.description.abstract","The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion."],["dc.description.abstract","Cells are surrounded by a plasma membrane that acts like a barrier to help to keep the cell intact. Proteins are embedded in this plasma membrane; and some of these membrane proteins act as channels that allow molecules to enter and leave the cell, while others allow the cell to communicate with its surroundings. Like all proteins, membrane proteins are chains of amino acids that are joined together by a molecular machine called a ribosome. Most membrane proteins are inserted into the membrane as they are being built. All bacteria contain a protein called YidC that inserts proteins into the plasma membrane of bacterial cells. However, the mechanism behind this activity and the parts of the YidC protein that interact with the ribosome and plasma membrane are unknown. Wickles et al. have now used data from a range of sources to predict the three-dimensional structure of the YidC protein taken from a bacterium called E. coli. The model shows how the YidC protein is threaded back-and-forth through the membrane, a total of five times. Some of the protein also extends into the inside of the bacterial cell. Wickles et al. then used a technique called cyro-electron microscopy to look at the structure of a YidC protein bound to a ribosome that is building a new protein. Fitting the more detailed model of YidC into this overall structure of the whole complex revealed how a single YidC protein might interact with the ribosome to insert a newly built protein into a membrane. Wickles et al. then used a combination of theoretical modeling and other experiments to identify the amino acids in the YidC protein that bind to the ribosome: as expected, the binding takes place where the newly formed protein chain exits the ribosome. Further experiments also identified the amino acids in the YidC protein that interact with the newly built membrane protein, thus revealing where it might leave the YidC protein and be inserted into the membrane. The next challenge will be to investigate how the YidC protein assists the folding of new membrane proteins into their own highly specific three-dimensional structure."],["dc.identifier.doi","10.7554/eLife.03035"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103043"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","2050-084X"],["dc.rights.uri","http://creativecommons.org/licenses/by/4.0/"],["dc.title","A structural model of the active ribosome-bound membrane protein insertase YidC"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1305"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","1310"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Wehmer, Marc"],["dc.contributor.author","Rudack, Till"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Aufderheide, Antje"],["dc.contributor.author","Pfeifer, Günter"],["dc.contributor.author","Plitzko, Jürgen M."],["dc.contributor.author","Förster, Friedrich"],["dc.contributor.author","Schulten, Klaus"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Sakata, Eri"],["dc.date.accessioned","2022-03-01T11:46:24Z"],["dc.date.available","2022-03-01T11:46:24Z"],["dc.date.issued","2017"],["dc.description.abstract","In eukaryotic cells, the ubiquitin–proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA + ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA + ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis."],["dc.description.abstract","In eukaryotic cells, the ubiquitin–proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA + ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA + ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis."],["dc.identifier.doi","10.1073/pnas.1621129114"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103655"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.rights.uri","http://www.pnas.org/site/misc/userlicense.xhtml"],["dc.title","Structural insights into the functional cycle of the ATPase module of the 26S proteasome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","48"],["dc.bibliographiccitation.journal","MC: Die Microcomputer-Zeitschrift"],["dc.bibliographiccitation.lastpage","65"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Heller, H."],["dc.contributor.author","Grubmüller, H."],["dc.contributor.author","Schulten, K."],["dc.date.accessioned","2018-04-29T14:04:44Z"],["dc.date.available","2018-04-29T14:04:44Z"],["dc.date.issued","1988"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13789"],["dc.language.iso","de"],["dc.notes.status","final"],["dc.title","Eine CRAY für 'jedermann'"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","83"],["dc.bibliographiccitation.lastpage","94"],["dc.contributor.author","Heller, H."],["dc.contributor.author","Boehncke, K."],["dc.contributor.author","Grubmüller, H."],["dc.contributor.author","Schulten, K."],["dc.contributor.editor","Wagner, Alan S."],["dc.date.accessioned","2018-04-29T14:00:56Z"],["dc.date.available","2018-04-29T14:00:56Z"],["dc.date.issued","1990"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13788"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.publisher","North American Transputer Users Group, IOS Press"],["dc.publisher.place","Van Diemenstraat 94, 1013 CN Amsterdam, The Netherlands"],["dc.relation.ispartof","Transputer research and applications"],["dc.title","Molecular dynamics simulations on a systolic ring of transputers"],["dc.type","book_chapter"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]