Ban, David

[["dc.bibliographiccitation.firstpage","10367"],["dc.bibliographiccitation.issue","39"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","10371"],["dc.bibliographiccitation.volume","53"],["dc.contributor.author","Michielssens, Servaas"],["dc.contributor.author","Peters, Jan Henning"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Seeliger, Daniel"],["dc.contributor.author","Sharma, Monika"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Sabo, Thomas Michael"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:45:30Z"],["dc.date.available","2017-09-07T11:45:30Z"],["dc.date.issued","2014"],["dc.description.abstract","In a conformational selection scenario, manipulating the populations of binding-competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground-state ensemble between open and closed substates that have a similar population in the wild-type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin's binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding-competent substates."],["dc.identifier.doi","10.1002/anie.201403102"],["dc.identifier.gro","3142049"],["dc.identifier.isi","000342760700013"],["dc.identifier.pmid","25115701"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3978"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","A Designed Conformational Shift To Control Protein Binding Specificity"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","184a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","185a"],["dc.bibliographiccitation.volume","108"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:52:26Z"],["dc.date.available","2017-09-07T11:52:26Z"],["dc.date.issued","2015"],["dc.description.abstract","Motion is involved in a large number of protein functions. Relaxation dispersion (RD) NMR experiments sensitively probe microsecond to millisecond motions. We conducted an in-depth RD analysis of the backbone and side chain methyl groups of ubquitin. This survey showed a large number of atoms (>30) with microsecond fluctuations. These atoms are distributed throughout the structure. Strikingly, nearly all show the same exchange rate, which suggests that ubiquitin undergoes collective motion involving both the backbone and side chains. Furthermore, comparison of different methyl nuclei indicates that the nature of the side chain fluctuations is almost entirely due to changes in rotamer populations. Thus, collective microsecond backbone motion is coupled to redistribution of side chain rotamer populations through a mechanism we term “population shuffling”. We present a single collective mode of motion that yields a reaction coordinate corresponding to the relaxation dispersion data. The resulting model indicates that a localized conformational switch distant from the binding interface propagates changes throughout the structure. Analysis of crystal structures confirms this allosteric network and suggests that the microsecond motion modulates binding to particular interaction partners."],["dc.identifier.doi","10.1016/j.bpj.2014.11.1020"],["dc.identifier.gro","3144936"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2615"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","0006-3495"],["dc.title","Microsecond Motion Modulates Ubiquitin Binding through an Allosteric Backbone/Side Chain Network"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","73"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","82"],["dc.bibliographiccitation.volume","57"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Mazur, Adam"],["dc.contributor.author","Carneiro, Marta G."],["dc.contributor.author","Sabo, T. Michael"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Koharudin, Leonardus M. I."],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Gronenborn, Angela M."],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:47:37Z"],["dc.date.available","2017-09-07T11:47:37Z"],["dc.date.issued","2013"],["dc.description.abstract","Micro-to-millisecond motions of proteins transmit pivotal signals for protein function. A powerful technique for the measurement of these motions is nuclear magnetic resonance spectroscopy. One of the most widely used methodologies for this purpose is the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment where kinetic and structural information can be obtained at atomic resolution. Extraction of accurate kinetics determined from CT-CPMG data requires refocusing frequencies that are much larger than the nuclei's exchange rate between states. We investigated the effect when fast processes are probed by CT-CPMG experiments via simulation and show that if the intrinsic relaxation rate is not known a priori the extraction of accurate kinetics is hindered. Errors on the order of 50 % in the exchange rate are attained when processes become fast, but are minimized to 5 % with a priori information. To alleviate this shortcoming, we developed an experimental scheme probing with large amplitude spin-lock fields, which specifically contains the intrinsic proton longitudinal Eigenrelaxation rate. Our approach was validated with ubiquitin and the Oscillatoria agardhii agglutinin (OAA). For OAA, an underestimation of 66 % in the kinetic rates was observed if is not included during the analysis of CT-CPMG data and result in incorrect kinetics and imprecise amplitude information. This was overcome by combining CT-CPMG with measured with a high power R-1 rho experiment. In addition, the measurement of removes the ambiguities in choosing between different models that describe CT-CPMG data."],["dc.identifier.doi","10.1007/s10858-013-9769-z"],["dc.identifier.gro","3142293"],["dc.identifier.isi","000323673800009"],["dc.identifier.pmid","23949308"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6676"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Max Planck Society; EU (ERC) [233227]; NIH [GM080642]"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Springer"],["dc.relation.issn","0925-2738"],["dc.title","Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","30a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Peters, Jan Henning"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:52:31Z"],["dc.date.available","2017-09-07T11:52:31Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.203"],["dc.identifier.gro","3144937"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2616"],["dc.notes.intern","Crossref Import"],["dc.notes.status","public"],["dc.publisher","Elsevier BV"],["dc.relation.issn","0006-3495"],["dc.title","Molecular Recognition through Concerted Ubiquitin Backbone and Side Chain Motion Determined from NMR and MD Simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3269"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","3274"],["dc.bibliographiccitation.volume","113"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Paulat, Maria"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:54:34Z"],["dc.date.available","2017-09-07T11:54:34Z"],["dc.date.issued","2016"],["dc.description.abstract","Many biological processes depend on allosteric communication between different parts of a protein, but the role of internal protein motion in propagating signals through the structure remains largely unknown. Through an experimental and computational analysis of the ground state dynamics in ubiquitin, we identify a collective global motion that is specifically linked to a conformational switch distant from the binding interface. This allosteric coupling is also present in crystal structures and is found to facilitate multispecificity, particularly binding to the ubiquitin-specific protease (USP) family of deubiquitinases. The collective motion that enables this allosteric communication does not affect binding through localized changes but, instead, depends on expansion and contraction of the entire protein domain. The characterization of these collective motions represents a promising avenue for finding and manipulating allosteric networks."],["dc.identifier.doi","10.1073/pnas.1519609113"],["dc.identifier.gro","3141707"],["dc.identifier.isi","000372488200052"],["dc.identifier.pmid","26961002"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/180"],["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","Allosteric switch regulates protein-protein binding through collective motion"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.journal","Journal of Magnetic Resonance (1969)"],["dc.bibliographiccitation.lastpage","4"],["dc.bibliographiccitation.volume","221"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Gossert, Alvar D."],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:48:29Z"],["dc.date.available","2017-09-07T11:48:29Z"],["dc.date.issued","2012"],["dc.description.abstract","Internal motions in the microsecond timescale have been proposed to play an active part in a protein's biological function. Nuclear magnetic resonance (NMR) relaxation dispersion is a robust method sensitive to this timescale with atomic resolution. However, due to technical limitations, the observation of motions faster than similar to 40 mu s for N-15 nuclei was not possible. We show that with a cryogenically cooled NMR probehead, a high spin-lock field strength can be generated that is able to detect motions as fast as 25 mu s. We apply this high spin-lock field strength in an NMR experiment used for characterizing dynamical processes. An on-resonance rotating-frame transverse relaxation experiment was implemented that allows for the detection of a 25 mu s process from a dispersion curve, and transverse relaxation rates were compared at low and high spin-lock field strengths showing that at high field strengths contributions from chemical exchange with lifetimes up to 25 mu s can be removed. Due to the increase in sensitivity towards fast motion, relaxation dispersion for a residue that undergoes smaller chemical shift variations due to dynamics was identified. This technique reduces the previously inaccessible window between the correlation time and the relaxation dispersion window that covers four orders of magnitude by a factor of 2. (C) 2012 Elsevier Inc. All rights reserved."],["dc.identifier.doi","10.1016/j.jmr.2012.05.005"],["dc.identifier.gro","3142490"],["dc.identifier.isi","000307414500001"],["dc.identifier.pmid","22743535"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/8847"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Academic Press Inc Elsevier Science"],["dc.relation.issn","1090-7807"],["dc.title","Exceeding the limit of dynamics studies on biomolecules using high spin-lock field strengths with a cryogenically cooled probehead"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","439a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","106"],["dc.contributor.author","Michielssens, Servaas"],["dc.contributor.author","Peters, Jan Henning"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Sabo, Thomas Michael"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:57:57Z"],["dc.date.available","2021-03-05T08:57:57Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1016/j.bpj.2013.11.2471"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79942"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Controlling Protein Binding Specificity by a Conformational Shift"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","11437"],["dc.bibliographiccitation.issue","48"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","11440"],["dc.bibliographiccitation.volume","50"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Funk, Michael"],["dc.contributor.author","Gulich, Rudolf"],["dc.contributor.author","Egger, Dalia"],["dc.contributor.author","Sabo, T. Michael"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Fenwick, R. Bryn"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Pichierri, Fabio"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Lange, Oliver F."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Salvatella, Xavier"],["dc.contributor.author","Wolf, Martin"],["dc.contributor.author","Loidl, Alois"],["dc.contributor.author","Kree, Reiner"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Lunkenheimer, Peter"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:45:04Z"],["dc.date.available","2017-09-07T11:45:04Z"],["dc.date.issued","2011"],["dc.description.abstract","The lifetime of interconversion among the ground states of a protein ensemble representation could only be assigned to a time window that is four orders of magnitude large and ranges from 4 ns to 50 μs. By combining temperature-dependent NMR relaxation dispersion (RD) experiments and dielectric relaxation (DR) spectroscopy in solution, the lifetime was now identified to a value of (10±9) μs at 309 K."],["dc.identifier.doi","10.1002/anie.201105086"],["dc.identifier.gro","3142794"],["dc.identifier.isi","000297863900026"],["dc.identifier.pmid","22113802"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/238"],["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","1433-7851"],["dc.title","Kinetics of Conformational Sampling in Ubiquitin"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","207"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","210"],["dc.bibliographiccitation.volume","54"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Schwiegk, Claudia"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:44:42Z"],["dc.date.available","2017-09-07T11:44:42Z"],["dc.date.issued","2015"],["dc.description.abstract","Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of microseconds, have been extensively characterized. On the other hand, the dynamics of the ground state are widely unexplored. Newly developed high-power relaxation dispersion experiments allow the detection of motions up to a one-digit microsecond timescale. These experiments showed that side chains in the hydrophobic core as well as at protein-protein interaction surfaces of both ubiquitin and the third immunoglobulin binding domain of proteinG move on the microsecond timescale. Both proteins exhibit plasticity to this microsecond motion through redistribution of the populations of their side-chain rotamers, which interconvert on the picosecond to nanosecond timescale, making it likely that this population shuffling process is a general mechanism."],["dc.identifier.doi","10.1002/anie.201408890"],["dc.identifier.gro","3141974"],["dc.identifier.isi","000347065100028"],["dc.identifier.pmid","25377083"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3146"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Max Planck Society; EU (ERC) [233227]; Alexander von Humboldt Foundation"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","Population Shuffling of Protein Conformations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]