Ban, David

[["dc.bibliographiccitation.firstpage","81"],["dc.bibliographiccitation.journal","Archives of Biochemistry and Biophysics"],["dc.bibliographiccitation.lastpage","91"],["dc.bibliographiccitation.volume","628"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2018-01-17T11:31:26Z"],["dc.date.available","2018-01-17T11:31:26Z"],["dc.date.issued","2017"],["dc.description.abstract","Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique capable of studying timescales of motion that range from those faster than molecular reorientation on the picosecond timescale to those that occur in real-time. Across this entire regime, NMR observables can report on the amplitude of atomic motion, and the kinetics of atomic motion can be ascertained with a wide variety of experimental techniques from real-time to milliseconds and several nanoseconds to picoseconds. Still a four orders of magnitude window between several nanoseconds and tens of microseconds has remained elusive. Here, we highlight new relaxation dispersion NMR techniques that serve to cover this \"hidden-time\" window up to hundreds of nanoseconds that achieve atomic resolution while studying the molecule under physiological conditions."],["dc.identifier.doi","10.1016/j.abb.2017.05.016"],["dc.identifier.pmid","28576576"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11679"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1096-0384"],["dc.title","Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["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","287"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","301"],["dc.bibliographiccitation.volume","58"],["dc.contributor.author","Sabo, T. Michael"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Mazur, Adam"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:46:22Z"],["dc.date.available","2017-09-07T11:46:22Z"],["dc.date.issued","2014"],["dc.description.abstract","Residual dipolar couplings (RDCs) are NMR parameters that provide both structural and dynamic information concerning inter-nuclear vectors, such as N-H-N and C alpha-H alpha bonds within the protein backbone. Two approaches for extracting this information from RDCs are the model free analysis (MFA) (Meiler et al. in J Am Chem Soc 123:6098-6107, 2001; Peti et al. in J Am Chem Soc 124:5822-5833, 2002) and the direct interpretation of dipolar couplings (DIDCs) (Tolman in J Am Chem Soc 124:12020-12030, 2002). Both methods have been incorporated into iterative schemes, namely the self-consistent RDC based MFA (SCRM) (Lakomek et al. in J Biomol NMR 41:139-155, 2008) and iterative DIDC (Yao et al. in J Phys Chem B 112:6045-6056, 2008), with the goal of removing the influence of structural noise in the MFA and DIDC formulations. Here, we report a new iterative procedure entitled Optimized RDC-based Iterative and Unified Model-free analysis (ORIUM). ORIUM unifies theoretical concepts developed in the MFA, SCRM, and DIDC methods to construct a computationally less demanding approach to determine these structural and dynamic parameters. In all schemes, dynamic averaging reduces the actual magnitude of the alignment tensors complicating the determination of the absolute values for the generalized order parameters. To readdress this scaling issue that has been previously investigated (Lakomek et al. in J Biomol NMR 41:139-155, 2008; Salmon et al. in Angew Chem Int Edit 48:4154-4157, 2009), a new method is presented using only RDC data to establish a lower bound on protein motion, bypassing the requirement of Lipari-Szabo order parameters. ORIUM and the new scaling procedure are applied to the proteins ubiquitin and the third immunoglobulin domain of protein G (GB3). Our results indicate good agreement with the SCRM and iterative DIDC approaches and signify the general applicability of ORIUM and the proposed scaling for the extraction of inter-nuclear vector structural and dynamic content."],["dc.identifier.doi","10.1007/s10858-013-9775-1"],["dc.identifier.gro","3142155"],["dc.identifier.isi","000334598500006"],["dc.identifier.pmid","24013952"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5144"],["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.publisher","Springer"],["dc.relation.eissn","1573-5001"],["dc.relation.issn","0925-2738"],["dc.title","ORIUM: Optimized RDC-based Iterative and Unified Model-free analysis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6462"],["dc.bibliographiccitation.issue","22"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","6465"],["dc.bibliographiccitation.volume","54"],["dc.contributor.author","Carneiro, Marta G."],["dc.contributor.author","Koharudin, Leonardus M. I."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Sabo, T. Michael"],["dc.contributor.author","Trigo-Mourino, Pablo"],["dc.contributor.author","Mazur, Adam"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Gronenborn, Angela M."],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:44:23Z"],["dc.date.available","2017-09-07T11:44:23Z"],["dc.date.issued","2015"],["dc.description.abstract","Lectins from different sources have been shown to interfere with HIV infection by binding to the sugars of viral-envelope glycoproteins. Three-dimensional atomic structures of a number of HIV-inactivating lectins have been determined, both as free proteins and in glycan-bound forms. However, details on the mechanism of recognition and binding to sugars are elusive. Herein we focus on the anti-HIV lectin OAA from Oscillatoria agardhii: We show that in the absence of sugars in solution, both the sugar-free and sugar-bound protein conformations that were observed in the X-ray crystal structures exist as conformational substates. Our results suggest that glycan recognition occurs by conformational selection within the ground state; this model differs from the popular excited-state model. Our findings provide further insight into molecular recognition of the major receptor on the HIV virus by OAA. These details can potentially be used for the optimization and/or development of preventive anti-HIV therapeutics."],["dc.identifier.doi","10.1002/anie.201500213"],["dc.identifier.gro","3141897"],["dc.identifier.isi","000355229800007"],["dc.identifier.pmid","25873445"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2289"],["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","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","9566"],["dc.bibliographiccitation.issue","33"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","9569"],["dc.bibliographiccitation.volume","55"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Sabo, T. Michael"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Fenwick, R. Bryn"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Salvatella, Xavier"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:44:44Z"],["dc.date.available","2017-09-07T11:44:44Z"],["dc.date.issued","2016"],["dc.description.abstract","Protein dynamics occurring on a wide range of timescales play a crucial role in governing protein function. Particularly, motions between the globular rotational correlation time (tau(c)) and 40 mu s (supra-tau(c) window), strongly influence molecular recognition. This supra-tau(c) window was previously hidden, owing to a lack of experimental methods. Recently, we have developed a high-power relaxation dispersion (RD) experiment for measuring kinetics as fast as 4 mu s. For the first time, this method, performed under super-cooled conditions, enabled us to detect a global motion in the first mu beta-turn of the third IgG-binding domain of protein G (GB3), which was extrapolated to 371 +/- 115 ns at 310 K. Furthermore, the same residues show the plasticity in the model-free residual dipolar coupling (RDC) order parameters and in an ensemble encoding the supra-tau(c) dynamics. This beta-turn is involved in antibody binding, exhibiting the potential link of the observed supra-tau(c) motion with molecular recognition."],["dc.identifier.doi","10.1002/anie.201603501"],["dc.identifier.gro","3141635"],["dc.identifier.isi","000383372700016"],["dc.identifier.pmid","27345359"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3678"],["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","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","221a"],["dc.bibliographiccitation.issue","3, Supplement 1"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","110"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Mazur, Adam"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2017-09-07T11:52:26Z"],["dc.date.available","2017-09-07T11:52:26Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1016/j.bpj.2015.11.1226"],["dc.identifier.gro","3144935"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2614"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","0006-3495"],["dc.title","Allostery through Protein Motion at Different Length and Time Scales"],["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","65"],["dc.bibliographiccitation.journal","Journal of Magnetic Resonance (1969)"],["dc.bibliographiccitation.lastpage","69"],["dc.bibliographiccitation.volume","269"],["dc.contributor.author","Chakrabarti, Kalyan S."],["dc.contributor.author","Ban, David"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Reddy, Jithender G."],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2017-09-07T11:44:45Z"],["dc.date.available","2017-09-07T11:44:45Z"],["dc.date.issued","2016"],["dc.description.abstract","Exchange-mediated saturation transfer (EST) provides critical information regarding dynamics of molecules. In typical applications EST is studied by either scanning a wide range of N-15 chemical shift offsets where the applied N-15 irradiation field strength is on the order of hundreds of Hertz or, scanning a narrow range of N-15 chemical shift offsets where the applied N-15 irradiation field-strength is on the order of tens of Hertz during the EST period. The H-1 decoupling during the EST delay is critical as incomplete decoupling causes broadening of the EST profile, which could possibly result in inaccuracies of the extracted kinetic parameters and transverse relaxation rates. Currently two different H-1 decoupling schemes have been employed, intermittently applied 180 pulses and composite-pulse-decoupling (CPD), for situations where a wide range, or narrow range of N-15 chemical shift offsets are scanned, respectively. We show that high-power CPD provides artifact free EST experiments, which can be universally implemented regardless of the offset range or irradiation field-strengths. (C) 2016 Elsevier Inc. All rights reserved."],["dc.identifier.doi","10.1016/j.jmr.2016.05.013"],["dc.identifier.gro","3141641"],["dc.identifier.isi","000381239900007"],["dc.identifier.pmid","27240144"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/4344"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Max Planck Society; EU (ERC) [233227]; James Graham Brown Foundation"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Academic Press Inc Elsevier Science"],["dc.relation.eissn","1096-0856"],["dc.relation.issn","1090-7807"],["dc.title","High-power H-1 composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]