Smith, Colin A.

[["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","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.journal","Nature Reviews Neurology"],["dc.contributor.author","Watson, Neil"],["dc.contributor.author","Brandel, Jean-Philippe"],["dc.contributor.author","Green, Alison"],["dc.contributor.author","Hermann, Peter"],["dc.contributor.author","Ladogana, Anna"],["dc.contributor.author","Lindsay, Terri"],["dc.contributor.author","Mackenzie, Janet"],["dc.contributor.author","Pocchiari, Maurizio"],["dc.contributor.author","Smith, Colin"],["dc.contributor.author","Pal, Suvankar"],["dc.date.accessioned","2021-06-01T09:41:41Z"],["dc.date.available","2021-06-01T09:41:41Z"],["dc.date.issued","2021"],["dc.identifier.doi","10.1038/s41582-021-00488-7"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85003"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.eissn","1759-4766"],["dc.relation.issn","1759-4758"],["dc.title","The importance of ongoing international surveillance for Creutzfeldt–Jakob disease"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["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","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.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","858"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Journal of the American Chemical Society"],["dc.bibliographiccitation.lastpage","869"],["dc.bibliographiccitation.volume","141"],["dc.contributor.author","Rovó, Petra"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Gauto, Diego"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Schanda, Paul"],["dc.contributor.author","Linser, Rasmus"],["dc.date.accessioned","2021-03-05T08:58:24Z"],["dc.date.available","2021-03-05T08:58:24Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1021/jacs.8b09258"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80124"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1520-5126"],["dc.relation.issn","0002-7863"],["dc.title","Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["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","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"]]

[["dc.bibliographiccitation.firstpage","27"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","43"],["dc.bibliographiccitation.volume","74"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","Mazur, Adam"],["dc.contributor.author","Rout, Ashok K."],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2021-03-05T09:05:22Z"],["dc.date.available","2021-03-05T09:05:22Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1007/s10858-019-00288-8"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80450"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1573-5001"],["dc.relation.issn","0925-2738"],["dc.title","Enhancing NMR derived ensembles with kinetics on multiple timescales"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]