Lakomek, Nils-Alexander

[["dc.bibliographiccitation.firstpage","23"],["dc.bibliographiccitation.issue","1-2"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","44"],["dc.bibliographiccitation.volume","45"],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Frank, Benedikt T. C."],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:46:50Z"],["dc.date.available","2017-09-07T11:46:50Z"],["dc.date.issued","2009"],["dc.description.abstract","This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time tau (c). In fact, the average amplitude of motion expressed in terms of order parameters S (2) associated with the supra-tau (c) window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains."],["dc.identifier.doi","10.1007/s10858-009-9354-7"],["dc.identifier.gro","3143062"],["dc.identifier.isi","000269079100005"],["dc.identifier.pmid","19652920"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/534"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0925-2738"],["dc.title","Accessing ns-mu s side chain dynamics in ubiquitin with methyl RDCs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1433"],["dc.bibliographiccitation.journal","Biochemical Society transactions"],["dc.bibliographiccitation.lastpage","1437"],["dc.bibliographiccitation.volume","36"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Lange, Oliver F."],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Egger, Dalia"],["dc.contributor.author","Lunkenheimer, Peter"],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:48:08Z"],["dc.date.available","2017-09-07T11:48:08Z"],["dc.date.issued","2008"],["dc.description.abstract","RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time tau(c), and 50 mu s. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein-protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism."],["dc.identifier.doi","10.1042/BST0361433"],["dc.identifier.gro","3143198"],["dc.identifier.isi","000261749200066"],["dc.identifier.pmid","19021570"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/686"],["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","0300-5127"],["dc.title","Residual dipolar couplings as a tool to study molecular recognition of ubiquitin"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1471"],["dc.bibliographiccitation.issue","5882"],["dc.bibliographiccitation.journal","Science"],["dc.bibliographiccitation.lastpage","1475"],["dc.bibliographiccitation.volume","320"],["dc.contributor.author","Lange, Oliver F."],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Schroeder, Gunnar F."],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:48:17Z"],["dc.date.available","2017-09-07T11:48:17Z"],["dc.date.issued","2008"],["dc.description.abstract","Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost."],["dc.identifier.doi","10.1126/science.1157092"],["dc.identifier.gro","3143280"],["dc.identifier.isi","000256676400038"],["dc.identifier.pmid","18556554"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/776"],["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","0036-8075"],["dc.title","Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","10336"],["dc.bibliographiccitation.issue","27"],["dc.bibliographiccitation.journal","Journal of the American Chemical Society"],["dc.bibliographiccitation.lastpage","10339"],["dc.bibliographiccitation.volume","133"],["dc.contributor.author","Bryn Fenwick, R."],["dc.contributor.author","Esteban-Martin, Santi"],["dc.contributor.author","Richter, Barbara"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Milovanovic, Dragomir"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Salvatella, Xavier"],["dc.date.accessioned","2017-09-07T11:44:07Z"],["dc.date.available","2017-09-07T11:44:07Z"],["dc.date.issued","2011"],["dc.description.abstract","Long-range correlated motions in proteins are candidate mechanisms for processes that require information transfer across protein structures, such as allostery and signal transduction. However, the observation of backbone correlations between distant residues has remained elusive, and only local correlations have been revealed using residual dipolar couplings measured by NMR spectroscopy. In this work, we experimentally identified and characterized collective motions spanning four beta-strands separated by up to 15 angstrom in ubiquitin. The observed correlations link molecular recognition sites and result from concerted conformational changes that are in part mediated by the hydrogen-bonding network."],["dc.identifier.doi","10.1021/ja200461n"],["dc.identifier.gro","3142698"],["dc.identifier.isi","000293149800004"],["dc.identifier.pmid","21634390"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/131"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Amer Chemical Soc"],["dc.relation.issn","0002-7863"],["dc.title","Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","139"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","155"],["dc.bibliographiccitation.volume","41"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Lange, Oliver F."],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Brueschweiler, Rafael"],["dc.contributor.author","Munk, Axel"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:48:16Z"],["dc.date.available","2017-09-07T11:48:16Z"],["dc.date.issued","2008"],["dc.description.abstract","Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of internuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 mu s). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters independent of the details of the structure used for alignment tensor calculation-as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors < S-rdc(2)> = 0: 72 +/- 0: 02 compared to < S-LS(2)> = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S-rdc(2) (NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-tau(c) time scale (S-rdc(2) (NH) = 0.59 +/- 0.03), while it is inconspicuous (S-LS(2) (NH) = 0.82) on the sub-tau(c) as well as on mu s-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data."],["dc.identifier.doi","10.1007/s10858-008-9244-4"],["dc.identifier.gro","3143271"],["dc.identifier.isi","000257224700004"],["dc.identifier.pmid","18523727"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11216"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/766"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: NIGMS NIH HHS [GM 066041, R01 GM066041]"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0925-2738"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4154"],["dc.bibliographiccitation.issue","23"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","4157"],["dc.bibliographiccitation.volume","48"],["dc.contributor.author","Salmon, Loic"],["dc.contributor.author","Bouvignies, Guillaume"],["dc.contributor.author","Markwick, Phineus"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Showalter, Scott"],["dc.contributor.author","Li, Da-Wei"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Brueschweiler, Rafael"],["dc.contributor.author","Blackledge, Martin"],["dc.date.accessioned","2017-09-07T11:47:34Z"],["dc.date.available","2017-09-07T11:47:34Z"],["dc.date.issued","2009"],["dc.identifier.doi","10.1002/anie.200900476"],["dc.identifier.gro","3143164"],["dc.identifier.isi","000266527800014"],["dc.identifier.pmid","19415702"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/648"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Wiley-v C H Verlag Gmbh"],["dc.relation.issn","1433-7851"],["dc.title","Protein Conformational Flexibility from Structure-Free Analysis of NMR Dipolar Couplings: Quantitative and Absolute Determination of Backbone Motion 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","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"]]