Pratihar, Supriya

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Chakrabarti, Kalyan S."],["dc.contributor.author","Olsson, Simon"],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Overkamp, Kerstin"],["dc.contributor.author","Lee, Ko On"],["dc.contributor.author","Gapsys, Vytautas"],["dc.contributor.author","Ryu, Kyoung-Seok"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Noé, Frank"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2022-09-01T09:50:00Z"],["dc.date.available","2022-09-01T09:50:00Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract\n Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin’s paradigmatic interaction with an SH3 (Src-homology 3) domain. By contrast, the SH3 domain recognizes ubiquitin in a two-state binding process. Subsequent molecular dynamics simulations and Markov state modeling reveal that the ubiquitin conformation selected for binding exhibits a characteristically extended C-terminus. Our framework is robust and expandable for implementation in other binding scenarios with the potential to show that conformational selection might be the design principle of the hubs in protein interaction networks."],["dc.identifier.doi","10.1038/s41467-022-31374-5"],["dc.identifier.pii","31374"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/113597"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-597"],["dc.relation.eissn","2041-1723"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","A litmus test for classifying recognition mechanisms of transiently binding proteins"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","9"],["dc.contributor.author","Reddy, Jithender G."],["dc.contributor.author","Pratihar, Supriya"],["dc.contributor.author","Frischkorn, Sebastian"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2018-01-17T11:30:39Z"],["dc.date.available","2018-01-17T11:30:39Z"],["dc.date.issued","2017"],["dc.description.abstract","Molecular dynamics play a significant role in how molecules perform their function. A critical method that provides information on dynamics, at the atomic level, is NMR-based relaxation dispersion (RD) experiments. RD experiments have been utilized for understanding multiple biological processes occurring at micro-to-millisecond time, such as enzyme catalysis, molecular recognition, ligand binding and protein folding. Here, we applied the recently developed high-power RD concept to the Carr-Purcell-Meiboom-Gill sequence (extreme CPMG; E-CPMG) for the simultaneous detection of fast and slow dynamics. Using a fast folding protein, gpW, we have shown that previously inaccessible kinetics can be accessed with the improved precision and efficiency of the measurement by using this experiment."],["dc.identifier.doi","10.1007/s10858-017-0155-0"],["dc.identifier.pmid","29188417"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11678"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1573-5001"],["dc.title","Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments"],["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","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","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"]]

[["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","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","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"]]