publication . Article . Other literature type . Conference object . 2017

The Exact Nuclear Overhauser Enhancement: Recent Advances.

Julien Orts; Celestine N. Chi; Alexandra Born; Morkos A. Henen; Simon Olsson; Dean Strotz; Beat Vögeli; Parker J. Nichols; Peter Güntert;
Open Access English
  • Published: 01 Jul 2017 Journal: Molecules (issn: 1420-3049, Copyright policy)
  • Publisher: MDPI AG
Abstract
Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of protei...
Subjects
free text keywords: NMR, biological macromolecules, proteins, dynamics, correlated dynamics, exact NOE, structure calculation, structure ensemble, allostery, conformational space, Organic chemistry, QD241-441, Review, Biochemistry and Molecular Biology, Biokemi och molekylärbiologi, dynamics; correlated dynamics; structure ensemble; structure calculation; NMR; biological macromolecules; exact NOE; allostery; conformational space; proteins, Chemistry, Relaxation (NMR), WW domain, biology.protein, biology, Nuclear magnetic resonance, Statistical physics, Protein dynamics, Cyclophilin A
67 references, page 1 of 5

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Law, A.B., Sapienza, P.J., Zhang, J., Zuo, X., Petit, C.M.. Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery. J. Am. Chem. Soc.. 2017; 139: 3599-3602 [OpenAIRE] [PubMed] [DOI]

Kim, T.H., Mehrabi, P., Ren, Z., Sljoka, A., Ing, C., Bezginov, A., Ye, L., Pomès, R., Prosser, R.S., Pai, E.F.. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science. 2017; 355: eaag2355 [OpenAIRE] [PubMed] [DOI]

Capdevila, D.A., Braymer, J.J., Edmonds, K.A., Wu, H., Giedroc, D.P.. Entropy redistribution controls allostery in a metalloregulatory protein. Proc. Natl. Acad. Sci. USA. 2017; 114: 4424-4429 [OpenAIRE] [PubMed] [DOI]

Berlow, R.B., Dyson, H.J., Wright, P.E.. Hypersensitive termination of the hypoxic response by a disordered protein switch. Nature. 2017 [OpenAIRE] [PubMed] [DOI]

Papaleo, E., Saladino, G., Lambrughi, M., Lindorff-Larsen, K., Gervasio, F.L., Nussinov, R.. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem. Rev.. 2016; 116: 6391-6423 [OpenAIRE] [PubMed] [DOI]

Chi, C.N., Bach, A., Engström, Å., Wang, H., Strømgaard, K., Gianni, S., Jemth, P.. A Sequential Binding Mechanism in a PDZ Domain. Biochemistry. 2009; 48: 7089-7097 [OpenAIRE] [PubMed] [DOI]

Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O.. Atomic-level characterization of the structural dynamics of proteins. Science. 2011; 330: 341-346 [OpenAIRE] [PubMed] [DOI]

Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E.. How Fast-Folding Proteins Fold. Science. 2011; 334: 517-520 [OpenAIRE] [PubMed] [DOI]

Eichmann, C., Preissler, S., Riek, R., Deuerling, E.. Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy. Proc. Natl. Acad. Sci. USA. 2010; 107: 9111-9116 [OpenAIRE] [PubMed] [DOI]

Fersht, A.. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. 1999; Volume 13409

Zhuravlev, P.I., Papoian, G.A.. Protein functional landscapes, dynamics, allostery: A tortuous path towards a universal theoretical framework. Q. Rev. Biophys.. 2010; 43: 295-332 [OpenAIRE] [PubMed] [DOI]

Chill, J.H., Naider, F.. A solution NMR view of protein dynamics in the biological membrane. Curr. Opin. Struct. Biol.. 2011; 21: 627-633 [OpenAIRE] [PubMed] [DOI]

67 references, page 1 of 5
Abstract
Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of protei...
Subjects
free text keywords: NMR, biological macromolecules, proteins, dynamics, correlated dynamics, exact NOE, structure calculation, structure ensemble, allostery, conformational space, Organic chemistry, QD241-441, Review, Biochemistry and Molecular Biology, Biokemi och molekylärbiologi, dynamics; correlated dynamics; structure ensemble; structure calculation; NMR; biological macromolecules; exact NOE; allostery; conformational space; proteins, Chemistry, Relaxation (NMR), WW domain, biology.protein, biology, Nuclear magnetic resonance, Statistical physics, Protein dynamics, Cyclophilin A
67 references, page 1 of 5

Van den Bedem, H., Fraser, J.S.. Integrative, dynamic structural biology at atomic resolution—It’s about time. Nat. Methods. 2015; 12: 307-318 [OpenAIRE] [PubMed] [DOI]

Barends, T.R.M., Foucar, L., Ardevol, A., Nass, K., Aquila, A., Botha, S., Doak, R.B., Falahati, K., Hartmann, E., Hilpert, M.. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science. 2015; 350: 445-450 [OpenAIRE] [PubMed] [DOI]

Hekstra, D.R., White, K.I., Socolich, M.A., Henning, R.W., Ranganathan, R., Biology, C.. Electric field-stimulated protein mechanics. Nature. 2016; 540: 1-18 [OpenAIRE] [PubMed] [DOI]

Law, A.B., Sapienza, P.J., Zhang, J., Zuo, X., Petit, C.M.. Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery. J. Am. Chem. Soc.. 2017; 139: 3599-3602 [OpenAIRE] [PubMed] [DOI]

Kim, T.H., Mehrabi, P., Ren, Z., Sljoka, A., Ing, C., Bezginov, A., Ye, L., Pomès, R., Prosser, R.S., Pai, E.F.. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science. 2017; 355: eaag2355 [OpenAIRE] [PubMed] [DOI]

Capdevila, D.A., Braymer, J.J., Edmonds, K.A., Wu, H., Giedroc, D.P.. Entropy redistribution controls allostery in a metalloregulatory protein. Proc. Natl. Acad. Sci. USA. 2017; 114: 4424-4429 [OpenAIRE] [PubMed] [DOI]

Berlow, R.B., Dyson, H.J., Wright, P.E.. Hypersensitive termination of the hypoxic response by a disordered protein switch. Nature. 2017 [OpenAIRE] [PubMed] [DOI]

Papaleo, E., Saladino, G., Lambrughi, M., Lindorff-Larsen, K., Gervasio, F.L., Nussinov, R.. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem. Rev.. 2016; 116: 6391-6423 [OpenAIRE] [PubMed] [DOI]

Chi, C.N., Bach, A., Engström, Å., Wang, H., Strømgaard, K., Gianni, S., Jemth, P.. A Sequential Binding Mechanism in a PDZ Domain. Biochemistry. 2009; 48: 7089-7097 [OpenAIRE] [PubMed] [DOI]

Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O.. Atomic-level characterization of the structural dynamics of proteins. Science. 2011; 330: 341-346 [OpenAIRE] [PubMed] [DOI]

Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E.. How Fast-Folding Proteins Fold. Science. 2011; 334: 517-520 [OpenAIRE] [PubMed] [DOI]

Eichmann, C., Preissler, S., Riek, R., Deuerling, E.. Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy. Proc. Natl. Acad. Sci. USA. 2010; 107: 9111-9116 [OpenAIRE] [PubMed] [DOI]

Fersht, A.. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. 1999; Volume 13409

Zhuravlev, P.I., Papoian, G.A.. Protein functional landscapes, dynamics, allostery: A tortuous path towards a universal theoretical framework. Q. Rev. Biophys.. 2010; 43: 295-332 [OpenAIRE] [PubMed] [DOI]

Chill, J.H., Naider, F.. A solution NMR view of protein dynamics in the biological membrane. Curr. Opin. Struct. Biol.. 2011; 21: 627-633 [OpenAIRE] [PubMed] [DOI]

67 references, page 1 of 5
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