Literature DB >> 19841630

NMR spectroscopy brings invisible protein states into focus.

Andrew J Baldwin1, Lewis E Kay.   

Abstract

Molecular dynamics are essential for protein function. In some cases these dynamics involve the interconversion between ground state, highly populated conformers and less populated higher energy structures ('excited states') that play critical roles in biochemical processes. Here we describe recent advances in NMR spectroscopy methods that enable studies of these otherwise invisible excited states at an atomic level and that help elucidate their important relation to function. We discuss a range of examples from molecular recognition, ligand binding, enzyme catalysis and protein folding that illustrate the role that motion plays in 'funneling' conformers along preferred pathways that facilitate their biological function.

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Year:  2009        PMID: 19841630     DOI: 10.1038/nchembio.238

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  90 in total

1.  Direct observation of protein-ligand interaction kinetics.

Authors:  Tanja Mittag; Brian Schaffhausen; Ulrich L Günther
Journal:  Biochemistry       Date:  2003-09-30       Impact factor: 3.162

2.  Millisecond protein folding studied by NMR spectroscopy.

Authors:  Markus Zeeb; Jochen Balbach
Journal:  Protein Pept Lett       Date:  2005-02       Impact factor: 1.890

3.  A consensus view of protein dynamics.

Authors:  Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

4.  The mechanism of rate-limiting motions in enzyme function.

Authors:  Eric D Watt; Hiroko Shimada; Evgenii L Kovrigin; J Patrick Loria
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-05       Impact factor: 11.205

5.  Complete tyrosine assignments in the high field 1H nuclear magnetic resonance spectrum of the bovine pancreatic trypsin inhibitor.

Authors:  G H Snyder; R Rowan; S Karplus; B D Sykes
Journal:  Biochemistry       Date:  1975-08-26       Impact factor: 3.162

6.  Measurement of methyl axis orientations in invisible, excited states of proteins by relaxation dispersion NMR spectroscopy.

Authors:  Andrew J Baldwin; D Flemming Hansen; Pramodh Vallurupalli; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2009-08-26       Impact factor: 15.419

7.  Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy.

Authors:  Philipp Neudecker; Arash Zarrine-Afsar; Wing-Yiu Choy; D Ranjith Muhandiram; Alan R Davidson; Lewis E Kay
Journal:  J Mol Biol       Date:  2006-08-22       Impact factor: 5.469

8.  Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?

Authors:  D Flemming Hansen; Pramodh Vallurupalli; Patrik Lundström; Philipp Neudecker; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2008-02-01       Impact factor: 15.419

9.  Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network.

Authors:  Rieko Ishima; James Baber; John M Louis; Dennis A Torchia
Journal:  J Biomol NMR       Date:  2004-06       Impact factor: 2.835

10.  Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease.

Authors:  Chun Tang; John M Louis; Annie Aniana; Jeong-Yong Suh; G Marius Clore
Journal:  Nature       Date:  2008-10-02       Impact factor: 49.962

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  165 in total

1.  Siderocalin Q83 exhibits differential slow dynamics upon ligand binding.

Authors:  Nicolas Coudevylle; Leonhard Geist; Matthias Hoetzinger; Martin Tollinger; Robert Konrat
Journal:  J Biomol NMR       Date:  2011-09-27       Impact factor: 2.835

2.  Structural biology: Proteins in dynamic equilibrium.

Authors:  Pau Bernadó; Martin Blackledge
Journal:  Nature       Date:  2010-12-23       Impact factor: 49.962

3.  Alternate states of proteins revealed by detailed energy landscape mapping.

Authors:  Michael D Tyka; Daniel A Keedy; Ingemar André; Frank Dimaio; Yifan Song; David C Richardson; Jane S Richardson; David Baker
Journal:  J Mol Biol       Date:  2010-11-10       Impact factor: 5.469

4.  IDPs: Less Disordered and More Ordered than Expected.

Authors:  Robert Konrat
Journal:  Biophys J       Date:  2015-10-06       Impact factor: 4.033

5.  Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts.

Authors:  Zhanglong Liu; Thomas M Casey; Mandy E Blackburn; Xi Huang; Linh Pham; Ian Mitchelle S de Vera; Jeffrey D Carter; Jamie L Kear-Scott; Angelo M Veloro; Luis Galiano; Gail E Fanucci
Journal:  Phys Chem Chem Phys       Date:  2016-02-17       Impact factor: 3.676

Review 6.  Solution NMR Spectroscopy for the Study of Enzyme Allostery.

Authors:  George P Lisi; J Patrick Loria
Journal:  Chem Rev       Date:  2016-01-06       Impact factor: 60.622

7.  Backbone resonance assignment of N15, N30 and D10 T cell receptor β subunits.

Authors:  Robert J Mallis; Ellis L Reinherz; Gerhard Wagner; Haribabu Arthanari
Journal:  Biomol NMR Assign       Date:  2015-08-15       Impact factor: 0.746

8.  Characterization of Chemical Exchange Using Relaxation Dispersion of Hyperpolarized Nuclear Spins.

Authors:  Mengxiao Liu; Yaewon Kim; Christian Hilty
Journal:  Anal Chem       Date:  2017-08-09       Impact factor: 6.986

9.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

Review 10.  Regulated unfolding of proteins in signaling.

Authors:  Diana M Mitrea; Richard W Kriwacki
Journal:  FEBS Lett       Date:  2013-02-20       Impact factor: 4.124

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