Literature DB >> 19784810

Methyl groups as probes of supra-molecular structure, dynamics and function.

Amy M Ruschak1, Lewis E Kay.   

Abstract

The development of new protein labeling strategies, along with optimized experiments that exploit the label, have significantly impacted on the types of biochemical problems that can now be addressed by solution NMR spectroscopy. Here we describe how methyl labeling of key residues in a highly deuterated protein background has facilitated studies of the structure, dynamics and interactions of supra-molecular particles. The methyl-labeling approach is briefly reviewed, followed by a summary of applications to three different molecular machines so as to illustrate the types of questions that can now be addressed. Areas where future innovations will lead to yet further improvements are highlighted as well.

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Year:  2009        PMID: 19784810     DOI: 10.1007/s10858-009-9376-1

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  70 in total

1.  NMR analysis of a 900K GroEL GroES complex.

Authors:  Jocelyne Fiaux; Eric B Bertelsen; Arthur L Horwich; Kurt Wüthrich
Journal:  Nature       Date:  2002-07-11       Impact factor: 49.962

2.  An isotope labeling strategy for methyl TROSY spectroscopy.

Authors:  Vitali Tugarinov; Lewis E Kay
Journal:  J Biomol NMR       Date:  2004-02       Impact factor: 2.835

3.  Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.

Authors:  G M Clore; A M Gronenborn
Journal:  Science       Date:  1991-06-07       Impact factor: 47.728

4.  The contact interface of a 120 kD CheA-CheW complex by methyl TROSY interaction spectroscopy.

Authors:  Damon J Hamel; Frederick W Dahlquist
Journal:  J Am Chem Soc       Date:  2005-07-13       Impact factor: 15.419

5.  Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR.

Authors:  Ioannis Gelis; Alexandre M J J Bonvin; Dimitra Keramisanou; Marina Koukaki; Giorgos Gouridis; Spyridoula Karamanou; Anastassios Economou; Charalampos G Kalodimos
Journal:  Cell       Date:  2007-11-16       Impact factor: 41.582

6.  Dynamic inter-subunit interactions in thermophilic F(1)-ATPase subcomplexes studied by cross-correlated relaxation-enhanced polarization transfer NMR.

Authors:  Masumi Kobayashi; Hiromasa Yagi; Toshio Yamazaki; Masasuke Yoshida; Hideo Akutsu
Journal:  J Biomol NMR       Date:  2008-01-05       Impact factor: 2.835

7.  Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies.

Authors:  Carlos Amero; Paul Schanda; M Asunción Durá; Isabel Ayala; Dominique Marion; Bruno Franzetti; Bernhard Brutscher; Jérôme Boisbouvier
Journal:  J Am Chem Soc       Date:  2009-03-18       Impact factor: 15.419

8.  Heterotropic effectors promote a global conformational change in aspartate transcarbamoylase.

Authors:  E Eisenstein; D W Markby; H K Schachman
Journal:  Biochemistry       Date:  1990-04-17       Impact factor: 3.162

9.  Surface, subunit interfaces and interior of oligomeric proteins.

Authors:  J Janin; S Miller; C Chothia
Journal:  J Mol Biol       Date:  1988-11-05       Impact factor: 5.469

10.  NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein.

Authors:  Mara Kreishman-Deitrick; Erin D Goley; Lyle Burdine; Carilee Denison; Coumaran Egile; Rong Li; Nagarajan Murali; Thomas J Kodadek; Matthew D Welch; Michael K Rosen
Journal:  Biochemistry       Date:  2005-11-22       Impact factor: 3.162

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  68 in total

1.  NMR studies of large protein systems.

Authors:  Shiou-Ru Tzeng; Ming-Tao Pai; Charalampos G Kalodimos
Journal:  Methods Mol Biol       Date:  2012

2.  Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy.

Authors:  Hechao Sun; Raquel Godoy-Ruiz; Vitali Tugarinov
Journal:  J Biomol NMR       Date:  2012-03       Impact factor: 2.835

Review 3.  Enlightening molecular mechanisms through study of protein interactions.

Authors:  Josep Rizo; Michael K Rosen; Kevin H Gardner
Journal:  J Mol Cell Biol       Date:  2012-06-26       Impact factor: 6.216

4.  Structural insights into calmodulin-regulated L-selectin ectodomain shedding.

Authors:  Jessica L Gifford; Hiroaki Ishida; Hans J Vogel
Journal:  J Biol Chem       Date:  2012-06-18       Impact factor: 5.157

5.  The proteasome antechamber maintains substrates in an unfolded state.

Authors:  Amy M Ruschak; Tomasz L Religa; Sarah Breuer; Susanne Witt; Lewis E Kay
Journal:  Nature       Date:  2010-10-14       Impact factor: 49.962

6.  (13)CHD2-CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins.

Authors:  Enrico Rennella; Rui Huang; Algirdas Velyvis; Lewis E Kay
Journal:  J Biomol NMR       Date:  2015-08-14       Impact factor: 2.835

7.  Independent valine and leucine isotope labeling in Escherichia coli protein overexpression systems.

Authors:  Roman J Lichtenecker; Katharina Weinhäupl; Lukas Reuther; Julia Schörghuber; Walther Schmid; Robert Konrat
Journal:  J Biomol NMR       Date:  2013-11       Impact factor: 2.835

8.  Cooperative dynamics across distinct structural elements regulate PTP1B activity.

Authors:  Kristiane R Torgeson; Michael W Clarkson; Ganesan Senthil Kumar; Rebecca Page; Wolfgang Peti
Journal:  J Biol Chem       Date:  2020-07-31       Impact factor: 5.157

9.  Improving yields of deuterated, methyl labeled protein by growing in H2O.

Authors:  Evan S O'Brien; Danny W Lin; Brian Fuglestad; Matthew A Stetz; Travis Gosse; Cecilia Tommos; A Joshua Wand
Journal:  J Biomol NMR       Date:  2018-08-02       Impact factor: 2.835

10.  The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site.

Authors:  Naima G Sharaf; Zhaoyong Xi; Rieko Ishima; Angela M Gronenborn
Journal:  Proteins       Date:  2017-09-26
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