Related ArticlesVisualizing Side-chains of Invisible Protein Conformers by Solution NMR.
J Mol Biol. 2013 Nov 7;
Authors: Bouvignies G, Vallurupalli P, Kay LE
Abstract
Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic resolution description of these rare states. Yet they are difficult to study because they cannot be observed using standard biophysical techniques. In the past decade NMR methods have been developed for structural studies of these elusive conformers, focusing primarily on backbone (1)H, (15)N and (13)C nuclei. Here we extend the methodology to include side-chains by developing a (13)C-based Chemical Exchange Saturation Transfer experiment for the assignment of side-chain aliphatic (13)C chemical shifts in uniformly (13)C labeled proteins. A pair of applications is provided, involving the folding of ?-sheet Fyn SH3 and ?-helical FF domains. Over 96% and 89% of the side-chain (13)C chemical shifts for excited states corresponding to the unfolded conformation of the Fyn SH3 domain and a folding intermediate of the FF domain, respectively, have been obtained, providing insight into side-chain packing and dynamics.
PMID: 24211467 [PubMed - as supplied by publisher]
Visualizing Side-chains of Invisible Protein Conformers by Solution NMR
Visualizing Side-chains of Invisible Protein Conformers by Solution NMR
Publication date: Available online 8 November 2013
Source:Journal of Molecular Biology</br>
Author(s): Guillaume Bouvignies , Pramodh Vallurupalli , Lewis E. Kay</br>
Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic resolution description of these rare states. Yet they are difficult to study because they cannot be observed using standard biophysical...
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11-08-2013 01:42 PM
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
J Biomol NMR. 2011 Sep 25;
Authors: Huang W, Varani G, Drobny GP
Abstract
Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived...
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09-30-2011 06:00 AM
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
J Biomol NMR. 2011 Sep 25;
Authors: Huang W, Varani G, Drobny GP
Abstract
Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived...
nmrlearner
Journal club
0
09-30-2011 05:59 AM
Interactions of protein side chains with RNA defined with REDOR solid state NMR
Interactions of protein side chains with RNA defined with REDOR solid state NMR
Abstract Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a...
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09-27-2011 07:04 AM
[NMR paper] NMR assignment of protein side chains using residue-correlated labeling and NOE spect
NMR assignment of protein side chains using residue-correlated labeling and NOE spectra.
Related Articles NMR assignment of protein side chains using residue-correlated labeling and NOE spectra.
J Magn Reson. 2003 Dec;165(2):237-47
Authors: Mueller GA, Kirby TW, DeRose EF, London RE
A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., amino acids,...
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11-24-2010 09:16 PM
[NMR paper] The effects of mutations on motions of side-chains in protein L studied by 2H NMR dyn
The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings.
Related Articles The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings.
J Mol Biol. 2003 Jun 6;329(3):551-63
Authors: Millet O, Mittermaier A, Baker D, Kay LE
Recently developed 2H spin relaxation experiments are applied to study the dynamics of methyl-containing side-chains in the B1 domain of protein L and in a pair of point mutants of the domain, F22L and A20V. X-ray and...
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11-24-2010 09:01 PM
[NMR paper] Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N r
Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.
Related Articles Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.
J Am Chem Soc. 2001 Feb 7;123(5):967-75
Authors: Mulder FA, Skrynnikov NR, Hon B, Dahlquist FW, Kay LE
A new NMR experiment is presented for...
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11-19-2010 08:32 PM
[NMR paper] Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide
Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study.
J Biol Chem. 1999 Mar 26;274(13):8411-20
Authors: Yuan T, Ouyang H, Vogel HJ
Binding of calcium to calmodulin (CaM) causes a conformational...
Visualizing Side-chains of Invisible Protein Conformers by Solution NMR.
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