Related ArticlesClusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein.
J Mol Biol. 2013 Jan 16;
Authors: Gangadhara BN, Laine JM, Kathuria SV, Massi F, Matthews CR
Abstract
Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in selected buried positions in ?-helices and pervasively in the underlying ?-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the ?(7)(??)(8)(??)(1-2) and ?(2)(??)(3-6)?(7) segments of the (??)(8) barrel. The most densely packed region of the large cluster, ?(3)(??)(4-6)?(7), correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology.
PMID: 23333740 [PubMed - as supplied by publisher]
[NMR paper] Solid-state NMR study reveals Collagen I structural modifications of amino-acid side chains upon fibrillogenesis.
Solid-state NMR study reveals Collagen I structural modifications of amino-acid side chains upon fibrillogenesis.
Related Articles Solid-state NMR study reveals Collagen I structural modifications of amino-acid side chains upon fibrillogenesis.
J Biol Chem. 2013 Jan 22;
Authors: De Sa Peixoto P, Laurent G, Azais T, Mosser G
Abstract
In vivo, collagen I, the major structural protein in human body, is found assembled into fibrils. In the present work, we study a high concentrated collagen sample in its soluble, fibrillar and denatured states...
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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...
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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] Microscopic stability of cold shock protein A examined by NMR native state hydrogen e
Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide.
Related Articles Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide.
Protein Sci. 2000 Feb;9(2):290-301
Authors: Jaravine VA, Rathgeb-Szabo K, Alexandrescu AT
Native state hydrogen exchange of cold shock protein A (CspA) has been characterized as a function of the denaturant urea and of the stabilizing agent...
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11-18-2010 09:15 PM
[NMR paper] Side-chains in native and random coil protein conformations. Analysis of NMR coupling
Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences.
Related Articles Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences.
J Mol Biol. 1998 Jul 31;280(5):867-77
Authors: West NJ, Smith LJ
The behaviour of amino acid side-chains in proteins in solution has been characterised by analysing NMR 3JHalphaH beta coupling constants and crystallographic chi1 torsion angles. Side-chains both in the...
Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein.
Linear Mode
