Related ArticlesHeteronuclear three-dimensional NMR spectroscopy of a partially denatured protein: the A-state of human ubiquitin.
J Biomol NMR. 1993 May;3(3):285-96
Authors: Stockman BJ, Euvrard A, Scahill TA
Human ubiquitin is a 76-residue protein that serves as a protein degradation signal when conjugated to another protein. Ubiquitin has been shown to exist in at least three states: native (N-state), unfolded (U-state), and, when dissolved in 60% methanol:40% water at pH 2.0, partially folded (A-state). If the A-state represents an intermediate in the folding pathway of ubiquitin, comparison of the known structure of the N-state with that of the A-state may lead to an understanding of the folding pathway. Insights into the structural basis for ubiquitin's role in protein degradation may also be obtained. To this end we determined the secondary structure of the A-state using heteronuclear three-dimensional NMR spectroscopy of uniformly 15N-enriched ubiquitin. Sequence-specific 1H and 15N resonance assignments were made for more than 90% of the residues in the A-state. The assignments were made by concerted analysis of three-dimensional 1H-15N NOESY-HMQC and TOCSY-HMQC data sets. Because of 1H chemical shift degeneracies, the increased resolution provided by the 15N dimension was critical. Analysis of short- and long-range NOEs indicated that only the first two strands of beta-sheet, comprising residues 2-17, remain in the A-state, compared to five strands in the N-state. NOEs indicative of an alpha-helix, comprising residues 25-33, were also identified. These residues were also helical in the N-state. In the N-state, residues in this helix were in contact with residues from the first two strands of beta-sheet. It is likely, therefore, that residues 1-33 comprise a folded domain in the A-state of ubiquitin. On the basis of 1H alpha chemical shifts and weak short-range NOEs, residues 34-76 do not adopt a rigid secondary structure but favor a helical conformation. This observation may be related to the helix-inducing effects of the methanol present. The secondary structure presented here differs from and is more thorough than that determined previously by two-dimensional 1H methods [Harding et al. (1991) Biochemistry, 30, 3120-3128].
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
J Am Chem Soc. 2010 Dec 27;
Authors: Esadze A, Li DW, Wang T, Bru?schweiler R, Iwahara J
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics...
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Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Alexandre Esadze, Da-Wei Li, Tianzhi Wang, Rafael Bru?schweiler and Junji Iwahara
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107847d/aop/images/medium/ja-2010-07847d_0007.gif
Journal of the American Chemical Society
DOI: 10.1021/ja107847d
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Two-dimensional heteronuclear saturation transfer difference NMR reveals detailed int
Two-dimensional heteronuclear saturation transfer difference NMR reveals detailed integrin αvβ6 protein-peptide interactions.
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Chem Commun (Camb). 2010 Sep 13;
Authors: Wagstaff JL, Vallath S, Marshall JF, Williamson RA, Howard MJ
We report the first example of peptide-protein heteronuclear two-dimensional (2D) saturation transfer difference nuclear magnetic resonance (STD NMR). This method, resulting in...
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[NMR paper] Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR expe
Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea.
Biochemistry. 1997 Jul 22;36(29):8977-91
Authors: Schwalbe H, Fiebig KM, Buck M, Jones JA, Grimshaw SB, Spencer A, Glaser SJ, Smith LJ, Dobson CM
...
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[NMR paper] Structures of larger proteins in solution: three- and four-dimensional heteronuclear
Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.
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Science. 1991 Jun 7;252(5011):1390-9
Authors: Clore GM, Gronenborn AM
Three- and four-dimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy offers dramatic improvements in spectral resolution by spreading through-bond and through-space correlations in three and four orthogonal frequency axes....
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[NMR paper] Characterization of a partially denatured state of a protein by two-dimensional NMR:
Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin.
Related Articles Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin.
Biochemistry. 1991 Mar 26;30(12):3120-8
Authors: Harding MM, Williams DH, Woolfson DN
A stable, partially structured state of ubiquitin, the A-state, is formed at pH 2.0 in 60% methanol/40% water at 298 K. Detailed characterization of the structure...
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[NMR paper] Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1 bet
Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1 beta in solution.
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Science. 1990 Jul 27;249(4967):411-4
Authors: Kay LE, Clore GM, Bax A, Gronenborn AM
A method is presented that dramatically improves the resolution of protein nuclear magnetic resonance (NMR) spectra by increasing their dimensionality to four. The power of this technique is demonstrated by the application of four-dimensional...
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Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
W. Trent Franks, Kathryn D. Kloepper, Benjamin J. Wylie and Chad M. Rienstra
Journal of Biomolecular NMR; 2007; 39(2); pp 107 - 131
Abstract:
Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation...