Related ArticlesStructural characterization of a peptoid with lysine-like side chains and biological activity using NMR and computational methods.
Org Biomol Chem. 2013 Jan 28;11(4):640-7
Authors: Sternberg U, Birtalan E, Jakovkin I, Luy B, Schepers U, Bräse S, Muhle-Goll C
Abstract
N-substituted glycine oligomers or peptoids with charged side chains are a novel class of cell penetrating peptide mimetics and have been shown to serve as drug delivery agents. Here, we investigated by NMR spectroscopy and quantum chemical calculations whether a Rhodamine B labelled peptoid [RhoB(Spiro)-Ahx]-[But](6A)NH(2) with lysine-like side chains adopts structural motifs similar to regular peptides. Due to a low chemical shift dispersion, high resolution structure determination with conventional NMR-derived distance restraints and J-couplings was not possible. Instead, a combined assignment and structure refinement strategy using the QM/MM force field COSMOS-NMR was developed to interpret the highly ambiguous chemical shift and distance constraints and obtain a medium resolution three-dimensional structural model. This allowed us to select for the all cis-amide conformation of the peptide with a pseudo-helical arrangement of extended side chains as a faithful representative structure of [RhoB(Spiro)-Ahx]-[But](6A)NH(2). We tested the biological activity of the peptoid by live-cell imaging, which showed that the cellular uptake of the peptoid was comparable to conventional cell-penetrating peptides.
[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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02-03-2013 10:19 AM
[Question from NMRWiki Q&A forum] selecting for side chains
selecting for side chains
Does anyone know of literature pointing to NMR experiments that can select for say -CH3 groups attached to -CH2?
Check if somebody has answered this question on NMRWiki QA forum
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06-05-2012 05:58 PM
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion [Biophysics and Computational Biology]
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion
Meinhold, D. W., Wright, P. E....
Date: 2011-05-31
Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use 15N, , and 13CO NMR R2 relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which...
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05-31-2011 11:41 PM
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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12-29-2010 04:04 PM
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
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/iFwgRBt-zto
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12-28-2010 05:27 AM
[NMR paper] NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor.
NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor.
Related Articles NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor.
Structure. 2005 Aug;13(8):1193-202
Authors: Arolas JL, D'Silva L, Popowicz GM, Aviles FX, Holak TA, Ventura S
The III-A intermediate constitutes the major rate-determining step in the oxidative folding of leech carboxypeptidase inhibitor...
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12-01-2010 06:56 PM
[NMR paper] Structural genomics and the metabolome: combining computational and NMR methods to id
Structural genomics and the metabolome: combining computational and NMR methods to identify target ligands.
Related Articles Structural genomics and the metabolome: combining computational and NMR methods to identify target ligands.
Curr Opin Drug Discov Devel. 2004 Jan;7(1):62-8
Authors: Parsons L, Orban J
One of the goals of structural genomics is to use three-dimensional structures to gain insights into the function of poorly understood or hypothetical proteins. Approximate functions are often apparent from the protein fold, but more...
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11-24-2010 09:25 PM
[NMR paper] Carbon-13 NMR studies of the lysine side chains of calmodulin and its proteolytic fra
Carbon-13 NMR studies of the lysine side chains of calmodulin and its proteolytic fragments.
Related Articles Carbon-13 NMR studies of the lysine side chains of calmodulin and its proteolytic fragments.
J Protein Chem. 1993 Dec;12(6):695-707
Authors: Huque ME, Vogel HJ
The pH-titration and dynamic behaviour of the seven lysine side chains in bovine calmodulin were studied by carbon-13 NMR. The amino groups of the calcium saturated protein and its proteolytic fragments TR1C (1-75) and TR2C (78-148) were dimethylated with carbon-13 labeled...
Structural characterization of a peptoid with lysine-like side chains and biological activity using NMR and computational methods.
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