Related ArticlesInsights into the molecular flexibility of ?-defensins by NMR relaxation analysis.
J Phys Chem B. 2014 Dec 11;118(49):14257-66
Authors: Conibear AC, Wang CK, Bi T, Rosengren KJ, Camarero JA, Craik DJ
Abstract
?-Defensins are mammalian cyclic peptides that have antimicrobial activity and show potential as stable scaffolds for peptide-based drug design. The cyclic cystine ladder structural motif of ?-defensins has been characterized using NMR spectroscopy and is important for their structure and stability. However, the effect of the pronounced elongated topology of ?-defensins on their molecular motion is not yet understood. Studies of molecular motion by NMR relaxation measurements have been facilitated by the recent development of a semirecombinant method for producing cyclic peptides that allows for isotopic labeling. Here we have undertaken a multifield (15)N NMR relaxation analysis of the anti-HIV ?-defensin, HTD-2, and interpreted the experimental data using various models of overall and internal molecular motion. We found that it was necessary to apply a model that includes internal motion to account for the variations in the experimental T1 and NOE data at different backbone amide sites in the peptide. Although an isotropic model with internal motion was the simplest model that provided a satisfactory fit with the experimental data, we cannot exclude the possibility that overall motion is anisotropic, especially considering the strikingly elongated topology of ?-defensins. The presence of flexible side chains, self-association, interactions with solvent, and internal motions are all potential contributors to the observed relaxation data. Internal motion consistent with the constraints imposed by the cyclic cystine ladder was observed in that the order parameters, S(2), show that residues in the turns are more flexible than those in the ?-sheet. This study provides insights into the dynamics of ?-defensins and information that might be useful in their application as scaffolds in drug design.
[NMR paper] General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
Related Articles General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
Biochem Biophys Res Commun. 2015 Jan 16;
Authors: Liu Q, Shi C, Yu L, Zhang L, Xiong Y, Tian C
Abstract
Internal backbone dynamic motions are essential for different protein functions and...
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General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations
General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations
Publication date: Available online 16 January 2015
Source:Biochemical and Biophysical Research Communications</br>
Author(s): Qing Liu , Chaowei Shi , Lu Yu , Longhua Zhang , Ying Xiong , Changlin Tian</br>
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and...
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01-17-2015 04:14 PM
[NMR paper] Heparin-Binding Proteins (Chemokines and Defensins) and their Complexes with Glycosaminoglycans from the Solution NMR Perspective.
Heparin-Binding Proteins (Chemokines and Defensins) and their Complexes with Glycosaminoglycans from the Solution NMR Perspective.
Related Articles Heparin-Binding Proteins (Chemokines and Defensins) and their Complexes with Glycosaminoglycans from the Solution NMR Perspective.
Curr Protein Pept Sci. 2014 Aug 25;
Authors: Pomin VH
Abstract
This review paper aims at discussing the major recent achievements in the field of the heparin-binding proteins (HBPs), primarily chemokines and defensins, and their complexes with...
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09-02-2014 11:17 PM
[NMR paper] Solid-State NMR in Macromolecular Systems: Insights on How Molecular Entities Move.
Solid-State NMR in Macromolecular Systems: Insights on How Molecular Entities Move.
Related Articles Solid-State NMR in Macromolecular Systems: Insights on How Molecular Entities Move.
Acc Chem Res. 2013 Mar 13;
Authors: Hansen MR, Graf R, Spiess HW
Abstract
The function of synthetic and natural macromolecularsystems critically depends on the packing and dynamics of the individual components of a given system. Not only can solid-state NMR provide structural information with atomic resolution, but it can also provide a way to characterize...
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03-14-2013 10:05 PM
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins.
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins.
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins.
Prion. 2011 Jul 1;5(3)
Authors: Santo KP, Berjanskii M, Wishart DS, Stepanova M
Abstract
Collective motions on ns-?s time scales are known to have a major impact on protein folding, stability, binding and enzymatic efficiency. It is also believed that these motions may have an...
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08-27-2011 04:53 PM
[NMR paper] Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation.
Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation.
Related Articles Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation.
J Mol Biol. 2002 Mar 22;317(2):263-78
Authors: Dayie KT, Brodsky AS, Williamson JR
Binding of the HIV tat protein to the TAR (transactivating response region) RNA element activates transcription of the HIV viral genome. The complex of TAR with argininamide serves as a model for the RNA conformation in the tat-TAR complex. The dynamics of the HIV-2 TAR-argininamide...
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11-24-2010 08:49 PM
[NMR paper] Thermodynamic insights into proteins from NMR spin relaxation studies.
Thermodynamic insights into proteins from NMR spin relaxation studies.
Related Articles Thermodynamic insights into proteins from NMR spin relaxation studies.
Curr Opin Struct Biol. 2001 Oct;11(5):555-9
Authors: Spyracopoulos L, Sykes BD
NMR spin relaxation measurements of picosecond to nanosecond timescale backbone and sidechain fluctuations of protein molecules, and subsequent entropic interpretation yield interesting, but sometimes counterintuitive, insights into proteins. The stabilities of proteins and protein interactions are achieved...
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11-19-2010 08:44 PM
[NMR paper] Insights into the local residual entropy of proteins provided by NMR relaxation.
Insights into the local residual entropy of proteins provided by NMR relaxation.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Insights into the local residual entropy of proteins provided by NMR relaxation.
Protein Sci. 1996 Dec;5(12):2647-50
Authors: Li Z, Raychaudhuri S, Wand AJ
A simple model is used to...
Insights into the molecular flexibility of ?-defensins by NMR relaxation analysis.
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