Within the past two decades, there has been an increase in the acquisition of residual dipolar couplings (RDC) for investigations of biomolecular structures. Their use however is still not as widely adopted as the traditional methods of structure determination by NMR, despite their potential for extending the limits in studies that examine both the structure and dynamics of biomolecules. This is in part due to the difficulties associated with the analysis of this information-rich data type. The software analysis tool REDCRAFT was previously introduced to address some of these challenges. Here we describe and evaluate a number of additional features that have been incorporated in order to extend its computational and analytical capabilities. REDCRAFTâ??s more traditional enhancements integrate a modified steric collision term, as well as structural refinement in the rotamer space. Other, non-traditional improvements include: the filtering of viable structures based on relative order tensor estimates, decimation of the conformational space based on structural similarity, and forward/reverse folding of proteins. Utilizing REDCRAFTâ??s newest features we demonstrate de-novo folding of proteins 1D3Z and 1P7E to within less than 1.6Â*Ã? of the corresponding X-ray structures, using as many as four RDCs per residue and as little as two RDCs per residue, in two alignment media. We also show the successful folding of a structure to less than 1.6Â*Ã? of the X-ray structure using {Ciâ??1â??Ni, Niâ??Hi, and Ciâ??1â??Hi} RDCs in one alignment medium, and only {Niâ??Hi} in the second alignment medium (a set of data which can be collected on deuterated samples). The program is available for download from our website at http://ifestos.cse.sc.edu.
Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings
Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings
Abstract Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural...
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06-26-2012 06:18 AM
Simultaneous measurement of 1Hâ??15N and Methyl 1Hmâ??13Cm residual dipolar couplings in large proteins
Simultaneous measurement of 1Hâ??15N and Methyl 1Hmâ??13Cm residual dipolar couplings in large proteins
Abstract A two-dimensional TROSY-based SIM-13Cmâ??1Hm/1Hâ??15N NMR experiment for simultaneous measurements of methyl 1 D CH and backbone amide 1 D NH residual dipolar couplings (RDC) in {U-; Ileδ1-; Leu,Val-}-labeled samples of large proteins is described. Significant variation in the alignment tensor of the 82-kDa enzyme Malate synthase G is observed as a function of only slight changes in experimental conditions. The SIM-13Cmâ??1Hm/1Hâ??15N data sets provide convenient means...
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09-30-2011 08:01 PM
Backbone resonance assignment and order tensor estimation using residual dipolar couplings
Backbone resonance assignment and order tensor estimation using residual dipolar couplings
Abstract An NMR investigation of proteins with known X-ray structures is of interest in a number of endeavors. Performing these studies through nuclear magnetic resonance (NMR) requires the costly step of resonance assignment. The prevalent assignment strategy does not make use of existing structural information and requires uniform isotope labeling. Here we present a rapid and cost-effective method of assigning NMR data to an existing structureâ??either an X-ray or computationally modeled...
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06-15-2011 02:31 AM
[NMR paper] Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
Related Articles Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
Eur Biophys J. 2005 Nov;34(8):1057-65
Authors: García-Mayoral MF, Pantoja-Uceda D, Santoro J, Martínez del Pozo A, Gavilanes JG, Rico M, Bruix M
(15)N-(1)H residual dipolar couplings (RDC) have been used as additional restraints to refine the solution structure of the ribotoxin alpha-sarcin. The RDC values were obtained by partial alignment of alpha-sarcin in the binary mixture...
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11-25-2010 08:21 PM
[NMR paper] Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: ne
Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination.
Related Articles Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination.
J Am Chem Soc. 2004 May 26;126(20):6232-3
Authors: Ding K, Gronenborn AM
A simple, sensitivity-enhanced experiment was devised for accurate measurement of backbone 15N-13Calpha and 1HN-13Calpha couplings in proteins. The measured residual dipolar couplings 2DHCA,...
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11-24-2010 09:51 PM
[NMR paper] Residual dipolar couplings in NMR structure analysis.
Residual dipolar couplings in NMR structure analysis.
Related Articles Residual dipolar couplings in NMR structure analysis.
Annu Rev Biophys Biomol Struct. 2004;33:387-413
Authors: Lipsitz RS, Tjandra N
Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide...
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11-24-2010 09:25 PM
[NMR paper] Protein structural motif recognition via NMR residual dipolar couplings.
Protein structural motif recognition via NMR residual dipolar couplings.
Related Articles Protein structural motif recognition via NMR residual dipolar couplings.
J Am Chem Soc. 2001 Feb 14;123(6):1222-9
Authors: Andrec M, Du P, Levy RM
NMR residual dipolar couplings have great potential to provide rapid structural information for proteins in the solution state. This information even at low resolution may be used to advantage in proteomics projects that seek to annotate large numbers of gene products for entire genomes. In this paper, we...
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11-19-2010 08:32 PM
Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bo
Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein
Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 30 July 2010</br>
Paul, Shealy , Mikhail, Simin , Sang Ho, Park , Stanley J., Opella , Homayoun, Valafar</br>
A strategy for simultaneous study of the structure and internal dynamics of a membrane protein is described using the REDCRAFT algorithm. The membrane-bound form of the Pf1 major coat protein (mbPf1) was used as an example. First, synthetic data is...
Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings
Linear Mode
