Related ArticlesProtein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
J Biomol NMR. 2005 May;32(1):71-81
Authors: Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ("PECAN", Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.
Mapping allostery through the covariance analysis of NMR chemical shifts [Biophysics and Computational Biology]
Mapping allostery through the covariance analysis of NMR chemical shifts
Selvaratnam, R., Chowdhury, S., VanSchouwen, B., Melacini, G....
Date: 2011-04-12
Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical...
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Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
Proteins. 2011 Feb 16;
Authors: Xu X, Ishima R, Ames JB
Recoverin, a member of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily, serves as a calcium sensor in retinal rod cells. Ca(2+) -induced conformational changes in recoverin promote extrusion of its...
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04-06-2011 10:54 AM
Mapping allostery through the covariance analysis of NMR chemical shifts.
Mapping allostery through the covariance analysis of NMR chemical shifts.
Mapping allostery through the covariance analysis of NMR chemical shifts.
Proc Natl Acad Sci U S A. 2011 Mar 28;
Authors: Selvaratnam R, Chowdhury S, Vanschouwen B, Melacini G
Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the...
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03-31-2011 06:24 PM
4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts
Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6â??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
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01-09-2011 12:46 PM
[NMR paper] Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis.
Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis.
Related Articles Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis.
J Am Chem Soc. 2005 Sep 7;127(35):12291-305
Authors: Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM
Magic-angle spinning...
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12-01-2010 06:56 PM
[NMR paper] Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plas
Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin. Metal-dependent differences in the hydrogen-bond network around the copper site.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin. Metal-dependent differences in the hydrogen-bond network around the copper site.
Eur J Biochem. 1996 Nov 15;242(1):132-47
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08-22-2010 02:20 PM
Analysis of and chemical shifts of cysteine and cystine residues in proteins: a quant
Abstract Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the
13\textC\upalpha and
13\textC\upbeta chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed...
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Analysis of NMR Chemical Shifts in Peptide & Protein Structure Determination-Wang '08
Analysis of NMR Chemical Shifts in Peptide and Protein Structure Determination
By Liya Wang (2008)
Amazon book description
Chemical shifts provide detailed information about non-covalent structure, solvent interactions, ionization constants, ring orientations, hydrogen bond interactions, and other phenomena. Since different chemical shift data sets are not necessarily comparable without corrections or adjustments, the applicability of statistical analysis of NMR chemical shifts to biomolecules has so far been limited. We use the term "congruent" to describe data sets that can be...
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its us
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