Related ArticlesAnalysis 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
Authors: Ubbink M, Lian LY, Modi S, Evans PA, Bendall DS
To compare cadmium-substituted plastocyanin with copper plastocyanin, the 1H-NMR spectra of CuI-, CuII- and Cd-plastocyanin from pea have been analyzed. Full assignments of the spectra of CuI- and Cd-plastocyanin indicate chemical shift differences up to 1 ppm. The affected protons are located in the four loops that surround the Cu site. The largest differences were found for protons in the hydrogen bond network which stabilizes this part of the protein. This suggests that the chemical shift differences are caused by very small but extensive structural changes in the network upon replacement of CuI by Cd. For CuII-plastocyanin the resonances of 72% of the protons observed in the CuI form have been identified. Protons within approximately 0.9 nm of the CuII were not observed due to fast paramagnetic relaxation. The protons between 0.9-1.7 nm from the CuII showed chemical shift differences up to 0.4 ppm compared to both CuI- and Cd-plastocyanin. These differences can be predicted assuming that they represent pseudocontact shifts. When corrected for the pseudocontact shift contribution, the CuII-plastocyanin chemical shifts were nearly all identical within error to those of the Cd form, but not of the CuI-plastocyanin, indicating that the CuII-plastocyanin structure, in as far as it can be observed, resembles Cd-rather than CuI-plastocyanin. In a single stretch of residues (64-69) chemical shift differences remained between all three forms after correction. The fact that pseudocontact shifts were observed for protons which were not broadened may be attributable to the weaker distance dependence of the pseudocontact shift effect compared to paramagnetic relaxation. This results in two shells around the Cu atom, an inner paramagnetic shell (0-0.9 nm), in which protons are not observed due to broadening, and an outer paramagnetic shell (0.9-1.7 nm), in which protons can be observed and show pseudocontact shifts. It is concluded that Cd-plastocyanin is a suitable redox-inactive substitute for Cu-plastocyanin.
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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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
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[NMR paper] Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its us
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
Related Articles Protein 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...
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11-25-2010 08:21 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...