Conformational heterogeneity

Meneni et al. [55] recorded 19F-NMR spectra of 16 fully paired 7-fluoro-2-a minofluorene (FAF)-modified 12mer duplexes (5 -CTTCTNG NCCTC-3 ), in which the bases (N = G, A, C, T) flanking the lesion (G ) were varied systematically. The purpose was to examine the effects of the flanking base sequences on 

T) [55], Specific S/B signal assignments were made based on ring current and H/D isotope effects, as well as NOESY/exchange characteristics [55, 56]. The 

S-conformer was more susceptible to a ring current effect, which enabled the base-displaced FAF to be better shielded than the B-conformer. The downfield B-conformer signals exhibited consistently greater H/D shielding effects (0.13-0.22 ppm) than the upfield S-conformer signals (below 0.06 ppm) measured at 20°C. 

Fluorescence spectroscopy was used to gain insights into the origins of the 3 -flanking sequence effects. Jain et al. [58] studied fully paired AG N duplexes (5 -CTTCT(2-AP)G NCCTC-3 ), in which the 5 A is replaced with the versatile 

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The multifrequency EPR and Mdssbauer properties of the [FesSJ in C. vinosum NiFe-hydrogenase are particularly interesting since they provide evidence of magnetic interactions with nearby paramagnetic species (151, 154, 155). The magnetically isolated form exhibits a well-resolved, almost axial EPR signal, g = 2.018, 2.016, 2.002, indicative of minimal conformational heterogeneity. However, a com-... 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

Davydov, D.R., Halpert, J.R., Renaud, J.P. and Hui Bon Hoa, G. (2003) Conformational heterogeneity of cytochrome P450 3A4 revealed by high pressure spectroscopy. Biochemical and Biophysical Research Communications, 312 (1), 121-130. 

A. G. Szabo, T. M. Stepanik, D. M. Wayner, and N. M. Young, Conformational heterogeneity of the copper binding site in azurin. A time-resolved fluorescence study,... 

Barton LL, editor. 1995. Sulfate-reducing bacteria. New York Plenum Press. Blanchard L, Marion D, Pollock B, et al. 1993. Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome C553 in Desulfovibrio desulfuricans G200 evidence of conformational heterogeneity in the oxidized protein by NMR. Eur J Biochem 218 293-301. 

The solution structure of Aspl3Cys, a thermostable mutant of Fd, has been solved by H-NMR and compared to that of the wild-type (WT) protein. The overall folding of the WT protein was maintained in the mutant, except for the immediate vicinity of the new cysteine. The geometry of the new cluster was a typical 4Fe-4S cubane, as monitored by the hyperfine shifts of the co-ordinated cysteines. Conformational heterogeneity, which was partly abolished by heat treatment, was observed and ascribed to a kinetic phenomenon. 

Xie, Z., Srividya, N., Sosnick, T. R., Pan, T., and Scherer, N. F. (2004). Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc. Natl. Acad. Sci. USA 101, 534-539. 

Conformationally heterogeneous states of proteins can be determined using NMR-derived structural data and suitable molecular dynamics techniques.100 Residual dipolar couplings have been shown to represent motions in ubiquitin slower than its correlation time.101 Using an extensive set of residual dipolar couplings, namely, 36 sets of amide NH, 6 sets of HNC and NC as well as 11... 

Breton, J., Bibikova, M., Oesterhelt, D., and Nabedryk, E., 1999, Conformational heterogeneity of the bacteriopheophytin electron acceptor in reaction centers from Rhodopseudomonas viridis revealed by Fourier transform infrared spectroscopy and site-directed mutagenesis. Biochemistry, 38 11541nll552. 

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