| 1. |
- Gutmanas, Aleksandras, et al.
(författare)
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Accurate relaxation parameters for large proteins.
- 2004
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Ingår i: Journal of magnetic resonance (San Diego, Calif. : 1997). - : Elsevier BV. - 1090-7807. ; 167:1, s. 107-13
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Tidskriftsartikel (refereegranskat)abstract
- The practical applicability, performance, and robustness of three-way decomposition (TWD) for the extraction of relaxation parameters are demonstrated for a large protein with 370 residues, the maltose binding protein. An ordinary set of seven relaxation-modulated (15)N HSQC spectra, recorded at another site, is systematically analyzed. For all 341 assigned backbone amide groups, including 21 pairs and one group of three overlapped peaks, T1 decay values were determined. On isolated peaks, TWD extracts T1 values with systematically lower error bounds compared to conventional tools, although for these simple cases the improvements remain limited. However, in the presence of spectral artifacts, the decrease in errors can become significant, demonstrating the higher robustness of TWD. For about half of the peaks in overlapped regions, the decomposition allowed separation of the signals, yielding significantly different T1 values between overlapping signals. For the rest, similarity of the decay times for the two or three overlapping signals could be confirmed within usually low error bounds. The use of TWD thus leads to a significant increase in the number of accessible relaxation probes in large proteins. With a newly implemented graphical user interface, the application of TWD requires merely a peak list, and thus no additional effort compared to conventional approaches is needed.
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| 3. |
- Zhuravleva, Anastasia, 1979, et al.
(författare)
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Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures.
- 2004
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Ingår i: Journal of molecular biology. - : Elsevier BV. - 0022-2836. ; 342:5, s. 1599-611
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic properties of electron transfer pathways in a small blue copper cupredoxin are explored using an extensive 15N NMR relaxation study of reduced Pseudomonas aeruginosa azurin at four magnetic fields (500-900 MHz) and at two temperatures chosen well below the melting point of the protein. Following a careful model-free analysis, several protein regions with different dynamic regimes are identified. Nanosecond time-scale mobility characterizes various residues of the hydrophobic surface patch believed to mark the natural entry point for electrons, notably the surface-exposed copper-ligand His117. These findings are consistent with a gated electron transfer process according to the "dynamic docking" model. Residues 47-49 along intramolecular pathways of electrons show rigidity that is remarkably conserved when increasing the temperature. Three different conformational exchange processes were observed in the millisecond range, one near the only disulfide bridge in the molecule and two near the copper ion. The latter two processes are consistent with previous data such as crystal structures at various pH values and NMR relaxation dispersion experiments; they may indicate an additional gated electron transfer mechanism at slower time-scales.
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