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Side-chain Dynamics (side-chain + dynamics)
Selected AbstractsDipolar dynamic frequency shifts in multiple-quantum spectra of methyl groups in proteins: correlation with side-chain motionMAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2006Vitali Tugarinov Abstract Small deviations from the expected relative positions of multiplet components in double- and zero-quantum 1H- 13C methyl correlation maps have been observed in spectra recorded on a 7-kDa protein. These dynamic frequency shifts (DFS) are the result of dipolar cross-correlations that derive from fields produced by the spins within the methyl groups. The shifts have been quantified and compared with values calculated from a Redfield analysis. Good agreement is noted between the signs of the predicted and experimentally observed relative shifts of lines in both F1 and F2 dimensions of spectra, as well as between the magnitudes of the calculated and observed shifts in the F2 (1H) dimension. The experimental DFS values show a reasonable correlation with 2H relaxation-derived measures of methyl side-chain dynamics, as expected from theory. This suggests that in cases where such shifts can be quantified, they can serve as qualitative measures of motion. Copyright © 2006 John Wiley & Sons, Ltd. [source] Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineeringPROTEIN SCIENCE, Issue 8 2006Koki Makabe Abstract Outer surface protein A (OspA) from Borrelia burgdorferi has an unusual dumbbell-shaped structure in which two globular domains are connected with a "single-layer" ,-sheet (SLB). The protein is highly soluble, and it has been recalcitrant to crystallization. Only OspA complexes with Fab fragments have been successfully crystallized. OspA contains a large number of Lys and Glu residues, and these "high entropy" residues may disfavor crystal packing because some of them would need to be immobilized in forming a crystal lattice. We rationally designed a total of 13 surface mutations in which Lys and Glu residues were replaced with Ala or Ser. We successfully crystallized the mutant OspA without a bound Fab fragment and extended structure analysis to a 1.15 Å resolution. The new high-resolution structure revealed a unique backbone hydration pattern of the SLB segment in which water molecules fill the "weak spots" on both faces of the antiparallel ,-sheet. These well-defined water molecules provide additional structural links between adjacent ,-strands, and thus they may be important for maintaining the rigidity of the SLB that inherently lacks tight packing afforded by a hydrophobic core. The structure also revealed new information on the side-chain dynamics and on a solvent-accessible cavity in the core of the C-terminal globular domain. This work demonstrates the utility of extensive surface mutation in crystallizing recalcitrant proteins and dramatically improving the resolution of crystal structures, and provides new insights into the stabilization mechanism of OspA. [source] The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinasePROTEIN SCIENCE, Issue 4 2004Anthony Mittermaier Abstract We have used 15N- and 2H-NMR spin relaxation experiments to study the response of backbone and side-chain dynamics when a leucine or valine is substituted for a completely buried phenylalanine residue in the SH3 domain from the Fyn tyrosine kinase. Several residues show differences in the time scales and temperature dependences of internal motions when data for the three proteins are compared. Changes were also observed in the magnitude of dynamics, with the valine, and to a lesser extent leucine mutant, showing enhanced flexibility compared to the wild-type (WT) protein. The motions of many of the same amide and methyl groups are affected by both mutations, identifying a set of loci where dynamics are sensitive to interactions involving the targeted side chain. These results show that contacts within the hydrophobic core affect many aspects of internal mobility throughout the Fyn SH3 domain. [source] Tryptophanyl fluorescence lifetime distribution of hyperthermophilic ,-glycosidase from molecular dynamics simulation: A comparison with the experimental dataPROTEIN SCIENCE, Issue 9 2000Ettore Bismuto Abstract A molecular dynamics simulation approach has been utilized to understand the unusual fluorescence emission decay observed for ,-glycosidase from the hyperthermophilic bacterium Solfolobus sulfataricus (S,gly), a tetrameric enzyme containing 17 tryptophanyl residues for each subunit. The tryptophanyl emission decay of (S,gly) results from a bimodal distribution of fluorescence lifetimes with a short-lived component centered at 2.5 ns and a long-lived one at 7.4 ns Bismuto E, Nucci R, Rossi M, Irace G, 1999, Proteins 27:71,79). From the examination of the trajectories of the side chains capable of causing intramolecular quenching for each tryptophan microenvironment and using a modified Stern,Volmer model for the emission quenching processes, we calculated the fluorescence lifetime for each tryptophanyl residue of S,gly at two different temperatures, i.e., 300 and 365 K. The highest temperature was chosen because in this condition S,lgy evidences a maximum in its catalytic activity and is stable for a very long time. The calculated lifetime distributions overlap those experimentally determined. Moreover, the majority of trytptophanyl residues having longer lifetimes correspond to those originally identified by inspection of the crystallographic structure. The tryptophanyl lifetimes appear to be a complex function of several variables, such as microenvironment viscosity, solvent accessibility, the chemical structure of quencher side chains, and side-chain dynamics. The lifetime calculation by MD simulation can be used to validate a predicted structure by comparing the theoretical data with the experimental fluorescence decay results. [source] Complex 1H,13C-NMR relaxation and computer simulation study of side-chain dynamics in solid polylysineBIOPOLYMERS, Issue 3 2005Alexey Krushelnitsky Abstract The side-chain dynamics of solid polylysine at various hydration levels was studied by means of proton spin,lattice relaxation times measurements in the laboratory and tilted (off-resonance) rotating frames at several temperatures as well as Monte Carlo computer simulations. These data were analyzed together with recently measured carbon relaxation data (A. Krushelnitsky, D. Faizullin, and D. Reichert, Biopolymers, 2004, Vol. 73, pp. 1,15). The analysis of the whole set of data performed within the frame of the model-free approach led us to a conclusion about three types of the side-chain motion. The first motion consists of low amplitude rotations of dihedral angles of polylysine side chains on the nanosecond timescale. The second motion is cis,trans conformational transitions of the side chains with correlation times in the microsecond range for dry polylysine. The third motion is a diffusion of dilating defects described in (W. Nusser, R. Kimmich, and F. Winter, Journal of Physical Chemistry, 1988, Vol. 92, pp. 6808,6814). This diffusion causes almost no reorientation of chemical bonds but leads to a sliding motion of side chains with respect to each other in the nanosecond timescale. This work evidently demonstrates the advantages of the simultaneous quantitative analysis of data obtained from different experiments within the frame of the same mathematical formalism, providing for the detailed description of the nature and geometry of the internal molecular dynamics. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 129,139, 2005 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||