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Relaxation Experiments (relaxation + experiment)
Selected AbstractsRole of the surface charges D72 and K8 in the function and structural stability of the cytochrome c6 from Nostoc sp.FEBS JOURNAL, Issue 13 2005PCC 711 We investigated the role of electrostatic charges at positions D72 and K8 in the function and structural stability of cytochrome c6 from Nostoc sp. PCC 7119 (cyt c6). A series of mutant forms was generated to span the possible combinations of charge neutralization (by mutation to alanine) and charge inversion (by mutation to lysine and aspartate, respectively) in these positions. All forms of cyt c6 were functionally characterized by laser flash absorption spectroscopy, and their stability was probed by urea-induced folding equilibrium relaxation experiments and differential scanning calorimetry. Neutralization or inversion of the positive charge at position K8 reduced the efficiency of electron transfer to photosystem I. This effect could not be reversed by compensating for the change in global charge that had been introduced by the mutation, indicating a specific role for K8 in the formation of the electron transfer complex between cyt c6 and photosystem I. Replacement of D72 by asparagine or lysine increased the efficiency of electron transfer to photosystem I, but destabilized the protein. D72 apparently participates in electrostatic interactions that stabilize the structure of cyt c6. The destabilizing effect was reduced when aspartate was replaced by the small amino acid alanine. Complementing the mutation D72A with a charge neutralization or inversion at position K8 led to mutant forms of cyt c6 that were more stable than the wild-type under all tested conditions. [source] Interflavin electron transfer in human cytochrome P450 reductase is enhanced by coenzyme bindingFEBS JOURNAL, Issue 12 2003Relaxation kinetic studies with coenzyme analogues The role of coenzyme binding in regulating interflavin electron transfer in human cytochrome P450 reductase (CPR) has been studied using temperature-jump spectroscopy. Previous studies [Gutierrez, A., Paine, M., Wolf, C.R., Scrutton, N.S., & Roberts, G.C.K. Biochemistry (2002) 41, 4626,4637] have shown that the observed rate, 1/,, of interflavin electron transfer (FADsq , FMNsq,FADox , FMNhq) in CPR reduced at the two-electron level with NADPH is 55 ± 2 s,1, whereas with dithionite-reduced enzyme the observed rate is 11 ± 0.5 s,1, suggesting that NADPH (or NADP+) binding has an important role in controlling the rate of internal electron transfer. In relaxation experiments performed with CPR reduced at the two-electron level with NADH, the observed rate of internal electron transfer (1/, = 18 ± 0.7 s,1) is intermediate in value between those seen with dithionite-reduced and NADPH-reduced enzyme, indicating that the presence of the 2,-phosphate is important for enhancing internal electron transfer. To investigate this further, temperature jump experiments were performed with dithionite-reduced enzyme in the presence of 2,,5,-ADP and 2,-AMP. These two ligands increase the observed rate of interflavin electron transfer in two-electron reduced CPR from 1/, = 11 s,1 to 35 ± 0.2 s,1 and 32 ± 0.6 s,1, respectively. Reduction of CPR at the two-electron level by NADPH, NADH or dithionite generates the same spectral species, consistent with an electron distribution that is equivalent regardless of reductant at the initiation of the temperature jump. Spectroelectrochemical experiments establish that the redox potentials of the flavins of CPR are unchanged on binding 2,,5,-ADP, supporting the view that enhanced rates of interdomain electron transfer have their origin in a conformational change produced by binding NADPH or its fragments. Addition of 2,,5,-ADP either to the isolated FAD-domain or to full-length CPR (in their oxidized and reduced forms) leads to perturbation of the optical spectra of both the flavins, consistent with a conformational change that alters the environment of these redox cofactors. The binding of 2,,5,-ADP eliminates the unusual dependence of the observed flavin reduction rate on NADPH concentration (i.e. enhanced at low coenzyme concentration) observed in stopped-flow studies. The data are discussed in the context of previous kinetic studies and of the crystallographic structure of rat CPR. [source] Non-ideal evolution of non-axisymmetric, force-free magnetic fields in a magnetarMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2008A. Mastrano ABSTRACT Recent numerical magnetohydrodynamic calculations by Braithwaite and collaborators support the ,fossil field' hypothesis regarding the origin of magnetic fields in compact stars and suggest that the resistive evolution of the fossil field can explain the reorganization and decay of magnetar magnetic fields. Here, these findings are modelled analytically by allowing the stellar magnetic field to relax through a quasi-static sequence of non-axisymmetric, force-free states, by analogy with spheromak relaxation experiments, starting from a random field. Under the hypothesis that the force-free modes approach energy equipartition in the absence of resistivity, the output of the numerical calculations is semiquantitatively recovered: the field settles down to a linked poloidal,toroidal configuration, which inflates and becomes more toroidal as time passes. A qualitatively similar (but not identical) end state is reached if the magnetic field evolves by exchanging helicity between small and large scales according to an ,-dynamo-like, mean-field mechanism, arising from the fluctuating electromotive force produced by the initial random field. The impossibility of matching a force-free internal field to a potential exterior field is discussed in the magnetar context. [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] Backbone dynamics of the human MIA protein studied by 15N NMR relaxation: Implications for extended interactions of SH3 domainsPROTEIN SCIENCE, Issue 3 2003Raphael Stoll MIA, melanoma inhibitory activity; NMR, nuclear magnetic resonance Abstract The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic melanoma stages III and IV. Here, we report the backbone dynamics of human MIA studied by 15N NMR relaxation experiments. The folded core of human MIA is found to be rigid, but several loops connecting ,-sheets, such as the RT-loop for example, display increased mobility on picosecond to nanosecond time scales. One of the most important dynamic features is the pronounced flexibility of the distal loop, comprising residues Asp 68 to Ala 75, where motions on time scales up to milliseconds occur. Further, significant exchange contributions are observed for residues of the canonical binding site of SH3 domains including the RT-loop, the n-Src loop, for the loop comprising residues 13 to 19, which we refer to as the"disulfide loop", in part for the distal loop, and the carboxyl terminus of human MIA. The functional importance of this dynamic behavior is discussed with respect to the biological activity of several point mutations of human MIA. The results of this study suggest that the MIA protein and the recently identified highly homologous fibrocyte-derived protein (FDP)/MIA-like (MIAL) constitute a new family of secreted proteins that adopt an SH3 domain-like fold in solution with expanded ligand interactions. [source] Definition of domain boundaries and crystallization of the SMN Tudor domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003Remco Sprangers Spinal muscular atropy (SMA) is the major genetic disease leading to childhood mortality and is caused by mutations in or deletions of the smn1 gene. The human survival of motor neurons (SMN) protein encoded by this gene plays an important role in the assembly of snRNPs (small nuclear ribonucleoprotein complexes) via binding to the spliceosomal Sm proteins. The tails of these Sm proteins contain symmetrically dimethylated arginines that are recognized by the central SMN Tudor domain. To gain insight in the molecular basis of this specific interaction, the SMN Tudor domain has been crystallized. The rapid crystallization of the protein and the high stability of the crystals is facilitated by redefinition of domain boundaries based on NMR relaxation experiments and the previously determined solution structure. The crystals diffract to high resolution (1.8,Å) and a complete data set has been collected from a hexagonal crystal form (P61/P65), with unit-cell parameters a = b = 27.65, c = 110.30,Å, , = , = 90, , = 120°. Crystal soaks and co-crystallization with peptides derived from the Sm protein tails have been initiated. Molecular replacement with the NMR coordinates is under way. [source] | ||||||||||