Protein structural dynamics

Rousseau F, Schymkowitz J. A systems biology perspective on protein structural dynamics and signal transduction. Curr Opin Struct Biol 2005 15 23-30. 

All these results are encouraging for investigators planning to use X-ray diffraction in mixed solvents at subzero temperatures and the rest of the present article will be devoted to a discussion of methods and preliminary results in this field. The methodology for cryoprotection of protein crystals, its physical-chemical basis, and the specific problems raised by the crystalline state, as well as the devices used to collect data at subzero temperatures, will be described. Limitations and perspectives of the procedure will be discussed critically. First attempts to determine the structure of productive enzyme-substrate intermediates through stop-action pictures will be described, as well as investigations showing that X-ray diffraction at selected normal and subzero temperatures can reveal protein structural dynamics. 

Bourgeois, D., Vallone, B., Schotte, F., Arcovito, A., Miele, A. E., Sciara, G., Wulff, M., Anfinrud, R, and Brunori, M. 2003. Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography. Proc. Natl. Acad. Sci. USA 100 8704-9. 

Mosberg HI, Sobczyk-Kojiro K. In Renugopalakrishnan V, Carey PR, Smith ICP, Huang SG, Storer AC, eds. Proteins Structure, Dynamics and Design. Leiden, The Netherlands ESCOM, 1991 105-109. 

The physical chemical properties of proteins inform their function and as such have been the object of intense investigation for over 50 years. Indeed, major progress in the understanding of protein structure, dynamics and thermodynamics, as well as their inter-relationships has been made thanks to advances in experimental and computational approaches. Despite this gain in fundamental understanding, a complete description of the factors that control these properties has not been achieved. In particular, the characterization of the role of solvent in controlling protein conformational transitions and stability remains to be accomplished [1]. 

Frauenfelder H, Petsko GA, TSemoglou D (1979) Tfemperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature (Lond) 280 558-563... 

Numerous investigations have used the Raman-active Fe-His vibration to probe heme protein interactions and protein structural dynamics for five-coordinate heme proteins. Identification of a similar vibrational probe for six-coordinate heme proteins wonld be valnable. Comparison with results on iron porphyrins snggests that the feature near 130 cm in the MbNO data (Figure 6) is a potential candidate for probing the Fe-His bond. We note the absence of this feature in the five-coordinate [Fe(PPIXDME)(NO)]. Further studies, including density functional theory (DFT) calculations, will clarify the character of this mode. However, the relatively small Fe amplitude with respect to the Fe His mode in deoxyMb indicates an altered mode character. 

The prerequisites for a DET can be derived from Marcus Theory [27,28]. The highly specific and directional protein-mediated electron transfer in biological systems is governed by factors such as the distance and the bonds between the redox centres, the redox-potential difference between donor and acceptor, an appropriate association of the redox couple and protein-structure dynamics coupled with electron transfer [24,27,29]. 

The essential role of protein structure dynamics as a mechanistic consideration in proton transport has focused attention on amino acids such as proline (3, 9), which can confer localized flexibility within and between helical segments. Except for the unique case of bacteriorhodopsin, which is amenable to spectroscopic examination (10), little is known about the nature of molecular dynamics in transport enzymes. 

J. N. Forkey, M. E. Quinlan and Y. E. Goldman, Protein. structural dynamics by. single-molecule fluorescence polarization, in Prog. Biophys. Mol. Biol. 2000. 74. 1-35. 

Frank, I. M. and Vavilov, S. I, 1931. Uber die WirkungssphSre der Ausldschungsvargange in den flureszierenden fliissigkeiten. Z. Phys. 69, 100 - 110. Franzen, L. E., Svensson, S. and Farm, O, 1980, Structural studies on the carbohydrate portion of human antithrombin III. Journal of Biological Chemistry. 255, 5090-5093. Frauenfelder, H., Petsko, C.A., and Tsernoglou, D, 1979, Temperature-dependent X-ray diffraction of a probe of protein structural dynamics. Nature 280, 558-563. 

Berendsen, H.J.C. Incomplete equilibration A source of error in free energy computations, in Renugopalakrishnan, V, Carey, P.R., Smith, l.C.P, Huang, S.G., Storer, A.C., editors. Proteins Structure, Dynamics, and Design. Leiden ESCOM 1991, p. 384-92. 

C. L. Brooks 111, in Computer Modelling of Fluid Polymers and Solids, C. R. A. Catlow, Ed., Kluwer Academic Publishers, Dordrecht, 1990, pp. 289-334. Molecular Simulations of Protein Structure, Dynamics and Thermodynamics. 

Slysz, G.W., Percy, A.J., Schriemer, D.C. (2008) Restraining expansion of the peak envelope in H/D exchange-MS and its application in detecting perturbations of protein structure/dynamics. Anal Chem, 80(18), 7004-7011. 

G. W. Slysz, A. J. Percy and D. C. Schriemer. (2008) Restraining Expansion of the Peak Envelope in H/D Exchange-MS and Its Application in Detecting Perturbations of Protein Structure/Dynamics, Analytical Chemistry, 80 (18), 7004-7011. 

Forkey, JN, Quinlan, ME, and Goldman, YE, Protein structural dynamics by single-molecule fluorescence polarization. Progress in Biophysics and Molecular Biology 74 (2000) 1-35. 

Applications of Time-resolved Mass Spectrometry in the Studies of Protein Structure Dynamics... 

R 191 LA. Kaltashov, S.J. Eyles and H. Xiao, Combination of Protein Hydrogen Exchange and Tandem Mass Spectrometry as an Emerging Tool to Probe Protein Structure, Dynamics and Function , p. 193... 

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