Protein dynamics spectroscopy

Deak J, Richard L, Pereira M, Chui H-L and Miller R J D 1994 Picosecond phase grating spectroscopy applications to bioenergetics and protein dynamics Meth. Enzymol. 232 322-60... 

NMR spectroscopy is one of the most widely used analytical tools for the study of molecular structure and dynamics. Spin relaxation and diffusion have been used to characterize protein dynamics [1, 2], polymer systems[3, 4], porous media [5-8], and heterogeneous fluids such as crude oils [9-12]. There has been a growing body of work to extend NMR to other areas of applications, such as material science [13] and the petroleum industry [11, 14—16]. NMR and MRI have been used extensively for research in food science and in production quality control [17-20]. For example, NMR is used to determine moisture content and solid fat fraction [20]. Multi-component analysis techniques, such as chemometrics as used by Brown et al. [21], are often employed to distinguish the components, e.g., oil and water. 

An advantage of NMR spectroscopy is the analysis of protein dynamics. Measurement and analysis of the relaxation parameters R1 R2, and the 15N NOE of 15N-labeled proteins leads to an order parameter (S2) that can describe the relative mobility of the backbone of the protein. Both collagenase-1 and stromelysin-1 have been studied either as inhibited complexes or the free protein [19, 52], Stromleysin-1 was studied with inhibitors binding to prime or nonprime subsites. Presence or absence of inhibitors in the nonprime sites had minor effects on the highly ordered structure of residues in these subsites, which are in contact with the... 

Fushman, D. and D. Cowburn, Nuclear magnetic resonance relaxation in determination of residue-specific 1SN chemical shift tensors in proteins in solution protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy, in Methods Enzymol. T. James, U. Schmitz, and V. Doetsch, Editors. 2001. p.109-126. 

Such ambiguity and also the low structural resolution of the method require that the spectroscopic properties of protein fluorophores and their reactions in electronic excited states be thoroughly studied and characterized in simple model systems. Furthermore, the reliability of the results should increase with the inclusion of this additional information into the analysis and with the comparison of the complementary data. Recently, there has been a tendency not only to study certain fluorescence parameters and to establish their correlation with protein dynamics but also to analyze them jointly, to treat the spectroscopic data multiparametrically, and to construct self-consistent models of the dynamic process which take into account these data as a whole. Fluorescence spectroscopy gives a researcher ample opportunities to combine different parameters determined experimentally and to study their interrelationships (Figure 2.1). This opportunity should be exploited to the fullest. 

Goodno, G. D., Astinov, V., and Miller, R. J. D. 1999. Diffractive optics-based heterodyne-detected grating spectroscopy Application to nltrafast protein dynamics. J. Phys. Chem.A 103 10619. 

Parak, R, Knapp, E. W., and Kucheida, D. 1982. Protein dynamics. Mossbauer spectroscopy on deoxymyoglobin crystals. J. Mol. Biol. 161 177-94. 

P R E CONTENTS Preface. Stable-Isotope Assisted Protein NMR Spectroscopy in Solution, Brian J. Stockman and John L. Mar-kley. 31P and 1H Two-Dimensional NMR and NOESY-Dis-tance Restrained Molecular Dynamics Methodologies for Defining Sequence-Specific Variations in Duplex Oligonucleotides, David G. Gorenstein, Robert P. Meadows, James T. Metz, Edward Nikonowcz and Carol Beth Post. NMR Study of B- and Z-DNA Hairpins of d[(CG) 3T4(CG)3] in Solution, Sa-toshi Ikuta and Yu-Sen Wang. Molecular Dynamics Simulations of Carbohydrate Molecules, J.W. Brady. Diversity in the Structure of Hemes, Russell Timkovich and Laureano L. Bon-doc. Index. Volume 2,1991, 180 pp. 112.50/E72.50 ISBN 1-55938-396-8... 

From the late 1960 s to the early 1970 s, more direct approaches to the investigation of protein dynamics were intensively developed. Such investigations featured the application of physical methods, such as physical labeling, NMR, optical spectroscopy, fluorescence, differential scanning calorimetry, and X-ray and neutron scattering. The purposeful application of the approaches made it possible to obtain detailed information on the mobility of different parts of protein globules and to compare this mobility with both the functional characteristics and stability of proteins, and with results of the theoretical calculation of protein dynamics. 

Likhtenshtein G.I. (1979b) Study of protein dynamics by spin-labeling, Mosbauer spectroscopy, and NMR, in Losche, A. (eds.), Special Collogue Amper on Dynamic Processes in Molecular Systems, Leipzig, Karl-Marx University, pp 100-107. 

Parak, F., Knapp, E.W., and Kucheida, D. (1982) Protein dynamics. Mossbauer spectroscopy on deoxymyoglobin crystal, 7. Mol. Biol., 161 177-194. paramagnetic center in spin-labeled proteins from the parameters of the saturation curve of the ESR spectrum of the label at 77K. Molecul. Biol. (Moscow) 10, 109-116. 

Proteins in the dry state are frozen. They only open up and start moving if some water is added, as in nature. It turns out that protein movements in, e.g., lysozyme are activated only when there is 0.15 g of water per gram of protein, a good example of the effect of hydration on living processes. However, it is difficult to examine protein dynamics in solution because to make a satisfactory interpretation of the observations, one would have first to do the corresponding spectroscopy in the dry state this is difficult because of the frozen state referred to and a tendency to decompose. 

Neutron spectroscopy is becoming a principal tool for the study of protein dynamics (Cusack, 1986, 1989 Middendorf, 1984 Middendorf et al., 1984). Current instruments cover motions with characteristic times from 10 to 10 sec. This range embraces essentially all protein modes excited at room temperature (the soft modes), including motions of the solvent shell and also low-frequency large-scale domain motions, like the hinge-bending motion of the lysozyme domains that form the... 

Full internal motions of protein Dynamic and thermodynamic coupling between hydration water and protein, seen in Mossbauer spectroscopy and computer simulations... 

In addition to the in vitro studies of well-defined systems that have been discussed here, NMR spectroscopy can also be applied to living systems or complex substance mixtures (146). This broad applicability is an advantage of NMR spectroscopy over X-ray crystallography. Early in vivo NMR studies that mostly identify small metabolite molecules by P or H ID experiments have led to different applications. In-cell NMR uses isotopic labeling combined with two or higher dimensional NMR experiments for structural studies of the phosphorylation state of a given protein in the cellular environment or of intrinsically unstructured proteins. In-cell NMR applications in prokaryotic systems cover structural and functional studies (i.e., protein-protein interactions, protein dynamics, automated structure determination, and de novo resonance assignments (147-149)). 

Protein dynamics, as a function of hydration, 191 Raman spectroscopy, and electrolytic solutions. 

M. Kataoka, H. Kamikubo, H. Nakagawa, S.F. Parker J.C. Smith (2003). Spectrosc-Int. J. 17, 529-535. Neutron inelastic scattering as a high-resolution vibrational spectroscopy New tool for the study of protein dynamics. 

Callendee, R., Dyee, R. B. (2002) Probing protein dynamics using temperature jump relaxation spectroscopy, Curr. Opin. Struct. Biol. 12, 628-633. 

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