Protein dynamics analysis

Equations (1-3) are widely used for protein dynamics analysis from relaxation measurements. The primary goals here are (A) to measure the spectral densities J(co) and, most important, (B) to translate them into an adequate picture of protein dynamics. The latter goal requires adequate theoretical models of motion that could be obtained from comparison with molecular dynamics simulations (see for example Ref. [23]). However, accurate analysis of experimental data is an essential prerequisite for such a comparison. 

Buck, M., Boyd, J., Redfield, C., MacKenzie, D.A., Jeenes, D.J., Archer, D.B., and Dobson, C. M. (1995) Stmctural determination of protein dynamics analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme, Biochemistry 34, 4041-4055. 

Tarek, M., Martina, GJ. and Tobias, D. (2000) Amplitude and frequency of protein dynamics analysis of discrepancies between neutron scattering and molecular dynamics simulations, J. Am. Chem. Soc. 122 10459-10451. 

The essential slow modes of a protein during a simulation accounting for most of its conformational variability can often be described by only a few principal components. Comparison of PGA with NMA for a 200 ps simulation of bovine pancreatic trypsic inhibitor showed that the variation in the first principal components was twice as high as expected from normal mode analy-si.s ([Hayward et al. 1994]). The so-called essential dynamics analysis method ([Amadei et al. 1993]) is a related method and will not be discussed here. 

Amadei et al. 1993] Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential Dynamics of Proteins. Proteins 17 (1993) 412-425 [Balsera et al. 1997] Balsera, M., Stepaniants, S., Izrailev, S., Oono, Y., Schiilten, K. Reconstructing Potential Energy Functions from Simulated Force-Induced Unbinding Processes. Biophys. J. 73 (1997) 1281-1287 [Case 1996] Case, D.A. Normal mode analysis of protein dynamics. Curr. Op. Struct. Biol. 4 (1994) 285-290... 

J. Gao, K. Kuczera, B. Tldor, and M. Karplus. Hidden thermodynamics of mutant proteins A molecular dynamics analysis. Science, 244 1069-1072, 1989. 

D. A. Case. Normal mode analysis of protein dynamics. Curr. Opin. Struc. Biol., 4 385-290, 1994. 

M. A. Balsera, W. Wriggers, Y. Oono, and K. Schulten. Principal component analysis and long time protein dynamics. J. Phys. Chem., 100 2567-2572, 1996. 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

Real-time spectroscopic methods can be used to measure the binding, dissociation, and internalization of fluorescent ligands with cell-surface receptors on cells and membranes. The time resolution available in these methods is sufficient to permit a detailed analysis of complex processes involved in cell activation, particularly receptor-G protein dynamics. A description of the kinetics and thermodynamics of these processes will contribute to our understanding of the basis of stimulus potency and efficacy. 

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... 

Strategies for the Analysis of Protein Dynamics from 15N Relaxation Data 291 ... 

Temperature consistency between measurements performed on different spectrometers is particularly critical for accurate interpretation of the data (see Refs. [19, 20] for post-acquisition temperature consistency tests). However, temperature control and equalization are also important for the combined analysis of T1, T2, and NOE data measured on the same spectrometer, because of the possible temperature differences between these measurements. Fig. 12.1 illustrates the sensitivity of relaxation parameters to temperature variations. Accurate measurement of protein dynamics requires that all experiments be done at the same temperature. To improve temperature consistency between Tlr T2, and... 

The overall tumbling of a protein molecule in solution is the dominant source of NH-bond reorientations with respect to the laboratory frame, and hence is the major contribution to 15N relaxation. Adequate treatment of this motion and its separation from the local motion is therefore critical for accurate analysis of protein dynamics in solution [46]. This task is not trivial because (i) the overall and internal dynamics could be coupled (e. g. in the presence of significant segmental motion), and (ii) the anisotropy of the overall rotational diffusion, reflecting the shape of the molecule, which in general case deviates from a perfect sphere, significantly complicates the analysis. Here we assume that the overall and local motions are independent of each other, and thus we will focus on the effect of the rotational overall anisotropy. 

Since the characterization of the overall rotational diffusion is a prerequisite for a proper analysis of protein dynamics from spin-relaxation data, we first focus on the theoretical basis of the method being used. 

The derivation of the SD or model-free parameters is just the beginning of the analysis of protein dynamics what one finally wants to achieve is a picture of protein dynamics in terms of motional models. 

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. 

A. P. Demchenko, Fluorescence analysis of protein dynamics, Essays Biochem. 22, 120-157 (1986). 

Only the presence of copper(II) quenched the fluorescence emission. Nevertheless, in ordinary biological systems, coppcr(II) ions are strongly bound to amino acids, peptides or proteins, and the ligands described may be therefore used for the dynamic analysis of the biologically important zinc(II) ions. 

Cinelli, R.A.G., Ferrari, A., Pellegrini, V., Tyagi, M., Giacca, M. and Beltram, F. (2004). The enhanced green fluorescent protein as a tool for the analysis of protein dynamics and localization Local fluorescence study at the single-molecule level. Photochemistry and Photobiology, 71, 771-776. 

Wales, T.E. and Engen, J.R. (2006) Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev., 25, 158-70. 

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