Protein , internal motions

Unlike for globular proteins, internal motions of IDPs can hardly be interpreted within the framework of the Lipari-Szabo model-free formalism. IDPs are dominated by segmental motions with low or negligible cooperativity between... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Direct experiment-simulation quasielastic neutron scattering comparisons have been perfonned for a variety of small molecule and polymeric systems, as described in detail in Refs. 4 and 18-21. The combination of simulation and neutron scattering in the analysis of internal motions in globular proteins was reviewed in 1991 [3] and 1997 [4]. 

A dynamic transition in the internal motions of proteins is seen with increasing temperamre [22]. The basic elements of this transition are reproduced by MD simulation [23]. As the temperature is increased, a transition from harmonic to anharmonic motion is seen, evidenced by a rapid increase in the atomic mean-square displacements. Comparison of simulation with quasielastic neutron scattering experiment has led to an interpretation of the dynamics involved in terms of rigid-body motions of the side chain atoms, in a way analogous to that shown above for the X-ray diffuse scattering [24]. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

For folded proteins, relaxation data are commonly interpreted within the framework of the model-free formalism, in which the dynamics are described by an overall rotational correlation time rm, an internal correlation time xe, and an order parameter. S 2 describing the amplitude of the internal motions (Lipari and Szabo, 1982a,b). Model-free analysis is popular because it describes molecular motions in terms of a set of intuitive physical parameters. However, the underlying assumptions of model-free analysis—that the molecule tumbles with a single isotropic correlation time and that internal motions are very much faster than overall tumbling—are of questionable validity for unfolded or partly folded proteins. Nevertheless, qualitative insights into the dynamics of unfolded states can be obtained by model-free analysis (Alexandrescu and Shortle, 1994 Buck etal., 1996 Farrow etal., 1995a). An extension of the model-free analysis to incorporate a spectral density function that assumes a distribution of correlation times on the nanosecond time scale has recently been reported (Buevich et al., 2001 Buevich and Baum, 1999) and better fits the experimental 15N relaxation data for an unfolded protein than does the conventional model-free approach. 

Thus, at present, fluorescence spectroscopy is capable of providing direct information on molecular dynamics on the nanosecond time scale and can estimate the results of dynamics occurring beyond this range. The present-day multiparametric fluorescence experiment gives new opportunities for interpretation of these data and construction of improved dynamic models. A further development of the theory which would provide an improved description of the dynamics in quantitative terms with allowance for the structural inhomogeneity of protein molecules and the hierarchy of their internal motions is required. 

C. K. Woodward and B. D. Hilton, Hydrogen exchange kinetics and internal motions in proteins, Annu. Rev. Biophys. Bioeng. 8, 99-128 (1979). 

J. W. Petrich, J. W. Longworth, and G. R. Fleming, Internal motion and electron transfer in proteins A picosecond fluorescence study of three homologous azurins. Biochemistry 26, 2711-2722 (1987). 

NMR is a powerful and versatile tool for structural studies of biological RNAs and complexes they form with other nucleic acids, proteins, and small molecules. The goal of these studies is to determine the role that structure and dynamics play in biological function. NMR has the capacity to determine high-resolution structures, as well as to map RNAiligand interfaces at low resolution. Most structures of RNA and RNA-ligand complexes are under 20 KDa in size however, recent advances allow for determination of solution structures of complexes up to 40 kDa. NMR can also probe dynamic motions in RNA on micro- to millisecond time scales. A number of biologically relevant internal motions such as... 

Another study used H T, T2 and 13C T, T p measurements to assess the molecular dynamics in dry and wet solid proteins bacterial RNAase, lysozyme and bovine serum albumin.115 All relaxation time data were analysed assuming three components for the molecular motion methyl group rotation and slow and fast oscillations of all atoms. An inhomogeneous distribution of correlation times was found for all samples, not surprisingly given the inhomogeneous nature of the samples. Interestingly, it was found that dehydration affected only the slow internal motions of the proteins and that the fast ones remained unaltered. 

Macromolecules display continuous motions. These motions can be of two main types the molecule can rotate on itself, following the precise axis of rotation, and it can have a local flexibility. Local flexibility, also called internal motions, allows different small molecules, such as solvent molecules, to diffuse along the macromolecule. This diffusion is generally dependent on the importance of the local internal dynamics. Also, the fact that solvent molecules can reach the interior hydrophobic core of macromolecules such as proteins clearly means that the term hydrophobicity should be considered as relative and not as absolute. Internal dynamics of proteins allow and facilitate a permanent contact between protein core and the solvent. Also, this internal motion permits small molecules such as oxygen to diffuse within the protein core. Since oxygen is a collisional quencher, analyzing the fluorescence data in the presence of different oxygen concentrations yields information on the internal dynamics of macromolecules. 

As mentioned earlier, regions of disorder in the spatial ensemble of calculated NMR structures can, in principle, be due to internal motions but can also reflect a relative lack of NOEs in such regions. A recent analysis83 suggests that ill-defined regions in structural ensembles often do reflect slow, large-amplitude motions, and so it is not always necessary to resort to relaxation time measurements if only a general idea of molecular motions is required for a particular protein. Even if relaxation measurements are done, it is often not necessary to undertake and extensive analysis to derive correlation... 

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