Internal motion model

Fig. 4 Experimental order parameters, S, of NH bond vectors in GB3 derived from iterative Direct Interpretation of Dipolar Couplings (DIDC) using all six sets of RDCs. The red line marks the order parameters derived from relaxation. Filled symbols represent residues for which the fully anisotropic model was required to get a satisfactory fit to the data, while, for open symbols, the isotropic internal motion model was able to fit the RDCs to within the experimental noise. (Reprinted with permission from [41])...

In fact, the adjustment often entails a 1 - 3 crankshaft type of motion. The conclusion fi-om the study of Keepers and James (1982) is that sugar-re-puckering motions and rotational wobbling in the phosphodiester moiety are most probably sources for the earlier conclusions of nanosecond motions. Furthermore, it would appear that any such motions are highly localized, being compensated by adjustments within a few bonds. It is noted that the best-fit internal motion model contains a contribution of 37% from the CSA mechanism at 40.5 MHz. 

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. 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

Having demonstrated that our simulation reproduces the neutron data reasonably well, we may critically evaluate the models used to interpret the data. For the models to be analytically tractable, it is generally assumed that the center-of-mass and internal motions are decoupled so that the total intermediate scattering function can be written as a product of the expression for the center-of-mass motion and that for the internal motions. We have confirmed the validity of the decoupling assumption over a wide range of Q (data not shown). In the next two sections we take a closer look at our simulation to see to what extent the dynamics is consistent with models used to describe the dynamics. We discuss the motion of the center of mass in the next section and the internal dynamics of the hydrocarbon chains in Section IV.F. 

Two physically reasonable but quite different models have been used to describe the internal motions of lipid molecules observed by neutron scattering. In the first the protons are assumed to undergo diffusion in a sphere [63]. The radius of the sphere is allowed to be different for different protons. Although the results do not seem to be sensitive to the details of the variation in the sphere radii, it is necessary to have a range of sphere volumes, with the largest volume for methylene groups near the ends of the hydrocarbon chains in the middle of the bilayer and the smallest for the methylenes at the tops of the chains, closest to the bilayer surface. This is consistent with the behavior of the carbon-deuterium order parameters,. S cd, measured by deuterium NMR ... 

Another way to describe deviations from the simple BPP spectral density is the so-called model-free approach of Lipari and Szabo [10]. This takes account of the reduction of the spectral density usually observed in NMR relaxation experiments. Although the model-free approach was first applied mainly to the interpretation of relaxation data of macromolecules, it is now also used for fast internal dynamics of small and middle-sized molecules. For very fast internal motions the spectral density is given by ... 

This simple relaxation theory becomes invalid, however, if motional anisotropy, or internal motions, or both, are involved. Then, the rotational correlation-time in Eq. 30 is an effective correlation-time, containing contributions from reorientation about the principal axes of the rotational-diffusion tensor. In order to separate these contributions, a physical model to describe the manner by which a molecule tumbles is required. Complete expressions for intramolecular, dipolar relaxation-rates for the three classes of spherical, axially symmetric, and asymmetric top molecules have been evaluated by Werbelow and Grant, in order to incorporate into the relaxation theory the appropriate rotational-diffusion model developed by Woess-ner. Methyl internal motion has been treated in a few instances, by using the equations of Woessner and coworkers to describe internal rotation superimposed on the overall, molecular tumbling. Nevertheless, if motional anisotropy is present, it is wiser not to attempt a quantitative determination of interproton distances from measured, proton relaxation-rates, although semiquantitative conclusions are probably justified by neglecting motional anisotropy, as will be seen in the following Section. 

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. 

Figure 15 The model molecule used to demonstrate the possibilities of HOESY experiments in terms of carbon-proton distances and reorientational anisotropy. To a first approximation, the molecule is devoid of internal motions and its symmetry determines the principal axis of the rotation-diffusion tensor. Note that H, H,., H,-, H,/ are non-equivalent. The arrows indicate remote correlations.

Up to this point only overall motion of the molecule has been considered, but often there is internal motion, in addition to overall molecular tumbling, which needs to be considered to obtain a correct expression for the spectral density function. Here we apply the model-free approach to treat internal motion where the unique information is specified by a generalized order parameter S, which is a measure of the spatial restriction of internal motion, and the effective correlation time re, which is a measure of the rate of internal motion [7, 8], The model-free approach only holds if internal motion is an order of magnitude (<0.3 ns) faster than overall reorientation and can therefore be separated from overall molecular tumbling. The spectral density has the following simple expression in the model-free formalism ... 

Li and coworkers49 reported a molecular motion of /1-carotene and a carotenopor-phyrin dyad (composed of a porphyrin, a trimethylene bridge and a carotenoid polyene) in solution. Internal rotational motions in carotenoid polyenes and porphyrins are of interest because they can mediate energy and electron transfer between these two moieties when the pigments are joined by covalent bonds. Such internal motions can affect the performance of synthetic model systems which mimic photosynthetic antenna function,... 

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. 

Yamakawa and co-workers have formulated a discrete helical wormlike chain model that is mechanically equivalent to that described above for twisting and bending/79111 117) However, their approach to determining the dynamics is very different. They do not utilize the mean local cylindrical symmetry to factorize the terms in r(t) into products of correlation functions for twisting, bending, and internal motions, as in Eq. (4.24). Instead, they... 

In the previous discussion, the electron-nucleus spin system was assumed to be rigidly held within a molecule isotropically rotating in solution. If the molecule cannot be treated as a rigid sphere, its motion is in general anisotropic, and three or five different reorientational correlation times have to be considered 79). Furthermore, it was calculated that free rotation of water protons about the metal ion-oxygen bond decreases the proton relaxation time in aqua ions of about 20% 79). A general treatment for considering the presence of internal motions faster than the reorientational correlation time of the whole molecule is the Lipari Szabo model free treatment 80). Relaxation is calculated as the sum of two terms 8J), of the type... 

A. Jones I don t feel the multiple internal rotations model is applicable for side chains any longer than or k carbons. As soon as it is longer than carbons, a crankshaft type of motion dominates Instead of multiple internal rotations. The viewpoint probably reflects some bias on my part. 

Constraints may be introduced either into the classical mechanical equations of motion (i.e., Newton s or Hamilton s equations, or the corresponding inertial Langevin equations), which attempt to resolve the ballistic motion observed over short time scales, or into a theory of Brownian motion, which describes only the diffusive motion observed over longer time scales. We focus here on the latter case, in which constraints are introduced directly into the theory of Brownian motion, as described by either a diffusion equation or an inertialess stochastic differential equation. Although the analysis given here is phrased in quite general terms, it is motivated primarily by the use of constrained mechanical models to describe the dynamics of polymers in solution, for which the slowest internal motions are accurately described by a purely diffusive dynamical model. 

Whereas many scientists shared Mulliken s initial skepticism regarding the practical role of theory in solving problems in chemistry and physics, the work of London (6) on dispersion forces in 1930 and Hbckel s 7t-electron theory in 1931 (7) continued to attract the interest of many, including a young scientist named Frank Westheimer who, drawing on the physics of internal motions as detailed by Pitzer (8), first applied the basic concepts of what is now called molecular mechanics to compute the rates of the racemization of ortho-dibromobiphenyls. The 1946 publication (9) of these results would lay the foundation for Westheimer s own systematic conformational analysis studies (10) as well as for many others, eg, Hendrickson s (11) and Allinger s (12). These scientists would utilize basic Newtonian mechanics coupled with concepts from spectroscopy (13,14) to develop nonquantum mechanical models of structures, energies, and reactivity. 

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