Relaxation data, dynamic information

This approach yields spectral densities. Although it does not require assumptions about the correlation function and therefore is not subjected to the limitations intrinsic to the model-free approach, obtaining information about protein dynamics by this method is no more straightforward, because it involves a similar problem of the physical (protein-relevant) interpretation of the information encoded in the form of SD, and is complicated by the lack of separation of overall and local motions. To characterize protein dynamics in terms of more palpable parameters, the spectral densities will then have to be analyzed in terms of model-free parameters or specific motional models derived e.g. from molecular dynamics simulations. The SD method can be extremely helpful in situations when no assumption about correlation function of the overall motion can be made (e.g. protein interaction and association, anisotropic overall motion, etc. see e.g. Ref. [39] or, for the determination of the 15N CSA tensor from relaxation data, Ref. [27]). 

Relaxation measurements provide a wealth of information both on the extent of the interaction between the resonating nuclei and the unpaired electrons, and on the time dependence of the parameters associated with the interaction. Whereas the dipolar coupling depends on the electron-nucleus distance, and therefore contains structural information, the contact contribution is related to the unpaired spin density on the various resonating nuclei and therefore to the topology (through chemical bonds) and the overall electronic structure of the molecule. The time-dependent phenomena associated with electron-nucleus interactions are related to the molecular system, and to the lifetimes of different chemical situations, for the resonating nucleus. Obtaining either structural or dynamic information, however, is only possible if an in-depth analysis of a series of experimental results provides sufficient data to characterize the system within the theoretical framework discussed in this chapter. 

Solid-state NMR magnetisation relaxation experiments provide a good method for the analysis of network structures. In the past two decades considerable progress has been made in the field of elastomer characterisation using transverse or spin-spin (T2) relaxation data [36-42]. The principle of the use of such relaxation experiments is based on the high sensitivity of the relaxation process to chain dynamics involving large spatial-scale chain motion in elastomers at temperatures well above the Tg and in swollen networks. Since chain motion is closely coupled to elastomer structure, chemical information can also be obtained in this way. 

This outline of the response theory has for simplicity been limited to molecules with axial symmetry of y and Aa and to the field on, field off cases, but can be extended in both respects without basic difficulties. Detailed comparisons with experiment have not yet been made, but it already is clear that Kerr effect relaxation data can now provide more valuable and better defined information about orientational dynamics of biopolymers and other molecules than was previously possible. With the increasing accuracy and time resolution of digital methods, it should be possible to study not only slow overall rotations of large molecules (microseconds or longer) but small conformational effects and small molecule reorientations on nano and picosecond time scales. Moreover, one can anticipate the possibilities, for simple problems at least, of extending response theory to other quadratic and higher order effects of strong electric fields on observable responses. 

One of the most widely used tools to assess protein dynamics are different heteronuclear relaxation parameters. These are in intimate connection with internal dynamics on time scales ranging from picoseconds to milliseconds and there are many approaches to extract dynamical information from a wide range of relaxation data (for a thorough review see Ref. 1). Most commonly 15N relaxation is studied, but 13C and 2H relaxation are the prominent tools to characterize side-chain dynamics.70 Earliest applications utilized 15N Ti, T2 relaxation as well as heteronuclear H- N) NOE experiments to characterize N-H bond motions in the protein backbone.71 The vast majority of studies applied the so-called model-free approach to translate relaxation parameters into overall and internal mobility. Its name contrasts earlier methods where explicit motional models of the N-H vector were used, for example diffusion-in-a-cone or two- or three-site jump, etc. Unfortunately, we cannot obtain information about the actual type of motion of the bond. As reconciliation, the model-free approach yields motional parameters that can be interpreted in each of these motional models. There is a well-established protocol to determine the exact combination of parameters to invoke for each bond, starting from the simplest set to the most complex one until the one yielding satisfactory description is reached. The scheme, a manifestation of the principle of Occam s razor is shown in Table l.72... 

The underlying strategy for extracting dynamical information from NMR relaxation data is based on the equations for either longitudinal (Tfl) or transverse (T2 ) relaxation rates. If relaxation is dominated by the magnetic dipole-dipole interaction between like-spin nuclei, then... 

This data can help understand activation processes in other kinases too. However, this picture is inherently incomplete as it relies upon the availability of structural data that covers the whole motion. Models based on analogy arguments have to be further tested whether motions inferred for PKA can in fact be transferred to other kinases. Solution-state NMR can act as a complement in providing a dynamic picture that links the static structures obtained by X-ray crystallography. Two NMR methods can provide information about conformational rearrangements of a protein at atomic resolution. NMR relaxation measurements yield information on the timescale of a process, whereas RDC can characterize the spatial nature of such a motion. 

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