Structural information, experimental techniques

The popularity of high resolution NMR is still unbroken and is based on its excellent information content with respect to molecular structures. New experimental techniques have opened new areas of application and improvements in spectrometer hard- and software not only fascilitate daily work of spectroscopists but bring NMR closer to the non-experienced user. 

It has been possible to determine transition structures computationally for many years, although not always easy. Experimentally, it has only recently become possible to examine reaction mechanisms directly using femtosecond pulsed laser spectroscopy. It will be some time before these techniques can be applied to all the compounds that are accessible computationally. Furthermore, these experimental techniques yield vibrational information rather than an actual geometry for the transition structure. 

The advantages of SEXAFS/NEXAFS can be negated by the inconvenience of having to travel to synchrotron radiation centers to perform the experiments. This has led to attempts to exploit EXAFS-Iike phenomena in laboratory-based techniques, especially using electron beams. Despite doubts over the theory there appears to be good experimental evidence that electron energy loss fine structure (EELFS) yields structural information in an identical manner to EXAFS. However, few EELFS experiments have been performed, and the technique appears to be more raxing than SEXAFS. 

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. 

No experimental technique exists for determining I-structures in either the liquid or the solid state. Techniques do exist for obtaining information on both the V- and D-structures of liquid water the results of applying these techniques are considered next. 

Hydropolymer gel has been considered as a possible candidate for an artificial articular cartilage in artificial joints because it exhibits very low friction when it is in contact with a solid. The origin of such low friction is considered to be associated with the water absorbed in the gel [83-86], some of which is squeezed out from the gel under the load and serves as a lubricant layer between the gel and solid surface, resulting in hydrodynamic lubrication [87, 88]. Although the structural information about the interfacial water is important to understand the role of water for the low frictional properties of hydrogel in contact with a solid and the molecular structure of lubricants other than water at solid/solid interfaces have been investigated theoretically [89-91] and experimentally [92-98], no experimental investigations on water structure at gel/solid interfaces have been carried out due to the lack of an effective experimental technique. 

In conclusion, rapid-mixing/rapid-freezing EPR is a wonderful technique to obtain unique molecular structural information on biochemical reaction intermediates with high time resolution, but it is also experimentally sufficiently involved that one should either build up a dedicated lab with dedicated operators or turn to one of the existing groups that have the equipment and, especially, the developed skills to do these experiments. Be prepared to provide at least an order of magnitude more sample than required for a static EPR experiment. 

These difficult experimental controversies show that there is a significant role for NMR, a non-perturbing non-destructive technique that provides structural information about the local atomic environment over several bonds. 

There are three potential methods by which a protein s three-dimensional structure can be visualized X-ray diffraction, NMR and electron microscopy. The latter method reveals structural information at low resolution, giving little or no atomic detail. It is used mainly to obtain the gross three-dimensional shape of very large (multi-polypeptide) proteins, or of protein aggregates such as the outer viral caspid. X-ray diffraction and NMR are the techniques most widely used to obtain high-resolution protein structural information, and details of both the principles and practice of these techniques may be sourced from selected references provided at the end of this chapter. The experimentally determined three-dimensional structures of some polypeptides are presented in Figure 2.8. 

Electron paramagnetic resonance (EPR) and NMR spectroscopy are quite similar in their basic principles and in experimental techniques. They detect different phenomena and thus yield different information. The major use of EPR spectroscopy is in the detection of free radicals which are uniquely characterised by their magnetic moment that arises from the presence of an unpaired electron. Measurement of a magnetic property of a material containing free radicals, like its magnetic susceptibility, provides the concentration of free radicals, but it lacks sensitivity and cannot reveal the structure of the radicals. Electron paramagnetic resonance spectroscopy is essentially free from these defects. 

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