Showing papers in "Progress in Biophysics & Molecular Biology in 1996"

Development and applications of in vivo clinical magnetic resonance spectroscopy

Abstract: 4.1 CURRENT STATUS. While an extensive clinical literature of MRS of muscle, brain, heart and liver has been achieved, the MRS technique is not considered essential for routine diagnosis because it is inherently insensitive and metabolic changes tend to be small. However, MRS techniques have proven to be of considerable value for prognosis in some circumstances, notably for predicting outcome following hypoxic-ischaemic injury in the newborn and also in predicting graft viability following organ transplantation. The chemical specificity of MRS has been illustrated, and exploiting the non-invasive nature of the technique, metabolic fingerprinting of pathophysiological processes throughout the natural history of a wide variety of diseases is now being accomplished. Particularly exciting are the applications of 13C MRS for measuring hepatic and muscle glycogen levels, for example in diabetics, and the use of hepatic 31P MRS for assessing liver function in cirrhosis. Other areas of excitement are the applications of 1H MRS in assessing neuronal function in epilepsy and stroke, and for measuring the evolution of lactate in stroke and hypoxic-ischaemic encephalopathy. Emphasis on technique development continues, and applications still tend to be technology-led. The availability of routine clinical MRI systems with spectroscopy capabilities has given MRS studies wider applicability. The recent improvements in spatial resolution have been impressive and the technique is slowly becoming more quantitative. 4.2. FUTURE PERSPECTIVES. Given the flexibility of clinical magnetic resonance techniques, particularly magnetic resonance imaging, it is likely that MRI will be the diagnostic tool of choice in a wider range of diseases, such as multiple sclerosis, stroke, neurodegenerative conditions, sports injuries and in staging malignancies. Since proton magnetic resonance spectroscopy packages have become a routine addition to many MRI systems, it is feasible to select the MRI sequences of most value in highlighting anatomical and pathological abnormalities and to incorporate specifically selected MRS sequences to emphasize biochemical differences. Improvements in technical methodologies are central to further developments. For example, use of internal coils, such as implantable or endoscopic coils, will enable small regions of tissue to be studied in considerable detail, which may otherwise be inaccessible to measurement. Chemical MRS studies have benefited from the use of higher magnetic fields, and the same may be expected for clinical MRS studies. Whole-body magnets up to 4 T have been used in a few centres, and certainly 3 T systems are becoming more widely available with the recent tremendous interest in functional imaging. Certainly, better control of artefacts can be expected; for example, improved definition of spectral changes due to voluntary or involuntary movements. Wider use of proton decoupling methods will improve the specificity of the spectra, by allowing definitive assignments of overlapping resonances, as well as the sensitivity. Comparing PET and MRS studies, it is becoming increasingly obvious that both will be required in parallel to explore parameters of brain metabolism and function. The ability to measure 13C MR signals in the brain has been demonstrated, which allows measurements of glutamate and glucose turnover. MRS measurements have the advantage of not requiring a radioactive isotope, as well as being insensitive to activity-related changes in regional cerebral blood flow. Also the study of cerebral glucose metabolism by MRS is very promising, allowing a resolution and sensitivity comparable to PET. A combination of MRS and PET studies will allow the pathogenesis of neuropsychiatric disorders to be better understood. (ABSTRACT TRUNCATED)

Orientational order determination by internal reflection infrared spectroscopy.

Abstract: PATIR-FTIR spectroscopy is a powerful technique for the determination of molecular order in thin films such as supported lipid membranes, but it relies on electromagnetic theory which is incomplete and potentially misleading. A complete derivation of the current theory for two, three and four phase system has been reported. The two phase and thin film approximations most commonly used in practice have been shown to represent the thickness-dependent expressions from which they are derived with a high degree of accuracy. However, these expressions are based on the macroscopic behavior of dielectric materials, and may not be accurate when applied to microscopic circumstances. The potential error introduced is qualitatively and quantitatively significant. Further experimental and theoretical work is needed to verify the accuracy of this theory, or to refute and refine it. This effort to do this is warranted by the power and increasing popularity of the technique.

The solution structure of paramagnetic metalloproteins.

Abstract: Paramagnetism causes broadening of the NMR lines and therefore makes dif®cult the detection of the constraints (NOEs and J) which are necessary for the determination of solution structures. The broadening is due to the fast nuclear relaxation rates, which are induced by the coupling of the nucleus with the unpaired electrons. Nevertheless, an NMR methodology has been developed, allowing the detection of classical constraints. This has allowed us to solve the ®rst solution structure of a paramagnetic metalloprotein in 1994. Since then, several solution structures of paramagnetic proteins have appeared. In addition, paramagnetism has been exploited in order to obtain new, nonclassical constraints. First, the nuclear relaxation has been exploited to obtain metal±proton distances. The position of nuclei with respect to the magnetic susceptibility tensor axes has been determined by the use of pseudocontact shifts. The contact shifts have been used as constraints after discovering or con®rming the shift dependence on dihedral angles. Paramagnetic molecules can be strongly magnetically anisotropic and therefore display partial orientation in strong external magnetic ®elds. These orientational effects result in dipolar contributions to the N-H J coupling. Such contributions can yield powerful structural constraints. In summary, the solution structure of many paramagnetic metalloproteins has been solved and described, and several new strategies have been developed for such solution structure determinations.

Nucleic acid crystallography: a view from the nucleic acid database.

Abstract: What are the future directions of the field of nucleic acid crystallography? Although there have been many duplex structures determined, the sample is still relatively small. This is especially true if one wants to derive enough information about the relationships between sequence and structure. Indeed, there are data for all the possible 10 dimer steps, but for some steps it is very limited. If the structural code resides in trimers or tetrad steps then there is simply not enough data to do meaningful statistical analyses. So the first direction that needs to be explored is the determination of more structures with more varied sequences. The other noticeable thing about the data is the shortness of the strands. While it is probably true that attempts to crystallize very long sequences will not meet with success, the idea of crystallizing sequences engineered to fit together via sticky ends such as has been done for the CAP-DNA complex (Schultz et al., 1990) should give data about the behavior of much longer stretches of DNA. The question of the effects of environment on the structure of DNA continues to be a very important one to address since DNA is rarely alone. The preliminary data we have analysed from the current sample shows that the conformation of some steps are very sensitive to packing type. Numerous studies of the hydration around DNA shows that there is a real synergy between the hydration structure and the base conformation. More data will allow further quantitation of these observations. RNA structure is the next very exciting frontier. The emerging structures of duplexes with internal loops, the two hammerhead ribozyme structures and the group I intron ribozyme have given us a glimpse of the complexity and elegance of this class of molecules. With the technology now in place to allow the determination of the structures of these molecules, the expectation is that now we will see a large increase in the number of these structures in the NDB.

Nucleic acid structure and recognition

Abstract: We review the global structures adopted by branched nucleic acids, including three- and four-way helical junctions in DNA and RNA. We find that some general folding principles emerge. First, all the structures exhibit a tendency to undergo pairwise coaxial helical stacking when permitted by the local stereochemistry of strand exchange. Second, metal ions generally play an important role in facilitating folding of branched nucleic acids. These principles can be applied to functionally important branched nucleic acids, such as the Holliday DNA junction of genetic recombination, and the hammerhead ribozyme in RNA.