Thermodynamics of specific protein-RNA interactions.

Abstract

Description of the recognition specificity between proteins and nucleic acids at the level of molecular interactions is one of the most challenging tasks in biophysics. It is key to understanding the course and control of gene expression and to the application of the thus acquired knowledge in chemotherapy. This review presents experimental results of thermodynamic studies and a discussion of the role of thermodynamics in formation and stability of functional protein-RNA complexes, with a special attention to the interactions involving mRNA 5' cap and cap-binding proteins in the initiation of protein biosynthesis in the eukaryotic cell. A theoretical framework for analysis of the thermodynamic parameters of protein-nucleic acid association is also briefly surveyed. Overshadowed by more spectacular achievements in structural studies, the thermodynamic investigations are of equal importance for full comprehension of biopolymers' activity in a quantitative way. In this regard, thermodynamics gives a direct insight into the energetic and entropic characteristics of complex macromolecular systems in their natural environment, aqueous solution, and thus complements the structural view derived from X-ray crystallography and multidimensional NMR. Further development of the thermodynamic approach toward interpretation of recognition and binding specificity in terms of molecular biophysics requires more profound contribution from statistical mechanics.

High-resolution synchrotron radiation studies on natural and thermally annealed scleractinian coral biominerals

“…Formic acid is known to dissolve not only mineral but also organic components (Waite & Andersen, 1980); therefore etching of the samples yields a distinct negative relief corresponding to regions (Figs. 1 and 2) enriched in organic content (see also Stolarski, 2003). The etched samples were rinsed with distilled water and air-dried.…”

“…Part of the samples (synthetic aragonite and biomineral ones) were thermally annealed to produce transformation of aragonite to calcite. The procedure involved heating of the samples in air at linear gradient (10 K min À1 ) from ambient 293 K to 773 K. The sample was kept at 773 K for 1 h and then allowed to cool slowly for ca 12 h. The experimental details were adjusted on the basis of our previous thermogravimetric measurements (Stolarski & Mazur, 2005). Under these conditions all aragonite is transformed to calcite, while further decomposition of the mineral to CaO is hindered.…”

“…In polished and etched sections of the natural skeleton of Favia and Desmophyllum two main regions are recognizable, described in biological literature as calcification centers [or centers of rapid accretion (CRAs) or early mineralization zones] and fibers (thickening deposits) (see Cuif et al, 2003;Stolarski, 2003). The calcification centers are greatly enriched in organic components and thus exhibit a strong negative relief in etched sections, whereas fibers, which contain less organic matter, show generally positive etching relief with some important exceptions; etching accentuates borders between bundles of fibers and their successive growth steps that are regularly distributed and dense in Favia (every research papers Sample of Favia (F. stelligera, ZPALV.31/1) (a) before and (b) after the annealing treatment at 773 K, at two SEM magnifications (a 1 ), (b 1 ) and (a 2 ), (b 2 ).…”

“…(a 1 , a 2 ) Polished and etched (formic acid, 1%, 20 s) transverse section of septal and wall skeleton with aragonite fibers radiating from CRAs. Black arrows indicate the negative etching relief of CRA regions that are particularly enriched in organic components (see Stolarski, 2003). (b 1 , b 2 ) The same skeleton annealed; the fibrous skeletal texture is replaced by irregularly arranged calcite grains.…”

“…Gré goire, 1967;Mutvei, 1969Mutvei, , 1979Currey & Kohn, 1976;Cuif & Dauphin, 2005a;Rousseau et al, 2005). Notably, the composite structure of the scleractinian coral skeleton was only recently elucidated, challenging the long-kept concept of their purely crystalline CaCO 3 (aragonite) composition (Cuif et al, 1997;Stolarski, 2003;Cuif & Dauphin, 2005b;Stolarski & Mazur, 2005). The occurrence of the intraskeletal organic components of coral skeletons has been assessed in the bulk samples by thermogravimetric (Cuif et al, 2004;Stolarski & Mazur, 2005), chromatographic (Dauphin, 2001) and spectroscopic (Cuif & Dauphin, 1998) methods, whereas their spatial distribution pattern has been studied by histological staining (Gautret et al, 2000;Stolarski, 2003) and synchrotron radiation (SR) mapping techniques (Cuif et al, 2003).…”