Nanosecond-pulse fluorometry study of S4 ribosomal protein

Ribosomal proteins: their structure and spatial arrangement in prokaryotic ribosomes

During the last 15 years of ribosomal protein study, enormous progress has been made. Each of the proteins from E. coli ribosomes has been isolated, sequenced, and immunologically and physically characterized. Ribosomal proteins from other sources (e.g., from some bacteria, yeast, and rat) have been isolated and studied as well. Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. Tremendous progress has also been made in deciphering the architecture of the ribosome. A battery of different methods has been used to provide the nearest neighbor distances of the ribosomal proteins in situ. Definitive measurements are now emanating from neutron-scattering experiments which also promise to give reasonably accurate radii of gyration of the proteins in situ. In turn, refined immune electron microscopy results supplement the neutron-scattering data and also position the proteins on the subunits themselves. This cannot be done by the other methods. Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combining the data from protein-RNA and from RNA-RNA cross-linking studies, the structure of the RNA in situ can be unraveled. Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers.

Rates of deactivation processes of indole derivatives in water-organic solvent mixtures--application to tryptophyl fluorescence of proteins

The fluorescence quantum yield and the fluorescence decay of indole, 3-methylindole, 1-methylindole and N-acetyltryptophanamide have been measured in different water-dioxane mixtures. For the first three derivatives, the fluorescence decays were found independent of the emission wavelength and were analyzed as single exponential functions. In the case of N-methylindole the rate of the non radiative deactivation processes knr increased linearly with the molar fraction of dioxane whereas for indole and scatole the variation of knr was biphasic. This behaviour can be explained by two excited state deactivations of these non N-methylated compounds in water and high water content mixtures; one of these deactivation processes occuring through an hydrogen bond between the N-H group and a water molecule. The rate of non radiative deactivation of N-acetyltryptophanamide was dominated by the internal quenching involving the intramolecular carbonyl. The rate of the radiative deactivation process kF of these four compounds increased linearly with the wavenumber of the fluorescence spectrum maximum. Data relative to the three non N-methylated derivatives fell practically on the same straight line. Data from other works have been gathered in order to check if a similar relation between the intrinsic kF and vF values can exist for the tryptophyl fluorescence emission of proteins.

Physical studies on the conformation of ribosomal protein S4 from Escherichia coli

Proton magnetic resonance, circular dichroism and infrared spectroscopy were used to investigate the secondary and tertiary structure of the 16-S RNA binding protein S4 from Escherichia coli ribosomes. The proton magnetic resonance spectra of protein S4 in ribosomal reconstitution and low-salt buffers were identical and showed little dipolar broadening of the peaks, suggesting that the protein had an open extended structure. A ring-current-shifted apolar methyl resonance in the high-field region of the spectrum, together with a perturbation of the tyrosine ring proton resonance in the low-field region, indicated the existence of a specific tertiary fold in the polypeptide chain. This structure disappeared on lowering the pH below 5 or on heating above 30 degrees C, both processes being reversible. Circular dichroism measurements on protein S4 showed an alpha-helix content of 32% in reconstitution buffer compared with 26% in low-salt buffer. Heating the protein solution in reconstitution buffer above 35 degrees C reversibly disrupted this extra helix. Infrared studies on both solid films and solutions of protein S4 indicated the presence of little or no beta-structure. These results correlate well with the known RNA binding properties of protein S4.