Types Of Biological Molecules Research Articles

Molecular mimicry: Quantitative methods to study structural similarity between protein and RNA

With rapidly increasing availability of three-dimensional structures, one major challenge for the post-genome era is to infer the functions of biological molecules based on their structural similarity. While quantitative studies of structural similarity between the same type of biological molecules (e.g., protein vs. protein) have been carried out intensively, the comparable study of structural similarity between different types of biological molecules (e.g., protein vs. RNA) remains unexplored. Here we have developed a new bioinformatics approach to quantitatively study the structural similarity between two different types of biopolymers--proteins and RNA--based on the spatial distribution of conserved elements. We applied it to two previously proposed tRNA-protein mimicry pairs whose functional relatedness between two molecules has been recently determined experimentally. Our method detected the biologically meaningful signals, which are consistent with experimental evidence.

Use of the same polymer for synthesis and purification of peptides

This work reveals an uncommon but valuable biotechnological approach regarding the use of a same polymer (benzhydrylamine-resin, BHAR) for synthesis and anion exchange purification of peptides. Initially, the octapeptide DRVYIHPF-NH2 was synthesized in 1% and 3% cross-linked BHAR, attaching 2.5 mmol g-1 ammonium groups. Due certainly to its less rigid polymeric backbone, higher synthesis yield (about 80%) was achieved with the former resin. Next, the negatively charged peptides DEVYEHPF-NH2 and DEVYEDPF-NH2 (-1 and -3 in neutral pH, respectively), both synthesized in 1% BHAR were submitted to chromatographic separation test in this same type of resin (1% and 3%). Following comparative results of peptide synthesis and swelling data of resin beads obtained by microscopy, an improved separation of both peptides occurred with 1% BHAR batch. These findings demonstrated that BHAR applied so far for peptide synthesis, when containing high amount of positively charged ammonium groups, can be also used alternatively as a solid support for chromatographic purification of this type of biological molecule.

45] Reactive absorption of ozone: An assay for reaction rates of ozone with sulfhydryl compounds and with other biological molecules

Publisher Summary Ozone is toxic to both plants and animals. Because the reactions of ozone with many types of biological molecules are extremely fast, ozone reacts very close to the surface of tissues that are in direct contact with the atmosphere. In animals, ozone reacts with biomolecules present in the fluid lining the air passages of lungs. In plants, ozone reacts with biomolecules within the cell walls lining the air passages of leaves. As ozone is consumed within tissues through reactions with biological molecules, more ozone is drawn into the tissues in a process called reactive absorption. Mathematical models of reactive absorption are well established and provide a means of calculating reaction rate constants for gases that react with nonvolatile solutes in liquids. While most of the development of these mathematical models has occurred within the chemical engineering literature, the measurement of reactive absorption can provide some unique insights about ozone reactions with biological molecules close to the surface of a solution. Using a very simple apparatus, it is possible to obtain values for even very large reaction rate constants.

Scanning force microscopy of nucleic acids and nucleoprotein assemblies

The scanning force microscope uses a sharp tip mounted on a flexible cantilever to touch and create images of a surface. During the past year, great progress has been made in the applications of SFM to imaging biological specimens. This progress has been made possible by advances in three areas: improved tip fabrication, development of better deposition methods; and control of sample environment. At present, SFM can reliably image most types of biological molecules at ~ 50–100 A resolution, depending on the system studied. The main technical advances of the past year, which often took place in connection with the imaging of nucleic acids and nucleoprotein assemblies, are reviewed. Potential solutions to present technical limitations and promising new developments now underway are also discussed.

Quenching of singlet oxygen by biomolecules from L1210 leukemia cells.

Singlet oxygen lifetimes for detergent-dispersed L1210 leukemia cells in deuterium oxide buffer were measured by following the decay of 1270 nm phosphorescence. Four photosensitizers and two detergents were studied. Stern-Volmer plots were linear over the cell concentration range studied (0-10(7) cells/mL). The singlet-oxygen quenching constants obtained depended somewhat upon the specific combination of detergent and photosensitizer used. Extrapolation of the singlet-oxygen lifetime data to "100%" cell concentration (1.39 +/- 0.04 x 10(9) cells/mL) and correction for the contribution of the water solvent gave a singlet-oxygen lifetime between 0.17 and 0.32 microseconds for the L1210 leukemia cell. The theoretical contributions of various types of biological molecules within the L1210 cell to the total singlet-oxygen quenching were calculated from their concentrations and their quenching constants. These calculations suggest that proteins will quench most of the singlet-oxygen. Only about 7% of the singlet-oxygen is quenched by water.