Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.     

Structure and internal mobility of proteins: a molecular dynamics study of hen egg white lysozyme

The structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high-resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root-mean-square deviations for backbone atoms of 2.3 Å and 1.1–1.3 Å, respectively, relative to the crystal structures; the different crystal structures have root-mean-square deviations of 0.73–0.81 Å for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β-sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side-chain atoms have larger fluctuations than main-chain atoms. Moreover, the regions that have large deviations among the x-ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.     

Cytogenetical effects of ageing in seeds

Freshly harvested seeds of soybean and barley were artificially aged. The progeny showed a marked decrease in mitotic index and chromosomal aberrations of various types increased at both mitosis and meiosis, resulting in a significant loss of pollen viability as the ageing advanced. Studies on the types and frequencies of chlorophyll deficients and phenodeviants also showed an overall increase, suggesting that ageing mimics irradiation effects and produces alterations in the gene complexes resulting in the segregation of different kinds of phenotypic mutations.     

Urine dopamine in starving obese subjects

In seven obese female subjects undergoing a period of therapeutic starvation, the excretion of sodium, potassium and dopamine and plasma levels of renin and aldosterone were measured. Sodium excretion increased during starvation and was maximal on the 2nd day. The urinary excretion of dopamine was significantly higher on day 4 and it remained elevated till the end of the study. Plasma renin activity and plasma aldosterone levels were also higher on the 4th-6th days of starvation. These findings suggest that dopamine may not play a significant role in the natriuresis of starvation.     

Effect of X-radiation on pollen tube growth and seed setting in crosses between Nicotiana tabacum and N. rustica

Summary In vitro andin vivo studies of the effect of irradiating pollen with different doses of X-rays were carried out inNicotiana rustica andN. tabacum. Dosages upto 9600 r were found to enhance the rate of growth of pollen tubers per unit time. Advantage was taken of this observation to overcome the incompatibility normally found in the crossN. tabacum x N. rustica as a result of the inadequate growth ofrustica pollen tubes intabacum style. Thus, whenrustica pollen exposed to 4800 r and 9600 r of X-rays were used to pollinatetabacum, fertilization resulting in the formation of viable hybrid seeds occurred. In the crossN. rustica×N. tabacum there is partial seed failure as a result of the hyperplastic development of the nucellar and endothelial cells. However, when X-rayedtabacum pollen were used in the cross, seed development registered a marked improvement. Since there is now evidence for suggesting that the contents of even those pollen tubes which do not participate in fertilization have some role to play in the development of the seed, it seems likely that radiation-induced biochemical changes in pollen may prove advantageous when conditions for seed development are abnormal as in instances of somatoplastic sterility. Besides such indirect biochemical effects, irradiation of pollen may also lead to genetic changes resulting in the inactivation of zygotic lethals. Thus, there is much scope for investigating the use of radiation to overcome inter-specific and inter-generic cross-incompatibility barriers.With 2 Figures in the Text     

Biodegradation of phenol by arthrobacter and modelling of the kinetics

The toxic effects of phenol, a common constituent of many industrial effluents, necessitates treatment of the polluted streams. Biodegradation is a popular technique and enjoys many advantages. The degradation of phenol with Arthrobacter species is studied in batch cultures and it is observed that the substrate is inhibiting. The fit of various models, including the model proposed earlier by us [17], to the experimental data is studied. The model is used to fit available data in literature, which unfortunately is very sparse. In all the cases the present model fits the data best.List of Symbols S mg/l substrate concentration - S ₀ mg/l threshold substrate concentration - K _I mg/l inhibition constant - K _m , K _s mg/l half saturation constant of growth kinetics - m, n constants - 1/h specific growth rate - _m 1/h maximal specific growth rate - X mg/l biomass concentration at time t - X ₀ mg/l initial biomass concentration Abbreviations MTCC Microbial Type Culture Collection - IMTECH Institute of Microbial Technology The cooperation of the staff of the Biosciences and Biotechnology Center, I.I.T. Madras is greatly appreciated.