Transglycosylation by Chitinase D from Serratia proteamaculans Improved through Altered Substrate Interactions

We describe the improvement of transglycosylation (TG) by chitinase D from Serratia proteamaculans (SpChiD). The SpChiD produced a smaller quantity of TG products for up to 90 min with 2 mm chitotetraose as the substrate and subsequently produced only hydrolytic products. Of the five residues targeted at the catalytic center, E159D resulted in substantial loss of both hydrolytic and TG activities. Y160A resulted in a product profile similar to SpChiD and a rapid turnover of substrate with slightly increased TG activity. The rest of the three mutants, M226A, Y228A, and R284A, displayed improved TG and decreased hydrolytic ability. Four of the five amino acid substitutions, F64W, F125A, G119S, and S116G, at the catalytic groove increased TG activity, whereas W120A completely lost the TG activity with a concomitant increase in hydrolysis. Mutation of Trp-247 at the solvent-accessible region significantly reduced the hydrolytic activity with increased TG activity. The mutants M226A, Y228A, F125A, S116G, F64W, G119S, R284A, and W247A accumulated approximately double the concentration of TG products like chitopentaose and chitohexaose, compared with SpChiD. The double mutant E159D/F64W regained the activity with accumulation of 6.0% chitopentaose at 6 h, similar to SpChiD at 30 min. Loss of chitobiase activity was unique to Y228A. Substitution of amino acids at the catalytic center and/or groove substantially improved the TG activity of SpChiD, both in terms of the quantity of TG products produced and the extended duration of TG activity.     

Photosynthesis and yield in cotton (Gossypium hirsutum L.) Var. Vikram after exclusion of ambient solar UV-B/A

The impact of ambient solar UV was studied on the photosynthesis and yield of cotton (Gossypium hirsutum) var. Vikram in a field experiment by excluding either UV-B (<315 nm) or UV-B/A (<400 nm) components of solar spectrum. Cotton plants were grown in cages covered with polyester filters that could specifically cut off UV-B or UV-B/A part of the solar spectrum. The control plants were grown under a filter transmissible to UV. Exclusion of UV enhanced plant height, leaf area, total biomass, and the yield parameters (number and weight of bolls, length of fiber and number of seeds) of cotton. Enhancement in the vegetative growth and yield of the plants could be related to enhanced rate of photosynthesis in the leaves. Polyphasic chlorophyll a fluorescence (OJIP) transients from UV excluded plants gave a higher fluorescence yield at I–P phase. Fluorescence measurements indicated enhanced F _v/F _m ratio and reduction capacity after exclusion of solar UV. Exclusion also enhanced stomatal conductance and intercellular CO₂ concentration and reduced the stomatal resistance. Total soluble proteins were higher after UV exclusion, and in SDS–PAGE analysis, bands corresponding to smaller subunits (14 kDa) of Rubisco were more intensely stained. Experiments indicated suppressive action of ambient UV on carbon fixation and yield of cotton plants. Exclusion of solar UV proved to be beneficial in enhancing the yield of cotton plants.     

Conformational analysis corresponding to intra-chain disulfide bridged peptides in proteins of known three-dimensional structure

We have carried out a systematic analysis in order to evaluate whether Intra-Chain Disulfide Bridged Peptides (ICDBPs) observed in proteins of known three-dimensional structure adopt structurally similar conformations as they may correspond to structural/functional motifs. 406 representative ICDBPs comprising between 3 to 17 amino acid residues could be classified according to peptide sequence length and main-chain secondary structure conformation into 146 classes. ICDBPs comprising 6 amino acid residues are maximally represented in the Protein Data Bank. They also represent the maximum number of main-chain secondary structure conformational classes. Individual ICDBPs in each class represent different protein superfamilies and correspond to different amino acid sequences. We identified 145 ICDBP pairs that had not less-than 0.5 A root mean square deviation value corresponding to their equivalent peptide backbone atoms. We believe these ICDBPs represent structural motifs and possible candidates in order to further explore their structure/function role in the corresponding proteins. The common conformational classes observed for ICDBPs defined according to the main-chain secondary structure conformations; H (helix), B (residue in a isolated beta bridge), C (coil), E (extended beta strand), G (3(10) helix), I (pi helix), S (bend), T (hydrogen-bonded turn) were; "CHHH", "CTTC", "CSSS" and "CSSC" (for ICDBP length 4), "CSSCC" (length 5), "EETTEE", "CCSSCC", "CCSSSC" (length 6), "EETTTEE" (length 7), "EETTTTEE" (length 8), "EEEETTEEEE" (length 10), "EEEETTTEEEE" (length 11) and "EEEETTTTEEEE" (length 12).     

A possible role of erythrocytes in storing and distributing arachidonic acid in rat

Young rats weighing 120g and having a packed red cell volume of 37.4% were maintained on a fat free diet. In eight weeks their body weights and packed red cell volume increased to 425g and 45.4%, respectively. However, the proportion of arachidonic acid (20:4) in the total fatty acids was unaltered in erythrocytes but was lowered in other tissues. In adipose tissue, which contained only trace levels of 20:4, about one third of the fatty acid was linoleic acid (18:2). Feeding fat free diet caused a depletion of most of 18:2 in the adipose tissue. Thus, during growth, when 18:2 is excluded from the diet, erythropoiesis is not inhibited. Furthermore, 20:4 produced from stored 18:2 may be used for the production of erythrocytes which retain the tetraenoic acid effectively.     

Impact of pre-sowing magnetic field exposure of seeds to stationary magnetic field on growth, reactive oxygen species and photosynthesis of maize under field conditions

Impact of pre-sowing exposure of seeds to static magnetic field were studied on 1 month old maize [Zea mays _. var: HQPM.1] plants under field conditions. Pre-standardized magnetic field strength of 100 mT (2 h) and 200 mT (1 h), which were proven best for improving different seedling parameters under laboratory condition, were used for this study. Magnetic field treatment altered growth, superoxide radical level, antioxidant enzymes and photosynthesis. Among the different growth parameters, leaf area and root length were the most enhanced parameters (78–40%, respectively), over untreated plants. Electron paramagnetic resonance spectroscopy study showed that superoxide radical was reduced and hydroxyl radical was unaffected after magnetic field treatment. With decrease in free radical content, antioxidant enzymes like superoxide dismutase and peroxidase were also reduced by 43 and 23%, respectively, in plants that emerged from magnetically treated seeds. Measurement of Chlorophyll a fluorescence by plant efficiency analyzer showed that the potential of processing light energy through photosynthetic machinery was enhanced by magnetic field treatment. Performance index of the plant enhanced up to two-fold and phenomenological leaf model showed more active reaction centers after magnetic field treatment. Among the two field strengths used, 200 mT (1 h) was more effective in altering all these parameters. It is concluded that pre-sowing magnetic field treatment can be effectively used for improving plant growth and development under field conditions.     

Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins.

The number of gamma-turns in a representative protein dataset selected from the current Protein Data Bank has increased almost seven times during the past decade. Eighty percent classic gamma-turns and 57% inverse gamma-turns are associated as multiple turns with either another y-turn or a beta-turn. We refer to these as multiple turns of the (gammabeta)1,2,3 or (betagamma)1,2,3 type, depending upon whether the gamma-turn is before or after the beta-turn along the protein chain, respectively. However, for multiple turns involving only gamma-turns, we follow the nomenclature analogous to that proposed earlier for the multiple (or double) beta-turns. Fifty-eight per cent beta-turns are associated as multiple turns with another beta-turn. We extracted multiple turns from the protein dataset and classified them on the basis of individual gamma- or beta-turn types and the number of overlapping residues. Furthermore, we evaluated the amino acid positional potentials and determined the statistically significant amino acid preferences, hydrogen bond/side-chain interaction preferences in the multiple turns and secondary structure preferences for residues immediately flanking these turns. The results of our analysis would be useful in the modeling, prediction or design of multiple turns in proteins. The amino acid sequence corresponding to the multiple turn, position in the protein chain, PDB Code/chain in which multiple turn is present and the individual turn types constituting the multiple turns are available from our website and this information would also be integrated in our Database of Structural Motifs in Proteins (http://www.cdfd.org.in/dsmp.html).     

CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms arecompared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globularprotein''s atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed indimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structurehas better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxinprotein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broadspectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. Thecarbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help inunderstanding the protein folding and function.