In silico analysis and homology modeling of strictosidine synthase involved in alkaloid biosynthesis in catharanthus roseus.

BACKGROUND: In this study, strictosidine synthase (STR) from Catharanthus roseus that plays an important role in alkaloid biosynthesis was selected. The purpose of this work was to perform in silico analysis and to predict the three-dimensional structure of this protein that is not available. RESULTS: Physicochemical characterization was performed by Expasy's Protparam server. The computed theoretical isoelectric point (pI) found to be less than 7 indicates the acidic nature of this protein. The aliphatic index 73.04 indicates the thermal stability of the protein. Grand average hydropathy (GRAVY) was predicted to be - 285; this lower value of GRAVY shows the possibility of better interaction of this protein with water. Functional analysis of these proteins was performed by SOSUI server which predicted the transmembrane helix. Secondary structure analysis was carried out by SOPMA that revealed that Alpha helix dominated among secondary structure elements followed by random coil, extended strand, and beta turns. The modeling of the three-dimensional structure of the STR was performed by Swiss model. The model was validated using protein structure checking tools PROCHECK and PROVE. CONCLUSIONS: This study reveals in silico analysis by Expasy Protparam server, SOPMA, and SOSUI server. Homology modeling of STR was performed by Swiss model.

Structure prediction of dihydroflavonol 4- reductase and anthocyanidin synthase from spinach.

Spinach is an important dietary vegetable associated with beneficial health effects. Flavonoids have various biological activities such as antioxidant, antibacterial, and anticancer effect Flavonoid including anthocyanin provides brilliant and colored pigments in different plant tissues. Anthocyanidin synthase and dihydroflavonol 4-reductase are responsible for anthocyanin biosynthesis. They contributed in plant protection against UV-B radiation, microbial and herbivore pathogens. A 3D structures of anthocyanidin synthase and dihydroflavonol 4-reductase from spinach are constructed in this study through homology modeling. The homology modeling is done by using the MODELLER 9v7 software. The energy of models was minimized by applying molecular mechanics method. The root mean square deviation (RMSD) for C atoms between the template and the homology-modeled structures was estimated by CE program. The final models were assessed by PROCHECK and WHATCHECK which showed that the final refined models are reliable.

Elucidating the site of action of oxalate in photosynthetic electron transport chain in spinach thylakoid membranes.

The effects of oxalate on PS II and PS I photochemistry were studied. The results suggested that in chloride-deficient thylakoid membranes, oxalate inhibited activity of PS II as well as PS I. To our knowledge, this is the only anion so far known which inhibits both the photosystems. Measurements of fluorescence induction kinetics, YZ* decay, and S2 state multiline EPR signal suggested that oxalate inhibited PS II at the donor side most likely on the oxygen evolving complex. Measurements of re-reduction of P700+ signal in isolated PS I particles in oxalate-treated samples suggested a binding site of oxalate on the donor, as well as the acceptor side of PS I.

Nitrite regulates distribution of excitation energy between the two photosystems by causing state transition.

The mechanism of distribution of absorbed excitation energy between the two photosystems in the presence of nitrite has been investigated in spinach (Spinacia oleracea L.) thylakoid membranes. Nitrite inhibited PS II activity (H(2)O --> DCPIP reaction) and enhanced PS I activity (DCPIPH(2) --> MV reaction). Nitrite decreased the F(v)/F(m) ratio measured at room temperature and increased the F(730)/F(685) ratio measured at low temperature (77 K). These results suggested that nitrite caused a decrease in the excitation energy available to PS II and transferred more energy to PS I by the mechanism of state transition. Measurement of fluorescence excitation spectra at 77 K showed that nitrite increased the absorption cross-section of PS I antenna at the expense of chlorophyll b and LHC II. Based on these observations we have suggested a role of nitrite in causing state transition.

A thermoluminescence study of the effects of nitrite on photosystem II in spinach thylakoids.

The site of action of nitrite on PS II was investigated by measuring the TL profile of nitrite-treated spinach thylakoid membranes. Three bands were observed in control, which were identified as the Q band (7 degrees C), the B band (24 degrees C) and the C band (57 degrees C). In the presence of 20 mmol/L nitrite, the intensity of the Q band decreased, the B band upshifted to 46 degrees C but the C band disappeared. The suppression of the Q band and the upshift of the B band suggested that nitrite caused inhibition at the water oxidizing complex. The effects of nitrite also remained the same in the presence of chloride. In case of ion-sufficient thylakoid membranes, nitrite decreased the Q band peak intensity and caused an upshift in the B band peak temperature. Nitrite showed similar effects in the presence of DCMU. This suggested that the site of action of nitrite is not at the acceptor side but at the donor side of PS II. The inhibition shown by nitrite has been found to be specific for nitrite anion. No other anions such as formate, fluoride or nitrate, were effective.