On the computation of the tertiary structure of globular proteins—IV. Use of secondary structure information

The distance geometry approach for computing the tertiary structure of globular proteins emphasized in this series of papers (Goelet al., J. theor. Biol. 99, 705–757, 1982) is developed further. This development includes incorporation of some secondary structure information—the location of alpha helices in the primary sequence—in the algorithm to compute the tertiary structure of alpha helical globular proteins. An algorithm is developed which estimates the interresidue distances between chain-proximate helices. These distances, in conjunction with the global statistical average distances obtainable from a database of real proteins and determined by the primary sequence of the protein under study, are used to determine the tertiary structure. Five proteins, parvalbumin, hemerythrin, human hemoglobin, lamprey hemoglobin, and sperm whale myoglobin, are investigated. The root mean square (RMS) errors between the calculated structures and those determined by X-ray diffraction range from 4.78 to 7.56 Å. These RMSs are 0.21–2.76 Å lower than those estimated without the secondary structure information. Contact maps and three-dimensional backbone representations also show considerable improvements with the introduction of secondary structure information.     

On the computation of the tertiary structure of globular proteins. III. Inter-residue distances and computed structures

An analysis of geometrical models for computing the tertiary structure of globular proteins from the primary structure is presented. The roles of initial configuration, input information on inter-residue distances and the errors in this information are delineated. It is shown that for local information like that on secondary structure, the calculated structure is very sensitive to errors and to the initial configuration. Thus, such information is far from adequate for predicting the tertiary structure. On the other hand, global information on all the inter-residue distances is quite insensitive to errors. A semi-empirical method is presented to estimate these distances and the calculated structures are given for two proteins—pancreatic trypsin inhibitor and parvalbumin. These structures have good resemblances to those determined by X-ray diffraction. A strategy for further refinement of the method is indicated.     

Lysis of mycelium ofFusarium oxysporum f. sp.udum in soil amended with organic matters

Summary Autoclaved or natural field soil amended with 0.1 to 5.0 per cent (W/W) of margosa cake, rice husk and sawdust with or without supplemental nitrogen were tested for lytic activity and bacterial numbers. Generally, non-amended autoclaved soil caused little or no lysis of mycelium ofF. oxysporum f. sp.udum; non-amended natural soil caused more lysis. Amendment of soil with margosa cake, rice husk or saw-dust with or without supplemental nitrogen greatly enhanced its lytic effect on the fungus. The degree of lysis depended on the dosage of amendment used and the stage of its decomposition in the soil. The extent of lysis increased as the bacterial population increased. Amongst bacteria,Bacillus subtilis was very common in most lytic zones.     

Bimodal oxygen uptake in juveniles and adults amphibious fish,Channa (= Ophiocephalus) marulius

Oxygen uptake of Channa marulius was studied under water with and without access to air. There was a significant increase in the oxygen uptake through the gills when access to air was prevented. However, this value (0.863 ± 0.058 mlO₂/indiv./h) was quite low in comparison to the total bimodal oxygen uptake (2.04 ± 0.14 mlO₂/indiv./h) in juveniles. In adult fish the oxygen uptake per unit time increased appreciably (4.673 ± 0.404 mlO₂/indiv./h). In juveniles as well as in adults the air breathing dominated over aquatic breathing. This fish showed a definite circadian rhythm in the bimodal oxygen uptake during different hours of the day.This work was performed in the Ichthyology Laboratory, P. G. Dept. of Zoology, Bhagalpur University, and was supported by a research grant from Bhagalpur University     

Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL

PINK1 is a mitochondrial kinase mutated in some familial cases of Parkinson's disease. It has been found to work in the same pathway as the E3 ligase Parkin in the maintenance of flight muscles and dopaminergic neurons in Drosophila melanogaster and to recruit cytosolic Parkin to mitochondria to mediate mitophagy in mammalian cells. Although PINK1 has a predicted mitochondrial import sequence, its cellular and submitochondrial localization remains unclear in part because it is rapidly degraded. In this study, we report that the mitochondrial inner membrane rhomboid protease presenilin-associated rhomboid-like protein (PARL) mediates cleavage of PINK1 dependent on mitochondrial membrane potential. In the absence of PARL, the constitutive degradation of PINK1 is inhibited, stabilizing a 60-kD form inside mitochondria. When mitochondrial membrane potential is dissipated, PINK1 accumulates as a 63-kD full-length form on the outer mitochondrial membrane, where it can recruit Parkin to impaired mitochondria. Thus, differential localization to the inner and outer mitochondrial membranes appears to regulate PINK1 stability and function.     

CDPK1 from Ginger Promotes Salinity and Drought Stress Tolerance without Yield Penalty by Improving Growth and Photosynthesis in Nicotiana tabacum

In plants, transient changes in calcium concentrations of cytosol have been observed during stress conditions like high salt, drought, extreme temperature and mechanical disturbances. Calcium-dependent protein kinases (CDPKs) play important roles in relaying these calcium signatures into downstream effects. In this study, a stress-responsive CDPK gene, ZoCDPK1 was isolated from a stress cDNA generated from ginger using rapid amplification of cDNA ends (RLM-RACE) – PCR technique and characterized its role in stress tolerance. An important aspect seen during the analysis of the deduced protein is a rare coupling between the presence of a nuclear localization sequence in the junction domain and consensus sequence in the EF-hand loops of calmodulin-like domain. ZoCDPK1 is abundantly expressed in rhizome and is rapidly induced by high-salt stress, drought, and jasmonic acid treatment but not by low temperature stress or abscissic acid treatment. The sub-cellular localization of ZoCDPK1-GFP fusion protein was studied in transgenic tobacco epidermal cells using confocal laser scanning microscopy. Over-expression of ginger CDPK1 gene in tobacco conferred tolerance to salinity and drought stress as reflected by the high percentage of seed germination, higher relative water content, expression of stress responsive genes, higher leaf chlorophyll content, increased photosynthetic efficiency and other photosynthetic parameters. In addition, transgenic tobacco subjected to salinity/drought stress exhibited 50% more growth during stress conditions as compared to wild type plant during normal conditions. T3 transgenic plants are able to grow to maturity, flowers early and set viable seeds under continuous salinity or drought stress without yield penalty. The ZoCDPK1 up-regulated the expression levels of stress-related genes RD21A and ERD1 in tobacco plants. These results suggest that ZoCDPK1 functions in the positive regulation of the signaling pathways that are involved in the response to salinity and drought stress in ginger and it is likely operating in a DRE/CRT independent manner.     

Influence of 2-(3,4 dichlorophenoxy)-triethylamine on photosynthesis of Phaseolus vulgaris L.

The effect of foliar sprays of the growth regulator 2-(3,4 dichlorophenoxy)-triethylamine (DCPTA) on net photosynthesis (P_n) by intact bean plants depended upon concentration and the stage of development of the leaves. A single foliar spray of 2.0 mM DCPTA reduced P_n when applied to young expanding leaves but had little effect on fully expanded leaves. Lower DCPTA concentrations (0.2 to 0.8 mM) had no effect on P_n, unless applied more than once which resulted in reduced P_n. The DCPTA-induced inhibition of P_n was associated with chlorosis and aberrations in chloroplast ultrastructure. DCPTA did not affect stomatal resistance. When applied to detached leaf disks in the dark, DCPTA retarded the normal loss of chlorophyll suggesting that DCPTA may have anti-seneseent properties.Abbreviations DCPTA 2-(3,4 dichlorophenoxy)-triethylamine - P_n net photosynthesis - I_s stomatal diffusive resistance     

Local but Not Systemic Administration of Uridine Prevents Development of Antigen-Induced Arthritis

Objective

Uridine has earlier been show to down modulate inflammation in models of lung inflammation. The aim of this study was to evaluate the anti-inflammatory effect of uridine in arthritis.

Methods

Arthritis was induced by intra-articular injection of mBSA in the knee of NMRI mice pre-immunized with mBSA. Uridine was either administered locally by direct injection into the knee joint or systemically. Systemic treatment included repeated injections or implantation of a pellet continuously releasing uridine during the entire experimental procedure. Anti-mBSA specific immune responses were determined by ELISA and cell proliferation and serum cytokine levels were determined by Luminex. Immunohistochemistry was used to identify cells, study expression of cytokines and adhesion molecules in the joint.

Results

Local administration of 25–100 mg/kg uridine at the time of arthritis onset clearly prevented development of joint inflammation. In contrast, systemic administration of uridine (max 1.5 mg uridine per day) did not prevent development of arthritis. Protection against arthritis by local administration of uridine did not affect the anti-mBSA specific immune response and did not prevent the rise in serum levels of pro-inflammatory cytokines associated with the triggering of arthritis. In contrast, local uridine treatment efficiently inhibited synovial expression of ICAM-1 and CD18, local cytokine production and recruitment of leukocytes to the synovium.

Conclusion

Local, but not systemic administration of uridine efficiently prevented development of antigen-induced arthritis. The protective effect did not involve alteration of systemic immunity to mBSA but clearly involved inhibition of synovial expression of adhesion molecules, decreased TNF and IL-6 production and prevention of leukocyte extravasation. Further, uridine is a small, inexpensive molecule and may thus be a new therapeutic option to treat joint inflammation in RA.