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RNA binding proteins play significant roles in many bio-macromolecular systems. Aromatic amino acid residues are vital for several biological functions. In the present work, the influences of π–π interactions in RNA binding proteins are analyzed. There are a total of 3,396 π-residues in RNA binding proteins out of which 1,547, 1,241, and 608 are phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), respectively. Among these 945, 634, and 356 Phe, Tyr, and Trp residues, respectively, are involved in π–π interactions. The observations indicate that majority of the aromatic residues in RNA binding proteins are involved in π–π interactions. Side chain–side chain π–π interactions are the predominant type of interactions in RNA binding proteins. These π–π interactions stabilize the core regions within RNA binding proteins. π–π interacting residues are evolutionary conserved. Residue-wise analysis indicates that π–π interacting residues have higher long-range contacts and hence they are important in the global conformational stability of these proteins. 相似文献
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K Sivasakthi M Tharanya M Zaman‐Allah J Kholov T Thirunalasundari V Vadez 《Plant biology (Stuttgart, Germany)》2020,22(5):769-780
- Terminal drought substantially reduces chickpea yield. Reducing water use at vegetative stage by reducing transpiration under high vapor pressure deficit (VPD), i.e. under dry/hot conditions, contributes to drought adaptation. We hypothesized that this trait could relate to differences in a genotype's dependence on root water transport pathways and hydraulics.
- Transpiration rate responses in conservative and profligate chickpea genotypes were evaluated under increasing VPD in the presence/absence of apoplastic and cell‐to‐cell transport inhibitors.
- Conservative genotypes ICC 4958 and ICC 8058 restricted transpiration under high VPD compared to the profligate genotypes ICC 14799 and ICC 867. Profligate genotypes were more affected by aquaporin inhibition of the cell‐to‐cell pathway than conservative genotypes, as measured by the root hydraulic conductance and transpiration under high VPD. Aquaporin inhibitor treatment also led to a larger reduction in root hydraulic conductivity in profligate than in conservative genotypes. In contrast, blockage of the apoplastic pathway in roots decreased transpiration more in conservative than in profligate genotypes. Interestingly, conservative genotypes had high early vigour, whereas profligate genotypes had low early vigour.
- In conclusion, profligate genotypes depend more on the cell‐to‐cell pathway, which might explain their higher root hydraulic conductivity, whereas water‐saving by restricting transpiration led to higher dependence on the apoplastic pathway. This opens the possibility to screen for conservative or profligate chickpea phenotypes using inhibitors, itself opening to the search of the genetic basis of these differences.
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Vaideeswaran Sivasakthi Parimelzaghan Anitha Kalavathi Murugan Kumar Susmita Bag Padmanaban Senthilvel Pandian Lavanya Rayapadi Swetha Anand Anbarasu Sudha Ramaiah 《Bioinformation》2013,9(8):432-439
Aromatic-aromatic hydrogen bonds are important in many areas of chemistry, biology and materials science. In this study we have
analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π
interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that
these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the
aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π
interactions and π-π networks play important roles in the structural stability of ILs and TNF proteins. 相似文献
4.
Vaideeswaran Sivaswamy Maxim I. Boyanov Brent M. Peyton Sridhar Viamajala Robin Gerlach William A. Apel Rajesh K. Sani Alice Dohnalkova Kenneth M. Kemner Thomas Borch 《Biotechnology and bioengineering》2011,108(2):264-276
Removal of hexavalent uranium (U(VI)) from aqueous solution was studied using a Gram‐positive facultative anaerobe, Cellulomonas sp. strain ES6, under anaerobic, non‐growth conditions in bicarbonate and PIPES buffers. Inorganic phosphate was released by cells during the experiments providing ligands for formation of insoluble U(VI) phosphates. Phosphate release was most probably the result of anaerobic hydrolysis of intracellular polyphosphates accumulated by ES6 during aerobic growth. Microbial reduction of U(VI) to U(IV) was also observed. However, the relative magnitudes of U(VI) removal by abiotic (phosphate‐based) precipitation and microbial reduction depended on the buffer chemistry. In bicarbonate buffer, X‐ray absorption fine structure (XAFS) spectroscopy showed that U in the solid phase was present primarily as a non‐uraninite U(IV) phase, whereas in PIPES buffer, U precipitates consisted primarily of U(VI)‐phosphate. In both bicarbonate and PIPES buffer, net release of cellular phosphate was measured to be lower than that observed in U‐free controls suggesting simultaneous precipitation of U and PO. In PIPES, U(VI) phosphates formed a significant portion of U precipitates and mass balance estimates of U and P along with XAFS data corroborate this hypothesis. High‐resolution transmission electron microscopy (HR‐TEM) and energy dispersive X‐ray spectroscopy (EDS) of samples from PIPES treatments indeed showed both extracellular and intracellular accumulation of U solids with nanometer sized lath structures that contained U and P. In bicarbonate, however, more phosphate was removed than required to stoichiometrically balance the U(VI)/U(IV) fraction determined by XAFS, suggesting that U(IV) precipitated together with phosphate in this system. When anthraquinone‐2,6‐disulfonate (AQDS), a known electron shuttle, was added to the experimental reactors, the dominant removal mechanism in both buffers was reduction to a non‐uraninite U(IV) phase. Uranium immobilization by abiotic precipitation or microbial reduction has been extensively reported; however, the present work suggests that strain ES6 can remove U(VI) from solution simultaneously through precipitation with phosphate ligands and microbial reduction, depending on the environmental conditions. Cellulomonadaceae are environmentally relevant subsurface bacteria and here, for the first time, the presence of multiple U immobilization mechanisms within one organism is reported using Cellulomonas sp. strain ES6. Biotechnol. Bioeng. 2011;108: 264–276. © 2010 Wiley Periodicals, Inc. 相似文献
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Viamajala S Peyton BM Gerlach R Sivaswamy V Apel WA Petersen JN 《Biotechnology and bioengineering》2008,101(6):1150-1162
Chromate (Cr(VI)) reduction studies were performed in bench scale flow columns using the fermentative subsurface isolate Cellulomonas sp. strain ES6. In these tests, columns packed with either quartz sand or hydrous ferric oxide (HFO)-coated quartz sand, were inoculated with strain ES6 and fed nutrients to stimulate growth before nutrient-free Cr(VI) solutions were injected. Results show that in columns containing quartz sand, a continuous inflow of 2 mg/L Cr(VI) was reduced to below detection limits in the effluent for durations of up to 5.7 residence times after nutrient injection was discontinued proving the ability of strain ES6 to reduce chromate in the absence of an external electron donor. In the HFO-containing columns, Cr(VI) reduction was significantly prolonged and effluent Cr(VI) concentrations remained below detectable levels for periods of up to 66 residence times after nutrient injection was discontinued. Fe was detected in the effluent of the HFO-containing columns throughout the period of Cr(VI) removal indicating that the insoluble Fe(III) bearing solids were being continuously reduced to form soluble Fe(II) resulting in prolonged abiotic Cr(VI) reduction. Thus, growth of Cellulomonas within the soil columns resulted in formation of permeable reactive barriers that could reduce Cr(VI) and Fe(III) for extended periods even in the absence of external electron donors. Other bioremediation systems employing Fe(II)-mediated reactions require a continuous presence of external nutrients to regenerate Fe(II). After depletion of nutrients, contaminant removal within these systems occurs by reaction with surface-associated Fe(II) that can rapidly become inaccessible due to formation of crystalline Fe-minerals or other precipitates. The ability of fermentative organisms like Cellulomonas to reduce metals without continuous nutrient supply in the subsurface offers a viable and economical alternative technology for in situ remediation of Cr(VI)-contaminated groundwater through formation of permeable reactive biobarriers (PRBB). 相似文献
6.
Parimelzaghan Anitha Vaideeswaran Sivasakthi Pandian Lavanya Susmita Bag Kalavathi Murugan Kumar Anand Anbarasu Sudha Ramaiah 《Bioinformation》2012,8(17):820-826
Metalloproteins have many different functions in cells such as enzymes; signal transduction, transport and storage proteins. About
one third of all proteins require metals to carry out their functions. In the present study we have analyzed the roles played by Arg
and Lys (cationic side chains) interactions with π (Phe, Tyr or Trp) residues and their role in the structural stability of
metalloproteins. These interactions might play an important role in the global conformational stability in metalloproteins. In spite
of its lower natural occurrence (1.76%) the number of Trp residues involved in energetically significant interactions is higher in
metalloproteins. 相似文献
7.
Dhurairajan Senthilnathan Sundararajan Vaideeswaran Ponnambalam Venuvanalingam Gernot Frenking 《Journal of molecular modeling》2011,17(3):465-475
The antitumor activities of bent metallocenes [Cp–M–Cp]2+ (M = Ti, V, Nb, Mo) and complexes of them with guanine, adenine, thymine and cytosine nucleotides have been probed using
electronic structure calculations. DFT/BP86 calculations have revealed that the bent metallocene–nucleotide interaction strongly
depends on the stability of the hydrolyzed form of the bent metallocene dichloride [Cp2M]2+ species, and in turn the stability of the [Cp2M]2+ species strongly depends on the electronic structure of [Cp2M]2+. Detailed electronic structure and Walsh energy analyses have been carried out for the hydrolyzed forms of four [Cp–M–Cp]2+ (M = Ti, V, Nb, Mo) species to find out why the bent structure is unusually stable. Energy changes that occur during the
bending process in frontier molecular orbitals as well as the p(π)–d(π) overlap have been invoked to account for the anticipated antitumor activities of these species. The bonding situation
and the interactions in bent metallocene–nucleotide adducts were elucidated by fragment analysis. Of the four nucleotides
complexed with the four bent metallocenes, adenine and guanine show better binding abilities than the other two nucleotides.
Metallocenes of second-row transition metals exhibit better binding with pyrimidine-base nucleotides. In particular, the Lewis
acidic bent metallocenes interact strongly with nucleotides. The antitumor activity is directly related to the binding strength
of the bent metallocene with nucleotide adducts, and the computed interaction energy values correlate very well with the experimentally
observed antitumor activities. 相似文献
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Murugesan Tharanya Jana Kholova Kaliamoorthy Sivasakthi Deepmala Seghal Charles Tom Hash Basker Raj Rakesh Kumar Srivastava Rekha Baddam Thiyagarajan Thirunalasundari Rattan Yadav Vincent Vadez 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2018,131(7):1509-1529
Key message
Four genetic regions associated with water use traits, measured at different levels of plant organization, and with agronomic traits were identified within a previously reported region for terminal water deficit adaptation on linkage group 2. Close linkages between these traits showed the value of phenotyping both for agronomic and secondary traits to better understand plant productive processes.Abstract
Water saving traits are critical for water stress adaptation of pearl millet, whereas maximizing water use is key to the absence of stress. This research aimed at demonstrating the close relationship between traits measured at different levels of plant organization, some putatively involved in water stress adaptation, and those responsible for agronomic performance. A fine-mapping population of pearl millet, segregating for a previously identified quantitative trait locus (QTL) for adaptation to terminal drought stress on LG02, was phenotyped for traits at different levels of plant organization in different experimental environments (pot culture, high-throughput phenotyping platform, lysimeters, and field). The linkages among traits across the experimental systems were analysed using principal component analysis and QTL co-localization approach. Four regions within the LG02-QTL were found and revealed substantial co-mapping of water use and agronomic traits. These regions, identified across experimental systems, provided genetic evidence of the tight linkages between traits phenotyped at a lower level of plant organization and agronomic traits assessed in the field, therefore deepening our understanding of complex traits and then benefiting both geneticists and breeders. In short: (1) under no/mild stress conditions, increasing biomass and tiller production increased water use and eventually yield; (2) under severe stress conditions, water savings at vegetative stage, from lower plant vigour and fewer tillers in that population, led to more water available during grain filling, expression of stay-green phenotypes, and higher yield.
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