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961.
Navneet Bung Meenakshi Pradhan Harini Srinivasan Gopalakrishnan Bulusu 《PLoS computational biology》2014,10(3)
Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle. 相似文献
962.
Rafael Guerrero-Preston Christina Michailidi Luigi Marchionni Curtis R Pickering Mitchell J Frederick Jeffrey N Myers Srinivasan Yegnasubramanian Tal Hadar Maartje G Noordhuis Veronika Zizkova Elana Fertig Nishant Agrawal William Westra Wayne Koch Joseph Califano Victor E Velculescu David Sidransky 《Epigenetics》2014,9(7):1031-1046
963.
964.
Siddiqui A McGuigan C Ballatore C Srinivasan S De Clercq E Balzarini J 《Bioorganic & medicinal chemistry letters》2000,10(4):381-384
A range of polyether para-substituted phosphoramidates were synthesised and found to have substantially elevated aqueous solubilities compared to the underivatised parent prodrug. A 30-fold increase in aqueous solubility could be achieved without a substantial decrease of in vitro activity against HIV-1. Replacement of the aryl (i.e. phenolic) moiety by tyrosine led to a substantial enhancement in aqueous solubility but also to a decrease in antiviral potency. A previously unobserved trend was identified, relating increased aryl substituent steric bulk to decreased antiviral activity. 相似文献
965.
The genesis of the spore coat of Dictyostelium represents an exquisite example of developmentally regulated protein secretion. The proteins that are destined to be assembled into the extracellular matrix of the spore coat are stored in unique prespore vesicles that are triggered to secrete their contents at terminal differentiation. The regulation of this process is being revealed by the identification of the individual proteins in these vesicles. 相似文献
966.
967.
Nithya Srinivasan 《BBA》2009,1787(9):1057-682
This review focuses on phylloquinone as an indispensable link between light-induced charge separation and subsequent charge stabilization in Photosystem I (PS I). Here, the role of the polypeptide in conferring the necessary kinetic and thermodynamic properties to phylloquinone so as to specify its functional role in PS I electron transfer is discussed. Photosynthetic electron transfer and the role of quinones in Type I and Type II reaction centers are introduced at the outset with particular emphasis on the determination of redox potentials of the cofactors. Currently used methodologies, particularly time-resolved optical spectroscopy and varieties of magnetic resonance spectroscopy that have become invaluable in uncovering the details of phylloquinone function are described in depth. Recent studies on the selective alteration of the protein environment and on the incorporation of foreign quinones either by chemical or genetic means are explored to assess how these studies have improved our understanding of protein-quinone interactions. Particular attention is paid to the function of the H-bond, methyl group and phytyl tail of the phylloquinone in interacting with the protein environment. 相似文献
968.
Richard L. Bell Chinnathambi Srinivasan Delores Lomberk 《In vitro cellular & developmental biology. Plant》2009,45(6):708-714
The influence of the nutrient composition of plant tissue culture media on axillary shoot proliferation and their preconditioning
effect on subsequent adventitious shoot regeneration from pear leaves was investigated. The goal was to improve both micropropagation
and regeneration of ‘Bartlett’ and ‘Beurre Bosc’ pear cultivars. Driver–Kuniyuki walnut (DKW) and Quoirin and Lepoivre (QL)
nutrient media were found to be superior to Murashige and Skoog (MS) and Woody Plant Medium (WPM) for axillary shoot proliferation.
Shoots on WPM exhibited some chlorosis. Axillary shoot culture on DKW would be preferred to that on QL due to the production
of excessively short thin shoots on the latter medium. DKW also was superior to QL and MS for production of young expanding
leaves for use as explants in adventitious regeneration. Leaf explants derived from shoot proliferation cultures grown on
DKW or QL media produced more adventitious shoots than leaf explants from MS. 相似文献
969.
Background
Clustering techniques are routinely used in gene expression data analysis to organize the massive data. Clustering techniques arrange a large number of genes or assays into a few clusters while maximizing the intra-cluster similarity and inter-cluster separation. While clustering of genes facilitates learning the functions of un-characterized genes using their association with known genes, clustering of assays reveals the disease stages and subtypes. Many clustering algorithms require the user to specify the number of clusters a priori. A wrong specification of number of clusters generally leads to either failure to detect novel clusters (disease subtypes) or unnecessary splitting of natural clusters. 相似文献970.
Characterization of proton production and consumption associated with microbial metabolism 总被引:1,自引:0,他引:1