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81.
Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence 总被引:11,自引:0,他引:11
Statistical analysis of 12 unstable and 32 stable proteins revealed that there are certain dipeptides, the occurrence of which is significantly different in the unstable proteins compared with those in the stable ones. Based on the impact of these dipeptides on the unstable proteins over the stable ones, a weight value of instability is assigned to each of the dipeptides. For a given protein the summation of these weight values normalized to the length of its sequence helps to distinguish between unstable and stable proteins. Results suggest that the in vivo instability of proteins is possibly determined by the order of certain amino acids in its sequence. An attempt is made to correlate metabolic stability of proteins with features of their primary sequence where weight values of instability for a protein of known sequence could thus be used as an index for predicting its stability characteristics. 相似文献
82.
A. Sharada Devi Tasneem Rehana A. S. Kolaskar M. W. Pandit 《Journal of biosciences》1989,14(2):133-142
Hydrophilicity index is used to locate antigenic determinants on two related groups of proteins-myoglobin and hemoglobin.
The data on 41 species (including 34 mammals) of myoglobin show that average hydrophilicity for the complete myoglobin molecules
as well as the average hydrophilicity for all hydrophilic regions put together seem to remain constant; the variation in the
size and location of the antigenic determinants in these species is very small indicating that the antigenic sites are not
shifted during evolution. In the case of both the proteins there is a good agreement between the antigenic sites picked up
by using hydrophilicity index and the experimentally determined antigenic sites. The data on 56 species of hemoglobin α-chains
and 44 species of hemoglobinβ-chains showed that although there are few sites on hemoglobin which have remained invariant during evolution, there is a
significant variation in other sites in terms of either a splitting of a site, or a drastic change in the hydrophilicity values
and/or a length of the site. Comparison of the hydrophilicity data on these two groups of proteins suggests that hemoglobins
which perform a variety of functions as compared to myoglobins are evolving faster than myoglobins supporting the contention
of earlier workers. 相似文献
83.
Nagendra K. Singh Deepak K. Gupta Pawan K. Jayaswal Ajay K. Mahato Sutapa Dutta Sangeeta Singh Shefali Bhutani Vivek Dogra Bikram P. Singh Giriraj Kumawat Jitendra K. Pal Awadhesh Pandit Archana Singh Hukum Rawal Akhilesh Kumar G. Rama Prashat Ambika Khare Rekha Yadav Ranjit S. Raje Mahendra N. Singh Subhojit Datta Bashasab Fakrudin Keshav B. Wanjari Rekha Kansal Prasanta K. Dash Pradeep K. Jain Ramcharan Bhattacharya Kishor Gaikwad Trilochan Mohapatra R. Srinivasan Tilak R. Sharma 《Journal of plant biochemistry and biotechnology.》2012,21(1):98-112
Pigeonpea (Cajanus cajan) is an important grain legume of the Indian subcontinent, South-East Asia and East Africa. More than eighty five percent of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. Here we present the first draft of the genome sequence of a popular pigeonpea variety ??Asha??. The genome was assembled using long sequence reads of 454 GS-FLX sequencing chemistry with mean read lengths of >550?bp and >10-fold genome coverage, resulting in 510,809,477?bp of high quality sequence. Total 47,004 protein coding genes and 12,511 transposable elements related genes were predicted. We identified 1,213 disease resistance/defense response genes and 152 abiotic stress tolerance genes in the pigeonpea genome that make it a hardy crop. In comparison to soybean, pigeonpea has relatively fewer number of genes for lipid biosynthesis and larger number of genes for cellulose synthesis. The sequence contigs were arranged in to 59,681 scaffolds, which were anchored to eleven chromosomes of pigeonpea with 347 genic-SNP markers of an intra-species reference genetic map. Eleven pigeonpea chromosomes showed low but significant synteny with the twenty chromosomes of soybean. The genome sequence was used to identify large number of hypervariable ??Arhar?? simple sequence repeat (HASSR) markers, 437 of which were experimentally validated for PCR amplification and high rate of polymorphism among pigeonpea varieties. These markers will be useful for fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications. This is the first plant genome sequence completed entirely through a network of Indian institutions led by the Indian Council of Agricultural Research and provides a valuable resource for the pigeonpea variety improvement. 相似文献
84.
Christopher J. Helal Zhijun Kang John C. Lucas Thomas Gant Michael K. Ahlijanian Joel B. Schachter Karl E.G. Richter James M. Cook Frank S. Menniti Kristin Kelly Scot Mente Jay Pandit Natalie Hosea 《Bioorganic & medicinal chemistry letters》2009,19(19):5703-5707
Utilizing structure-based drug design, a 4-aminoimidazole heterocyclic core was synthesized as a replacement for a 2-aminothiazole due to potential metabolically mediated toxicity. The synthetic route utilized allowed for ready synthesis of 1-substituted-4-aminoimidazoles. SAR exploration resulted in the identification of a novel cis-substituted cyclobutyl group that gave improved enzyme and cellular potency against cdk5/p25 with up to 30-fold selectivity over cdk2/cyclin E. 相似文献
85.
M. H. M. Ammar Awadhesh Pandit R. K. Singh S. Sameena M. S. Chauhan A. K. Singh P. C. Sharma Kishor Gaikwad T. R. Sharma Trilochan Mohapatra N. K. Singh 《Journal of plant biochemistry and biotechnology.》2009,18(2):139-150
Soil salinity and sodicity are major constraints to rice production in about twenty per cent of the irrigated crop land. Inbuilt genetic tolerance to salinity is the most economical and environmentally sustainable way to solve this problem. A mapping population of 200 F2 plants and their corresponding F3 families, derived from a cross between a salt tolerant indica rice variety CSR27 and a salt sensitive variety MI48 were used to map OTLs for salt tolerance. Seventeen different parameters, including seedling salt injury score, Na+, K+, CI? concentrations and Na+/K+ ratio in leaf and stem tissues at vegetative and reproductive stages were mapped. A framework linkage map was constructed using 79 SSR and EST markers distributed over the twelve rice chromosomes at an average interval of 20.7cM and total map distance of 1634.5 cM. Twenty five major OTLs, each explaining more than ten per cent of the trait phenotypic variance, were mapped on chromosomes 1, 2, 3 and 8. These included one OTL for seedling salt injury score, nine for Na+ concentration, three for K+ concentration and four for Cl? concentration in leaf and stem tissues at vegetative and reproductive stages. The Na+/K+ ratio, an important ion balancing parameter for the salt tolerance, was controlled by eight OTLs explaining phenotypic variance in the range of 42.88–52.63%. Four OTL intervals were robust with major effect and having OTLs for multiple salt tolerance parameters that might be governed by common or tightly linked genes. One major OTL for multiple salt tolerance parameters on chromosome 8 and three major OTLs for CI? ion concentration are novel for this study. The OTLs identified here will serve as a base for fine mapping, gene tagging and marker assisted selection for salt tolerance in rice. 相似文献
86.
87.
The objective of the present work was to add value to three different qualities of grain sorghum namely normal healthy, germinated, and blackened through production of glucose, and to intensify glucose production (yield) by means of ultrasound treatment. Liquefaction (using Bacillus licheniformis α-amylase) and saccharification (using amyloglucosidase) processes were optimized with use of normal sorghum flour as a starting material for the production of glucose. The effect of ultrasound treatment on the sorghum slurry prior to liquefaction was studied on the processes of liquefaction and saccharification under optimized conditions. Due to ultrasound treatment, liquefact DE increased by 10-25% depending upon sonication time and the intensity. Ultrasound treatment of 1 min at 100% amplitude was found to decrease the average particle size of the slurry from 302 μm to 115 μm, which resulted in an increased percentage of saccharification by about 8%. The reason for the increase in the percentage of saccharification was attributed to the availability of additional starch for hydrolysis due to ultrasound-assisted disruption of the protein matrix (surrounding starch granules) and the amylose-lipid complex. Integration of ultrasound treatment in the state of art of the production of glucose from dry-milled sorghum and its possible subsequent use in the bioethanol production may improve the overall economics of the process. 相似文献
88.
I. D. Godwin S. B. Williams P. S. Pandit H. K. C. Laidlaw 《In vitro cellular & developmental biology. Plant》2009,45(4):383-399
Cereals provide more than half the world population’s calorific intake, and have a variety of other important uses as food
and beverage ingredients, livestock feeds, and as sources of renewable energy and industrial components. The technology to
genetically modify many important cereals is now well-established, thereby presenting new opportunities to produce cereals
with enhanced quality and novel properties. In 2007, GM (genetically modified) maize with insect and herbicide resistance
was grown on over 30 million hectares worldwide, yet to date, there are no GM cereals with enhanced or novel grain (end-use)
qualities being grown in commercial farmers’ fields. This review will discuss some of the latest GM technology developments
reported to enhance the quality of cereals for food and other uses. Developments and opportunities involving gene manipulation
for starch and protein quality, as well as non-starch polysaccharides, phenolic compounds and micronutrients will also be
discussed. The current paucity of GM cereals with enhanced grain quality is not related to the absence of technological progress,
rather it is the regulatory and consumer acceptance issues that have slowed the release of these crops. 相似文献
89.
In a variety of threading methods, often poorly ranked (low z‐score) templates have good alignments. Here, a new method, TASSER_low‐zsc that identifies these low z‐score–ranked templates to improve protein structure prediction accuracy, is described. The approach consists of clustering of threading templates by affinity propagation on the basis of structural similarity (thread_cluster) followed by TASSER modeling, with final models selected by using a TASSER_QA variant. To establish the generality of the approach, templates provided by two threading methods, SP3 and SPARKS2, are examined. The SP3 and SPARKS2 benchmark datasets consist of 351 and 357 medium/hard proteins (those with moderate to poor quality templates and/or alignments) of length ≤250 residues, respectively. For SP3 medium and hard targets, using thread_cluster, the TM‐scores of the best template improve by ~4 and 9% over the original set (without low z‐score templates) respectively; after TASSER modeling/refinement and ranking, the best model improves by ~7 and 9% over the best model generated with the original template set. Moreover, TASSER_low‐zsc generates 22% (43%) more foldable medium (hard) targets. Similar improvements are observed with low‐ranked templates from SPARKS2. The template clustering approach could be applied to other modeling methods that utilize multiple templates to improve structure prediction. Proteins 2010. © 2010 Wiley‐Liss, Inc. 相似文献
90.