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101.
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Len J. Wade Violeta Bartolome Ramil Mauleon Vivek Deshmuck Vasant Sumeet Mankar Prabakar Muthukumar Chelliah Emi Kameoka K. Nagendra K. R. Kamalnath Reddy C. Mohan Kumar Varma Kalmeshwar Gouda Patil Roshi Shrestha Zaniab Al-Shugeairy Faez Al-Ogaidi Mayuri Munasinghe Veeresh Gowda Mande Semon Roel R. Suralta Vinay Shenoy Vincent Vadez Rachid Serraj H. E. Shashidhar Akira Yamauchi Ranganathan Chandra Babu Adam Price Kenneth L. McNally Amelia Henry 《PloS one》2015,10(4)
The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7–40.7 Mb) and on chromosome 8 (20.3–21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions. 相似文献
103.
Gopichandran Sowmya Edmond J Breen Shoba Ranganathan 《Protein science : a publication of the Protein Society》2015,24(9):1486-1494
Protein–protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure–function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. 相似文献
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Helena Jambor Alberto Antonietti Bradly Alicea Tracy L. Audisio Susann Auer Vivek Bhardwaj Steven J. Burgess Iuliia Ferling Magorzata Anna Gazda Luke H. Hoeppner Vinodh Ilangovan Hung Lo Mischa Olson Salem Yousef Mohamed Sarvenaz Sarabipour Aalok Varma Kaivalya Walavalkar Erin M. Wissink Tracey L. Weissgerber 《PLoS biology》2021,19(3)
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Recent work indicates a general architecture for proteins in which sparse networks of physically contiguous and coevolving amino acids underlie basic aspects of structure and function. These networks, termed sectors, are spatially organized such that active sites are linked to many surface sites distributed throughout the structure. Using the metabolic enzyme dihydrofolate reductase as a model system, we show that: (1) the sector is strongly correlated to a network of residues undergoing millisecond conformational fluctuations associated with enzyme catalysis, and (2) sector-connected surface sites are statistically preferred locations for the emergence of allosteric control in vivo. Thus, sectors represent an evolutionarily conserved "wiring" mechanism that can enable perturbations at specific surface positions to rapidly initiate conformational control over protein function. These findings suggest that sectors enable the evolution of intermolecular communication and regulation. 相似文献