Genome-wide analysis of PH and FYVE domains in Arabidopsis thaliana by computational methods
Item
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Title
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Genome-wide analysis of PH and FYVE domains in Arabidopsis thaliana by computational methods
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Identifier
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d_2009_2013:2038e883298a:09969
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identifier
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10007
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Creator
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Wywial, Ewa,
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Contributor
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Shaneen M. Singh
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Date
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2009
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Language
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English
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Publisher
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City University of New York.
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Subject
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Bioinformatics
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Abstract
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Phosphoinositide-binding domains have emerged as molecules responsible for trafficking and anchoring of membrane associated proteins in various organisms ranging from yeast to mammalian cells. Two such domains, i.e. the Pleckstrin Homology (PH) and Fab1p, YOTB, Vac1 and EEA1 (FYVE), are of special interest because of their unique membrane binding characteristics and genome wide prevalence. Structurally, the PH domains share a core fold of seven beta-strands followed by a C-terminal alpha-helix whereas the FYVE domains comprise two small double-stranded beta-sheets, a C-terminal alpha-helix and eight Zn 2+ ion-binding cysteines. The PH and FYVE domains are found in functionally diverse families in different organisms; some of these are well studied and others remain unexplored. Plants stand out from the rest of the organisms where most of protein families containing these domains remain largely uncharacterized. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PH and FYVE proteins, characterize their sequence and model/analyze their 3D structure. Integrating the sequence, structure and known experimental details for each of these domains, we propose a comprehensive genome-wide domain-based classification of both the Arabidopsis PH and FYVE proteins: we classify forty-nine Arabidopsis PH and fifteen Arabidopsis FYVE proteins into twelve and five classes, respectively. Our study provides valuable details on the biophysical traits of the individual modeled domains, family specific characteristics as well as genomic trends for these domains in Arabidopsis and predictions of their membrane binding behaviors. We report the exclusive presence of plant specific domain architectures, variant binding signatures and biophysical profiles in individual members or complete families of Arabidopsis PH and FYVE domain-containing proteins such as the PRAF proteins. Our study provides the first glimpse into the putative roles of these lipid-binding domains based on which we can begin to understand the role(s) they play in plants and how it compares to their role in other organisms.
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Type
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dissertation
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Source
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2009_2013.csv
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degree
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Ph.D.
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Program
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Biology
