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Author Mahtha S.K., Kumari K., Gaur V., Yadav G.
Title Cavity architecture based modulation of ligand binding tunnels in plant START domains.
<b>The S</b>teroidogenic <b>a</b>cute <b>r</b>egulatory <b>p</b>rotein (<b>StAR</b>)-<b>r</b>elated <b>l</b>ipid <b>t</b>ransfer (START) domain represents an evolutionarily conserved superfamily of <b>lipid transfer proteins</b> widely distributed across the tree of life. Despite significant expansion in plants, knowledge about this domain remains inadequate in plants. In this work, we explore the role of cavity architectural modulations in START protein evolution and functional diversity. We use deep-learning approaches to generate plant START domain models, followed by surface accessibility studies and a comprehensive structural investigation of the rice START family. We validate 28 rice START domain models, delineate binding cavities, measure pocket volumes, and compare these with mammalian counterparts to understand evolution of binding preferences. Overall, plant START domains retain the ancestral &#x3b1;/&#x3b2; helix-grip signature, but we find subtle variation in cavity architectures, resulting in significantly smaller ligand-binding tunnels in the plant kingdom. We identify cavity lining residues (CLRs) responsible for reduction in ancestral tunnel space, and these appear to be class specific, and unique to plants, providing a mechanism for the observed shift in domain function. For instance, mammalian cavity lining residues A135, G181 and A192 have evolved to larger CLRs across the plant kingdom, contributing to smaller sizes, minimal STARTs being the largest, while members of type-IV HD-Zip family show almost complete obliteration of lipid binding cavities, consistent with their present-day DNA binding functions. In summary, this work quantifies plant START structural & functional divergence, bridging current knowledge gaps.
Journal Comput Struct Biotechnol J
Country India
Volume 21
Pages 3946-3963
Year 2023
PubMed ID 37635766
PubMed Central ID 10448341
DOI 10.1016/j.csbj.2023.07.039
Gene HB4 HOX29 HOX33 HOX9 LF1 OUL1 ROC1 ROC2 ROC3 ROC4 ROC6 ROC7 ROC9 TF1 TF1L URL1 _ _ _ _ _ _ _ _ _ _ _ _
Strain Wild Core Collection -
Induced Mutation Lines(NIG Collection) -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain
Stages in Each Organ
- Muant Lines (Gene)
Cultivated Varieties(NIG Collection) -
Stages in Each Organ -