Pdr5 is a founding member of a large (pdr) subfamily of clinically and agriculturally significant fungal ABC transporters. The tremendous power of yeast genetics combined with biochemical and structural approaches revealed the astonishing asymmetry of this efflux pump. Asymmetry is manifested in Pdr5's ATP-binding sites, drug binding sites, signal transformation interface, and molecular exit gate. Even its mode of conformational switching is asymmetric with one half of the protein remaining nearly stationary. In the case of its ATP-binding sites, asymmetry is created by replacing a set of highly conserved residues with a characteristic set of deviant ones. This contrasts with the asymmetry of the molecular gate. There, a full complement of canonical residues is present, but structural features in the vicinity prevent some of these from forming a molecular plug during closure. Compared to their canonical-functioning counterparts, the deviant ATP site and these gating residues have different, essential functions. In addition to its remarkable asymmetry, the surprising observation that Pdr5 is a drug / proton co-transporter shines a new light on this remarkable protein.
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http://dx.doi.org/10.1016/j.drup.2023.101010 | DOI Listing |
Alzheimers Dement
December 2024
College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.
Background: The "Recruitment and Retention for Alzheimer's Disease Diversity Genetic Cohorts in the ADSP (READD-ADSP)" is developing a resource to expand ancestral diversity in Alzheimer disease (AD) studies to dissect the genetic architecture of AD across different populations. In addition to US sites, READD-ADSP includes four US sites and nine countries in sub-Saharan Africa through the Africa Dementia Consortium (AfDC). The overall goal of READD-ADSP is to identify genetically driven targets in diverse groups including African Americans and Hispanic/Latinos in US, and Africans.
View Article and Find Full Text PDFBiosci Biotechnol Biochem
December 2024
Department of Agricultural Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan.
Escherichia coli expressing SrPlsAR from Selenomonas ruminantium produces plasmalogen, comprising almost 60% of the total phospholipid content under anaerobic conditions. Both plasmenylethanolamine and plasmenylglycerol were detected, and the major acyl aldehyde derived from sn-1 vinyl ether was C16:1. Plasmalogen synthesis is affected by mutations in ATP-binding sites and Cys expected to be involved in the formation of the [4Fe-4S] cluster.
View Article and Find Full Text PDFMethods Mol Biol
December 2024
Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi, India.
Cavities in proteins perform diverse functions such as substrate binding, enzyme catalysis, passage for transportation of small molecules, and protein oligomerization. Often, the physical properties of these cavities are closely linked to the protein function; such as the hydrophobic lipid-binding cavities in lipid-binding proteins (LBPs) that protect lipid substrates from the larger aqueous milieu. Therefore, the characterization of protein cavities can provide valuable insights into protein structure-function relationships, hinting toward their mechanism of action while aiding in the identification of ligand binding sites that are essential for drug discovery approaches.
View Article and Find Full Text PDFJ Chem Inf Model
December 2024
Department of Computer Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea.
Accurate identification of adenosine triphosphate (ATP) binding sites is crucial for understanding cellular functions and advancing drug discovery, particularly in targeting kinases for cancer treatment. Existing methods face significant challenges due to their reliance on time-consuming precomputed features and the heavily imbalanced nature of binding site data without further investigations on their utility in drug discovery. To address these limitations, we introduced Multiview-ATPBind and ResiBoost.
View Article and Find Full Text PDFJ Biol Chem
December 2024
Department of Microbiology and Molecular Genetics. Electronic address:
While ATP-site inhibitors for protein-tyrosine kinases are often effective drugs, their clinical utility can be limited by off-target activity and acquired resistance mutations due to the conserved nature of the ATP-binding site. However, combining ATP-site and allosteric kinase inhibitors can overcome these shortcomings in a double-drugging framework. Here we explored the allosteric effects of two pyrimidine diamines, PDA1 and PDA2, on the conformational dynamics and activity of the Src-family tyrosine kinase Hck, a promising drug target for acute myeloid leukemia.
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