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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Structure-based functional annotation of hypothetical proteins from Candida dubliniensis: a quest for potential drug
Kundan Kumar1, Amresh Prakash1, Farah Anjum2
1Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
Abstract:
Candida dubliniensis is an emerging pathogenic yeast in humans and infections are usually restricted to mucosal parts of the body. However, its presence in specimens of immunocompromised individuals, especially in HIV-positive patients, is of major medical concern. There is a large fraction of genomes of C. dubliniensis in the database which are uncharacterized for their biochemical, biophysical, and/or cellular functions, and are identified as hypothetical proteins (HPs). Function annotation of Candida genome is, therefore, essentially required to facilitate the understanding of mechanisms of pathogenesis and biochemical pathways important for selecting novel therapeutic target. Here, we carried out an extensive analysis to explain the functional properties of genome, using available protein structure and function analysis tools. We successfully modeled the structures of eight HPs for which a template with moderate sequence similarity was available in the protein data bank. All modeled structures were analyzed and we found that these proteins may act as transporter, kinase, transferase, ketosteroid, isomerase, hydrolase, oxidoreductase, and binding targets for DNA and RNA. Since these unique HPs of Candida showed no homologs in humans, these proteins are expected to be a potential target for future antifungal therapy.
Insights
This study characterized hypothetical proteins (HPs) in Candida dubliniensis, an emerging fungal pathogen. These unique HPs, absent in humans, show potential as novel antifungal drug targets.
Area of Science:
- Medical Mycology
- Genomics
- Structural Biology
Background:
- Candida dubliniensis is an emerging human pathogen, particularly concerning in immunocompromised individuals.
- A significant portion of C. dubliniensis genomes comprises uncharacterized hypothetical proteins (HPs).
- Functional annotation of these HPs is crucial for understanding pathogenesis and identifying therapeutic targets.
Purpose of the Study:
- To functionally characterize hypothetical proteins (HPs) within the Candida dubliniensis genome.
- To identify potential novel therapeutic targets for antifungal drug development.
Main Methods:
- Utilized protein structure and function analysis tools for extensive genomic analysis.
- Modeled structures of eight HPs using available templates from the protein data bank.
- Analyzed modeled structures to predict protein functions.
Main Results:
- Successfully modeled structures for eight hypothetical proteins (HPs).
- Predicted functions include roles as transporters, kinases, transferases, isomerases, hydrolases, oxidoreductases, and DNA/RNA binding proteins.
- Identified unique HPs in C. dubliniensis with no human homologs.
Conclusions:
- The characterized hypothetical proteins (HPs) of Candida dubliniensis possess diverse predicted functions.
- These HPs represent promising, species-specific targets for the development of novel antifungal therapies.
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