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A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation.

ABSTRACT: BACKGROUND: The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. METHOD: In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B) are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. RESULTS: Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s) for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. CONCLUSION: The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome.The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from the parasite that could provide leads to identify novel drug targets against malaria.

SUBMITTER: Gangwar D

PROVIDER: S-EPMC2674469 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation.

Gangwar Deepti D Kalita Mridul K MK Gupta Dinesh D Chauhan Virander S VS Mohmmed Asif A

Malaria journal 20090418

<h4>Background</h4>The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of prot ...[more]

PMID: 19374766

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Project description:Emergence of drug-resistant Plasmodium falciparum has created an urgent need for new drug targets. DNA polymerase ? is an essential enzyme required for chromosomal DNA replication and repair, and therefore may be a potential target for anti-malarial drug development. However, little is known of the characteristics and function of this P. falciparum enzyme.The coding sequences of DNA polymerase ? catalytic subunit (PfPol?-cat), DNA polymerase ? small subunit (PfPol?S) and proliferating cell nuclear antigen (PfPCNA) from chloroquine- and pyrimethamine-resistant P. falciparum strain K1 were amplified, cloned into an expression vector and expressed in Escherichia coli. The recombinant proteins were analysed by SDS-PAGE and identified by LC-MS/MS. PfPol?-cat was biochemically characterized. The roles of PfPol?S and PfPCNA in PfPol?-cat function were investigated. In addition, inhibitory effects of 11 compounds were tested on PfPol?-cat activity and on in vitro parasite growth using SYBR Green I assay.The purified recombinant protein PfPol?-cat, PfPol?S and PfPCNA showed on SDS-PAGE the expected size of 143, 57 and 34 kDa, respectively. Predicted amino acid sequence of the PfPol?-cat and PfPol?S had 59.2 and 24.7 % similarity respectively to that of the human counterpart. The PfPol?-cat possessed both DNA polymerase and 3'-5' exonuclease activities. It used both Mg(2+) and Mn(2+) as cofactors and was inhibited by high KCl salt (>200 mM). PfPol?S stimulated PfPol?-cat activity threefolds and up to fourfolds when PfPCNA was included in the assay. Only two compounds were potent inhibitors of PfPol?-cat, namely, butylphenyl-dGTP (BuPdGTP; IC50 of 38 µM) and 7-acetoxypentyl-(3, 4 dichlorobenzyl) guanine (7-acetoxypentyl-DCBG; IC50 of 55 µM). The latter compound showed higher inhibition on parasite growth (IC50 of 4.1 µM).Recombinant PfPol?-cat, PfPol?S and PfPCNA were successfully expressed and purified. PfPolS and PfPCNA increased DNA polymerase activity of PfPol?-cat. The high sensitivity of PfPol? to BuPdGTP can be used to differentiate parasite enzyme from mammalian and human counterparts. Interestingly, 7-acetoxypentyl-DCBG showed inhibitory effects on both enzyme activity and parasite growth. Thus, 7-acetoxypentyl-DCBG is a potential candidate for future development of a new class of anti-malarial agents targeting parasite replicative DNA polymerase.

Dataset Information

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation.

Publications

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation.

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