Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite <i>Plasmodium falciparum</i> 3D7

Palanisamy, Balamurugan; Ekambaram, Rajasekaran; Heese, Klaus

doi:10.1093/bioinformatics/btt587

Cited by 3 publications

(2 citation statements)

References 32 publications

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“…Three of the A-D FAM72 aa variations are located near the potential transmembrane domain (aa 74 -aa 94) of FAM72 [17], and the major changes at aa positions 94 (L-->P), 99 (G-->R) and 125 (W-->R) ( Supplementary Fig. S2 [70,71]) may indicate opposing functions [48].…”

Section: Discussionmentioning

confidence: 99%

All-or-(N)One – an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci

et al. 2015

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FAM72 is a novel neuronal progenitor cell (NPC) self-renewal supporting protein expressed under physiological conditions at low levels in other tissues. Accumulating data indicate the potential pivotal tumourigenic effects of FAM72. Our in silico human genome-wide analysis (GWA) revealed that the FAM72 gene family consists of four human-specific paralogous members, all of which are located on chromosome (chr) 1. Unique asymmetric FAM72 segmental gene duplications are most likely to have occurred in conjunction with the paired genomic neighbour SRGAP2 (SLIT-ROBO Rho GTPase activating protein), as both genes have four paralogues in humans but only one vertebra-emerging orthologue in all other species. No species with two or three FAM72/SRGAP2 gene pairs could be identified, and the four exclusively human-defining ohnologues, with different mutation patterns in Homo neanderthalensis and Denisova hominin, may remain under epigenetic control through long non-coding (lnc) RNAs.

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Section: Discussionmentioning

confidence: 99%

All-or-(N)One – an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci

et al. 2015

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“…As the codons XAX and XTX (X=A, T, G or C) are playing an important role in producing proteins with adequate CFD. Producing mRNAs with this principle of CFD is important task for solving genetics diseases and production [7]. Similar studies with number of carbon rather than fraction can yield different results and observation.…”

Section: Resultsmentioning

confidence: 99%

CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

Ekambaram

Kannaiyan²,

Marimuthu

et al. 2014

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Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.

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Proteomic Atomics Reveals a Distinctive Uracil‐5‐Methyltransferase

Pramanik

Thaker

Perumal

et al. 2020

Molecular Informatics

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Carbon (C), hydrogen (H), nitrogen (N), oxygen (O), and sulfur (S) atoms intrigue as they are the foundation for amino acid (AA) composition and the folding and functions of proteins and thus define and control the survival of a cell, the smallest unit of life. Here, we calculated the proteomic atom distribution in > 1500 randomly selected species across the entire current phylogenetic tree and identified uracil-5-methyltransferase (U5MTase) of the protozoan parasite Plasmodium falciparum (Pf, strain Pf3D7), with a distinct atom and AA distribution pattern. We determined its apicoplast location and in silico 3D protein structure to refocus attention exclusively on U5MTase with tremendous potential for therapeutic intervention in malaria. Around 300 million clinical cases of malaria occur each year in tropical and subtropical regions of the world, resulting in over one million deaths annually, placing malaria among the most serious infectious diseases. Genomic and proteomic research of the clades of parasites containing Pf is progressing slowly and the functions of most of the~5300 genes are still unknown. We applied a 'bottom-up' comparative proteomic atomics analysis across the phylogenetic tree to visualize a protein molecule on its actual basis -i. e., its atomic level. We identified a protruding Pf3D7-specific U5MTase, determined its 3D protein structure, and identified potential inhibitory drug molecules through in silico drug screening that might serve as possible remedies for the treatment of malaria. Besides, this atomic-based proteome map provides a unique approach for the identification of parasite-specific proteins that could be considered as novel therapeutic targets.

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Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite Plasmodium falciparum 3D7

Cited by 3 publications

References 32 publications

All-or-(N)One – an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci

All-or-(N)One – an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci

CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

Proteomic Atomics Reveals a Distinctive Uracil‐5‐Methyltransferase

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