Possible functional proximity of various organisms based on the bioinformatics analysis of their taste receptors

Hassan, Sk. Sarif; Sil, Moumita; Chakraborty, Subhajit; Goswami, Arunava; Basu, Prabir; Nawn, Debaleena; Uversky, Vladimir N.

doi:10.1016/j.ijbiomac.2022.10.009

“…Count of every amino acid in a sequence, termed amino acid frequency, was computed for all 165 moonlighting protein [23, 24, 25]. Due to varied lengths of moonlighting protein sequences, percentage of amino acids in a sequence (obtained from dividing the amino acid frequencies by the length of that sequence and multiplied by 100) is termed the relative frequency of amino acids in that sequence.…”

Section: Methodsmentioning

confidence: 99%

“…Shannon entropy (SE) is a measure of the information content in a system [26]. SE of each moonlighting protein sequence is evaluated by the formula: p i is the count of amino acid i in that sequence divided by the length of that sequence [23]. SE reflects the degree of randomness in the amino acids count in a given sequence.…”

Section: Methodsmentioning

confidence: 99%

The Distal-Proximal Relationships Among the Human Moonlighting Proteins: Evolutionary hotspots and Darwinian checkpoints

Nawn,

Hassan,

Sil

et al. 2023

Preprint

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Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases.

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“…We performed the above two steps for all binary sequences. We checked our null hypothesis by performing a Studentt-test to check if the mean of z is significantly different from 0 [82,83].…”

Section: Data Acquisitionmentioning

confidence: 99%

Biology of Coital Behavior: Looking Through the Lens of Mathematical Genomics

Sil

¹

,

Nawn

²

,

Hassan³

et al. 2023

Preprint

0

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Research has shown that genetics and epigenetics regulate mating behavior across multiple species. Previous studies have generally focused on the signaling pathways involved and spatial distribution of the associated receptors. However a thorough quantitative characterization of the receptors involved may offer deeper insight into mating behavioral patterns. Here oxytocin, arginine-vasopressin 1a, dopamine 1, and dopamine 2 receptors were investigated across 76 vertebrate species. The receptor sequences were characterized by polarity-based randomness, amino acid frequency-based Shannon entropy and Shannon sequence variability, intrinsic protein disorder, binding affinity, stability and pathogenicity of homology-based SNPs, structural and physicochemical features. Hierarchical clustering of species was derived based on structural and physicochemical features of the four receptor sequences separately, which eventually led to proximal relationships among 29 species. Humans were found to be significantly distant phylogenetically from the prairie voles, a representative of monogamous species based on coital behavior. Furthermore, the mouse (polygamous), the prairie deer mouse (polygamous), and the prairie vole (monogamous) although being proximally related (based on quantitative genomics of receptors), differed in their coital behavioral pattern, mostly, due to behavioral epigenetic regulations. This study adds a perspective that receptor genomics does not directly translate to behavioral patterns.

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“…Where H is the Shannon entropy, P (i) is the frequency probability of occurrence of amino acid i, and the summation is over all possible amino acids [83]. The resulting value of H reflects the degree of diversity of frequency distribution of amino acids.…”

Section: Amino Acid Frequency Based Shannon Entropy Of Sequencementioning

confidence: 99%

“…To assess the single nucleotide polymorphism (SNP) across the remaining sequences for AVPR1a, DRD1, DRD2, and OXTR receptors, we used sp-Q9WTV9-V1AR MICOH, tr-E0V8E1-E0V8E1 MICOH D(1A), tr-E0V889-E0V889 MICOH D(2), and tr-E0V872-E0V872 MICOH as reference sequences, respectively. We used the Clustal Omega web-server to align the remaining sequences to the reference sequences and to identify similar nonsynonymous changes in the amino acid residues, which we referred to as "homology based SNPs" (in short simply "SNPs") [83].…”

Section: Determining Homology Based Snps Pathogenicity and Structural...mentioning

confidence: 99%

Biology of Coital Behavior: Looking Through the Lens of Mathematical Genomics

Sil¹,

Nawn

²

,

Hassan³

et al. 2023

Preprint

Self Cite

0

View full text Add to dashboard Cite

Research has shown that genetics and epigenetics regulate mating behavior across multiple species. Previous studies have generally focused on the signaling pathways involved and spatial distribution of the associated receptors. However a thorough quantitative characterization of the receptors involved may offer deeper insight into mating behavioral patterns. Here oxytocin, arginine-vasopressin 1a, dopamine 1, and dopamine 2 receptors were investigated across 76 vertebrate species. The receptor sequences were characterized by polarity-based randomness, amino acid frequency-based Shannon entropy and Shannon sequence variability, intrinsic protein disorder, binding affinity, stability and pathogenicity of homology-based SNPs, structural and physicochemical features. Hierarchical clustering of species was derived based on structural and physicochemical features of the four receptor sequences separately, which eventually led to proximal relationships among 29 species. Humans were found to be significantly distant phylogenetically from the prairie voles, a representative of monogamous species based on coital behavior. Furthermore, the mouse (polygamous), the prairie deer mouse (polygamous), and the prairie vole (monogamous) although being proximally related (based on quantitative genomics of receptors), differed in their coital behavioral pattern, mostly, due to behavioral epigenetic regulations. This study adds a perspective that receptor genomics does not directly translate to behavioral patterns.

show abstract

Possible functional proximity of various organisms based on the bioinformatics analysis of their taste receptors

Cited by 9 publications

References 40 publications

The Distal-Proximal Relationships Among the Human Moonlighting Proteins: Evolutionary hotspots and Darwinian checkpoints

The Distal-Proximal Relationships Among the Human Moonlighting Proteins: Evolutionary hotspots and Darwinian checkpoints

Biology of Coital Behavior: Looking Through the Lens of Mathematical Genomics

Biology of Coital Behavior: Looking Through the Lens of Mathematical Genomics

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