Physiochemical Properties Of Proteins Research Articles

Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius)

The two species of the Old World Camelini tribe, dromedary and Bactrian camels, show superior adaptability to the different environmental conditions they populate, e.g. desert, mountains and coastal areas, which might be associated with adaptive variations on their mitochondrial DNA. Here, we investigate signatures of natural selection in the 13-mitochondrial protein-coding genes of different dromedary camel populations from the Arabian Peninsula, Africa and southwest Asia. The full mitogenome sequences of 42 dromedaries, 38 domestic Bactrian, 29 wild Bactrian camels and 31 samples representing the New World Lamini tribe reveal species-wise genetic distinction among Camelidae family species, with no evidence of geographic distinction among dromedary camels. We observe gene-wide signals of adaptive divergence between the Old World and New World camels, with evidence of purifying selection among Old World camel species. Upon comparing the different Camelidae tribes, 27 amino acid substitutions across ten mtDNA protein-coding genes were found to be under positive selection, in which, 24 codons were defined to be under positive adaptive divergence between Old World and New World camels. Seven codons belonging to three genes demonstrated positive selection in dromedary lineage. A total of 89 codons were found to be under positive selection in Camelidae family based on investigating the impact of amino acid replacement on the physiochemical properties of proteins, including equilibrium constant and surrounding hydrophobicity. These mtDNA variants under positive selection in the Camelidae family might be associated with their adaptation to their contrasting environments.

An in silico approach towards identification of novel drug targets in Klebsiellaoxytoca

The prolonged use, incorrect diagnosis, unnecessary prescription, improper dosing over the year has transformed klebsiella organisms into resistant to antibiotics. The emergence of resistance to many antibiotics and drugs makes treatment options limited. Now, the antibiotic pipeline has become severely dry. So, there is a pressing necessity for a new drug against Klebsiella oxytoca infections as well as the identification of drug targets. In this study, a systematic proteome subtractive method is used to screen out the most potential drug targets of Klebsiella oxytoca that might facilitate the discovery of putative drug in the near future. The comparative proteome analysis of host and pathogen was made to identify the non-homologous proteins which showed no similarity with human host proteins. KEGG pathway analysis was made to identify common and unique metabolic pathways. A computational analysis was carried out to list out the indispensable non-homologous proteins of the pathogen. Essential proteins were predicted by the analysis of protein-protein interactions networks to reveal the proteins which are exigent for the survival of the pathogen, and these proteins also have a lethal effect when removed from the pathogen. In this study, 43 essential proteins were identified. To predict subcellular localization, CELLO (version 2.5) and PSORTb (version 3.00) tools were used. The druggability of proteins was predicted using the DrugBank database. Besides, the physiochemical properties of proteins were analyzed using the Protparam tool of ExPASy. After physiochemical properties analysis and the based on 3D structure availability in the Protein Data Bank, the homology model was built for only one influential drug target using MODELLER. In the end, molecular docking study was carried out to investigate the protein interactions with five different drugs.

Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development.

Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family have multiple potential roles in plant growth and development, particularly in flower induction and seed development. However, limited information is available about the functions of these genes in fruit plants, particularly in grapes. We identified 14 GASA genes in grapevine (Vitis vinifera L.) and performed comprehensive bioinformatics and expression analyses. In the bioinformatics analysis, the locations of genes on chromosomes, physiochemical properties of proteins, protein structure, and subcellular positions were described. We evaluated GASA proteins in terms of domain structure, exon-intron distribution, motif arrangements, promoter analysis, phylogenetic, and evolutionary history. According to the results, the GASA domain is conserved in all proteins and the proteins are divided into three well-conserved subgroups. Synteny analysis proposed that segmental and tandem duplication have played a role in the expansion of the GASA gene family in grapes, and duplicated gene pairs have negative selection pressure. Most of the proteins were predicted to be in the extracellular region, chloroplasts, and the vacuole. In silico promoter analysis suggested that the GASA genes may influence different hormone signaling pathways and stress-related mechanisms. Additionally, we performed a comparison of the expression between seedless (Thompson seedless) and seeded (Red globe) cultivars in different plant parts, including the ovule during different stages of development. Furthermore, some genes were differentially expressed in different tissues, signifying their role in grapevine growth and development. Several genes (VvGASA2 and 7) showed different expression levels in later phases of seed development in Red globe and Thompson seedless, suggesting their involvement in seed development. Our study presents the first genome-wide identification and expression profiling of grapevine GASA genes and provides the basis for functional characterization of GASA genes in grapes. We surmise that this information may provide new potential resources for the molecular breeding of grapes.

Structural characterization and physicochemical properties of protein extracted from soybean meal assisted by steam flash-explosion with dilute acid soaking.

The aim of this work was to analyze the influence of steam flash-explosion (SFE) with dilute acid soaking pretreatment on the structural characteristics and physiochemical properties of protein from soybean meal (SBM). The pretreatment led to depolymerisation of soy protein isolate (SPI) and formation of new protein aggregation through non-disulfide covalent bonds, which resulted in broader MW distribution of SPI. The analysis of CD spectroscopy showed that the SFE treatment induced minor changes in secondary structure, however, the intrinsic tryptophan fluorescence revealed that acid soaking and SFE treatment pronouncedly altered the tertiary structure of SPI. The protein zeta potential was shown to be increased after SFE treatment attributed to the changes in protein structure and the covalent coupling between carbohydrate and protein. These results contribute to clarifying the mechanisms of the effect of pretreatment on SPI structure, thus moving further toward implementing SFE in the processing chain of SPI.