The architectural network for protein secondary structure prediction

Over the past 25 years, the accuracy of proteins secondary structure prediction has improved substantially. Recently evolutionary information taken from the deviation of proteins in some structural family have again enhance prediction accuracy for all these residues predicted correctly is in one of the three sates helix, strands and others . The new methods developed over the past few years may be interesting in context of improvements which is achieved through combination of the existing methods. Evolutionary divergences profile posses’ adequate information to improve protein secondary structure prediction accuracy. These profiles can also able to correctly predict long stretches of identical residues in other secondary structure. This sequence structure relationship may help to help to developed tool which can efficiently predict the protein secondary structure from its amino acid sequence

Analyses of Burial Codon Bias Among the Species of Dipterocarpaceae Through Molecular and Phylogenetic Data

Introduction: DNA barcode, a molecular marker, is used to distinguish among the closely related species, and it can be applied across a broad range of taxa to understand ecology and evolution. MaturaseK gene ( matK ) and rubisco bisphosphate carboxylase/oxygenase form I gene ( rbcL ) of the chloroplast are highly conserved in a plant system, which are used as core barcode. This present endeavor entails the comprehensive examination of the under threat plant species based on success of discrimination on DNA barcode under selection pressure. Result: The family Dipterocarpaceae comprising of 15 genera is under threat due to some factors, namely, deforestation, habitat alteration, poor seed, pollen dispersal, etc. Species of this family was grouped into 6 clusters for matK and 5 clusters and 2 sub-clusters for rbcL in the phylogenetic tree by using neighbor-joining method. Cluster I to cluster VI of matK and cluster I to cluster V of rbcL genes were analyzed by various codon and substitution bias tools. Mutational pressure guided the codon bias which was favored by the avoidance of higher GC content and significant negative correlation between GC12 and GC3 (in sub-cluster I of cluster I [0.03 0.85) also showed the same result, which possibly could be due to the negative impact of very high and low transition rate than transversion. Conclusion: Through the analysis of inter-generic, inter/intra-specific variation and phylogenetic data, it was found that both selection and mutation played an important role in synonymous codon choice in these genes, but they acted inconsistently on the genes, both matK and rbcL . In vitro stable proteins of both matK and rbcL were selected through natural selection rather than mutational selection. matK gene had higher individual discrimination and barcode success compared with rbcL . These discriminatory approaches may describe the problem related to the extinction of plant species. Hence, it becomes very imperative to identify and detect the under threat plant species in advance

To analyze the nature and position of the salt bridges of different thermophilic and mesophilic proteins, we have used the software RasMol 2.7.5 a Molecular Graphics Visualisation Tool.

<p>To analyze the nature and position of the salt bridges of different thermophilic and mesophilic proteins, we have used the software RasMol 2.7.5 a Molecular Graphics Visualisation Tool.</p

Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges

<div><p>Introduction</p><p>Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications.</p><p>Methods</p><p>Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins.</p><p>Results</p><p>Present results strongly suggest that nonpolar smaller volume amino acids Ala (<i>χ</i>² = 238.54, p<0.001) and Gly (<i>χ</i>² = 73.35, p<0.001) are highly and Val moderately (<i>χ</i>² = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (<i>χ</i>²~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of <i>cis</i> peptide, loop/ turn and outlier in thermophiles. Pearson’s correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement.</p><p>Conclusions</p><p>Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.</p></div

Tyrosine phosphorylation is presented.

<p>The Tyr phosphorylation is evaluated at different ranges and presented in fifty thermophilic and their homologue fifty mesophilic proteins (used in salt bridge and physicochemical property study) (a). The mean number (mean ± SE) of Tyr which undergoes phosphorylation was calculated (50 thermophilic and 50 mesophilic proteins) as the percentage derived with respect to the total number of residues in the corresponding proteins. Level of significance *p<0.05.</p

Fifty thermophilic and their homologue fifty mesophilic proteins (which has their resolved 3D structure in PDB and has been utilized in the evaluation of physic-chemical properties) were selected.

<p>The salt-bridge analysis tool of Visual Molecular Dynamics, VMD (<a href="http://www.ks.uiuc.edu/" target="_blank">http://www.ks.uiuc.edu</a>) was utilized for this study. The number of total salt-bridges was calculated as the percentage derived with respect to the total number of residues in the corresponding proteins. The abundance rate of different important salt bridge dyads (ASP-ARG, ASP-HIS, ASP-LYS, GLU-ARG, GLU-HIS, GLU-LYS) were determined and calculated as the percentage of total number of salt bridges in those proteins. The level of significances of difference of mean are calculated by Student’s t test and represented on the bar as “*”. *p<0.05, **p<0.01 and ***p<0.001.</p

To analyze the nature and position of the salt bridges of different thermophilic and mesophilic proteins, we have used the software RasMol 2.7.5 a Molecular Graphics Visualisation Tool.

<p>To analyze the nature and position of the salt bridges of different thermophilic and mesophilic proteins, we have used the software RasMol 2.7.5 a Molecular Graphics Visualisation Tool.</p

This figure demonstrates the possible fates of a polypeptide having a significant hydrophilic and hydrophobic residues combination.

<p>Greater hydrophobicity results in the intrusion of that part into the core of the molecule which generates a compact structure. That minimizes the surface area to volume ration and hence the possibility of water contact.</p

Amino acid distributions are shown in 200 mesophilic and their 200 thermophilic homologue proteins.

<p>The database from the website <a href="http://www.uniprot.org/" target="_blank">http://www.uniprot.org/</a> was utilized for finding the amino acid sequences of thermophilic and mesophilic proteins. The percentage of 20 amino acids in each protein is calculated by accessing the website <a href="http://www.ebi.ac.uk/Tools/services/Pepstat" target="_blank">http://www.ebi.ac.uk/Tools/services/Pepstat</a>. The occurrences of amino acid are represented as different groups like 0–2%, 2–4%.....up to 18–20%. The distribution pattern in thermophilic versus mesophilic proteins are further analyzed by the Chi-square test.</p

The statistical analyses were done by using the SPSS for Windows statistical software package (SPSS Inc., Chicago, IL, USA, 2001).

<p>M stands for mesophilic, T- thermophilic, IPt- isoelectric point, C- charge, Hpl- hydrophilic, Hpb- hydrophobic, R- residue no.</p><p>Pearson correlation was utilized to evaluate the level of association of different physicochemical factors of 50 thermophilic and their homologue mesophilic proteins P value <0.05 is considered to be statistically significant.</p