The effects of alpha-helix on the stability of Asn residues: deamidation rates in peptides of varying helicity

Asn deamidation was monitored in Ala-based octadecapeptides of varying alpha-helicity. Gly was substituted for Ala residues at positions 6 and 16 to create a peptide with less helicity. Ala --> Gly substitutions were made at three or more residues from the Asn to negate known primary sequence effects on deamidation rates. The extent of helicity and rate of Asn deamidation for alkaline aqueous solutions of each peptide was measured as a function of temperature by circular dichroism and reversed-phase high-performance liquid chromatography, respectively. The rate of deamidation in the peptides was inversely proportional to the extent of alpha-helicity. The results support the conclusion that Asn deamidation only occurs in the nonhelical population of conformers.     

Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality

A large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome-wide. Sequence-tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 individuals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast . Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed.     

Epidemiology of asthma and associated factors in an urban Pakistani population: adult asthma study-Karachi

Background

This study was conducted in order to determine the prevalence of asthma and associated risk factors in the adult population of Karachi, Pakistan.

Methods

This multi-stage, cross-sectional survey was conducted from May 2014–August 2015; comprising 1629 adults in 75 randomly selected clusters in Karachi, Pakistan. Definitions included: ‘self-reported asthma’, ‘reversibility in FEV₁^’ and ‘respiratory symptoms and reversibility in FEV₁’.

Results

Prevalence of asthma was 1.8% (self-reported) (95% CI: 1.0–2.6), 11.3% (reversibility in FEV₁) (95% CI: 9.4–13.3) and 6.6% (symptoms and reversibility in FEV₁) (95% CI: 5.1–8.1). Asthmatics were more likely to belong to the age group ≥38?years according to ‘reversibility in FEV₁’ and ‘respiratory symptoms and reversibility in FEV₁’ (AOR: 1.9, 95% CI: 1.2–3.3) and (AOR: 2.1, 95% CI: 1.1–4.2), respectively. Asthmatics were more likely to report history of allergies (AOR: 1.9, 95% CI: 1.2–2.9) and (AOR: 2.8, 95% CI: 1.7–4.8); and were exposed to environmental tobacco smoke (AOR: 1.6, 95% CI: 1.1–2.5) and (AOR: 1.9, 95% CI: 1.1–3.3) according to ‘reversibility in FEV₁’ and ‘respiratory symptoms and reversibility in FEV₁’, respectively. Asthmatics were more likely to report pack years of smoking ≥5 (AOR: 2.3, 95% CI: 1.1–4.7) according to ‘respiratory symptoms and reversibility in FEV₁’.

Conclusion

This study reports a high prevalence of asthma among Pakistani adults and calls for developing appropriate public health policies for prevention and control of asthma in the country. Further studies should be conducted to determine the national prevalence as well as follow-up studies to identify preventable causes for adult asthma.

     

Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis

Bacillus thuringiensis is an insecticidal bacterium whose chitinolytic system has been exploited to improve insect resistance in crops. In the present study, we studied the CBP24 from B. thuringiensis using homology modeling and molecular docking. The primary and secondary structure analyses showed CBP24 is a positively charged protein and contains single domain that belongs to family CBM33. The 3D model after refinement was used to explore the chitin binding characteristics of CBP24 using AUTODOCK. The docking analyses have shown that the surface exposed hydrophilic amino acid residues Thr-103, Lys-112 and Ser-162 interact with substrate through H-bonding. While, the amino acids resides Glu-39, Tyr-46, Ser-104 and Asn-109 were shown to have polar interactions with the substrate. The binding energy values evaluation of docking depicts a stable intermolecular conformation of the docked complex. The functional characterization of the CBP24 will elucidate the substrate-interaction pathway of the protein in specific and the carbohydrate binding proteins in general leading towards the exploration and exploitation of the prokaryotic substrate utilization pathways.     

Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4

This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.     

Actin residue glu(93) is identified as an amino acid affecting myosin binding.

Many mutants have been described that affect the function of the actin encoded by the Drosophila melanogaster indirect flight muscle-specific actin gene, Act88F. We describe the development of procedures for purification of this actin from the other isoforms expressed in the fly as well as in vitro motility, single molecule force/displacement measurements, and stop-flow solution kinetic studies of the wild-type actin and that of the E93K mutation of the Act88F gene. We show that this mutation affects in vitro motility of F-actin, in both the presence and absence of methylcellulose, and the ability of the ACT88F actin to bind the S1 fragment of rabbit skeletal myosin. However, optical tweezer measurements of the actomyosin working stroke and the force transmitted from the rabbit heavy meromyosin to and through F-actin are unchanged by the mutation. These results support the proposal (Holmes, K. C. (1995) Biophys J. 68, (suppl.) 2-7) that actin residue Glu(93) is part of the secondary myosin binding site and suggest that myosin binding occurs first at the primary myosin binding site and then at the secondary site.     

Additions to the List of Graphidaceae (Lichenized Ascomycetes) in Pakistan

Biology Bulletin - As part of comprehensive study of lichen diversity of northern areas of Pakistan using molecular and morphological approaches, we found four species of the family Graphidaceae....