Systematic analysis of protein interaction network associated with azoospermia

Non-obstructive azoospermia is a severe infertility factor. Currently, the etiology of this condition remains elusive with several possible molecular pathway disruptions identified in the post-meiotic spermatozoa. In the presented study, in order to identify all possible candidate genes associated with azoospermia and to map their relationship, we present the first protein-protein interaction network related to azoospermia and analyze the complex effects of the related genes systematically. Using Online Mendelian Inheritance in Man, the Human Protein Reference Database and Cytoscape, we created a novel network consisting of 209 protein nodes and 737 interactions. Mathematical analysis identified three proteins, ar, dazap2, and esr1, as hub nodes and a bottleneck protein within the network. We also identified new candidate genes, CREBBP and BCAR1, which may play a role in azoospermia. The gene ontology analysis suggests a genetic link between azoospermia and liver disease. The KEGG analysis also showed 45 statistically important pathways with 31 proteins associated with colorectal, pancreatic, chronic myeloid leukemia and prostate cancer. Two new genes and associated diseases are promising for further experimental validation

Molecular dynamic simulation of V176G mutation associated with Gerstmann–Sträussler–Scheinker at elevated temperature

The transformation of cellular prion protein (PrPc) into pathogenic conformer (PrPSc) in transmissible spongiform encephalopathy is expedited by mutations in the prion protein. One recently reported novel mutation V176G is located in region of the protein known to cause Creutzfeldt-Jakob disease (CJD) but possess a unique neuropathological profile and spongiform alteration similar to Gerstmann–Sträussler–Scheinker syndrome (GSS). Using molecular dynamics simulations; the denaturation of the prion structure with V176G at 500K was studied to identify the dynamics in structural properties such as salt bridge, solvent accessibility, hydrogen bonds and hydrophobicity. The simulations revealed that the heat-induced unfolding caused destabilization of the native structure of PrP and affecting the ß-sheet region of the structure more than the a-helix. Unique salt bridge formation suggests conformational orientation that may be attributed to the V176G mutation. The mutation effects showed an increased fluctuation of the H1 region, gain of hydrogen bonds between H3 and H2 which may be part of the oligomerization pathway and determine the features of the PrPSc assemblies

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation

Substrate and cofactor binding interaction studies of galactitol -1- Phosphate 5- Dehydrogenase from Peptoclostridium difficile

Tagatose is a high value low calorie sweetener that is used as a sugar substitute in the food and pharmaceutical industry. The production of tagatose requires the conversion of galactitol-1-phosphate to tagatose-6-phosphate by galactitol-1-phosphate 5-dehydrogenase (PdGPDH). Theobjective of this work is to study the protein-ligand interaction between PdGPDH and its ligands; galactitol-1-phosphate, Zn2+ and NAD+. Understanding of this mechanism will provide an insight into the possible catalytic events in these domains, thus providing information for potential protein engineering to improve the tagatose production. A 3D model of PdGPDH was constructed to identify the catalytic and coenzyme binding domains. In order to understand the interaction of PdGPDH with its ligands, a docking analysis of PdGPDH-substrate, PdGPDH-Zn2+ and PdGPDH-NAD+ complex was performed using CDOCKER in Discovery Studio 4.0 (DS 4.0). A series of docking events were performed to find the most stable binding interaction for the enzyme and its ligands. This study found that Cys 37, His 58, Glu 59, Glu 142 residues from PdGPDH form an active site pocket similar to known GPDH. A catalytic Zn2+ binding domain and a cofactor NAD+binding domain with strong hydrogen bonding contacts with the substrate and the cofactor were identified. The binding pockets of the enzyme for galactitol-1-phosphate, NAD+ and Zn2+has been defined. The stability of PdGPDH with its ligand was verified by utilizing the molecular dynamic simulation of docked complex. The results from this study will assist future mutagenesis study and enzyme modification work to improve the tagatose production

Molecular phylogeny and structure prediction of rice RFT1 protein

Rice is one of the most important species in the family of Poaceae. As one of the major crop that is consumed by world population, it is cultivated commercially in many parts of the world. Hence, the phylogeny study of this crop is crucial as a step for improvement of its breeding programs. Phylogenetic relationship among 12 rice cultivars that originated from two common sub-species; Indica and Japonica were inferred by comparing protein sequence data sets derived from its flowering time gene, namely RFT1 and analyzed using maximum parsimony (MP) method. The predicted structure of RFT1 protein was generated by I-TASSER server and analyzed using YASARA software. The result showed that the cultivars were classified into two major groups, where the first group (Japonica) evolved first followed by the second group (Indica). The findings suggested that some cultivars had a close relationship with each other even it is originates from different varieties. The relationships among these cultivars provide useful information for better understanding of molecular evolution process and designing good breeding program in order to generate new cultivar

Effect of stored oil palm trunk sap towards methyl ester synthesis / Nurnuha Shamsir... [et al.]

Oil palm trunk (OPT) has highest content of sap, 80% of the overall weight. OPT sap contains free sugars which can be converted into valuable compounds such as ester. The objective of this study is to determine the changes of free sugars at different storage time and the effect on methyl ester synthesis. The sap was extracted and stored at different durations time (1, 7, 14, 21 and 28 days). 10ml of dried sap was added with 100mg Fe2(SO4)3 EFB and 15ml of methanol. The mixture was put into the autoclave to be heated at 160 oC for 150 minutes. Free sugars found in OPT sap were glucose, fructose and sucrose. The free sugars vary upon the storage time and highest concentration of glucose and fructose achieved at day 21. This is due to hydrolysis of sucrose. The GC-MS analysis identified and quantified several methyl ester such as methyl pyruvate, methyl levulinate, methyl-9- oxononanoate and methyl palmitate. These findings confirmed that the free sugars from OPT sap were possible to be an alternative carbon in ester synthesi

Characterization of a glucose-tolerant β-glucosidase from Anoxybacillus sp. DT3-1

Background: In general, biofuel production involves biomass pretreatment and enzymatic saccharification, followed by the subsequent sugar conversion to biofuel via fermentation. The crucial step in the production of biofuel from biomass is the enzymatic saccharification. Many of the commercial cellulase enzyme cocktails, such as Spezyme® CP (Genencor), Acellerase™ 1000 (Genencor), and Celluclast® 1.5L (Novozymes), are ineffectively to release free glucose from the pretreated biomass without additional β-glucosidase. Results: In this study, for the first time, a β-glucosidase DT-Bgl gene (1359 bp) was identified in the genome of Anoxybacillus sp. DT3-1, and cloned and heterologously expressed in Escherichia coli BL21. Phylogenetic analysis indicated that DT-Bgl belonged to glycosyl hydrolase (GH) family 1. The recombinant DT-Bgl was highly active on cello-oligosaccharides and p-nitrophenyl-β-d-glucopyranoside (pNPG). The DT-Bgl was purified using an Ni-NTA column, with molecular mass of 53 kDa using an SDS-PAGE analysis. It exhibited optimum activity at 70 °C and pH 8.5, and did not require any tested co-factors for activation. The K m and V max values for DT-Bgl were 0.22 mM and 923.7 U/mg, respectively, with pNPG as substrate. The DT-Bgl displayed high glucose tolerance, and retained 93 % activity in the presence of 10 M glucose. Conclusions: Anoxybacillus DT-Bgl is a novel thermostable β-glucosidase with low glucose inhibition, and converts long-chain cellodextrins to cellobiose, and further hydrolyse cellobiose to glucose. Results suggest that DT-Bgl could be useful in the development of a bioprocess for the efficient saccharification of lignocellulosic biomass

Draft genome sequences of longimonas halophila KCTC 42399 and longibacter salinarum KCTC 52045

Longimonas halophila and Longibacter salinarum are type strains of underexplored genera affiliated with Salisaetaceae. Herein, we report the draft genome sequences of two strains of these bacteria, L. halophila KCTC 42399 and L. salinarum KCTC 52045, with the intent of broadening knowledge of this family. Genome annotation and gene mining revealed that both bacteria exhibit amylolytic abilities

Genome analysis of a new Rhodothermaceae strain isolated from a hot spring

A bacterial strain, designated RA, was isolated from water sample of a hot spring on Langkawi Island of Malaysia using marine agar. Strain RA is an aerophilic and thermophilic microorganism that grows optimally at 50-60°C and is capable of growing in marine broth containing 1-10% (w/v) NaCl. 16S rRNA gene sequence analysis demonstrated that this strain is most closely related (<90% sequence identity) to Rhodothermaceae, which currently comprises of six genera: Rhodothermus (two species), Salinibacter (three species), Salisaeta (one species), Rubricoccus (one species), Rubrivirga (one species), and Longimonas (one species). Notably, analysis of average nucleotide identity (ANI) values indicated that strain RA may represent the first member of a novel genus of Rhodothermaceae. The draft genome of strain RA is 4,616,094 bp with 3630 protein-coding gene sequences. Its GC content is 68.3%, which is higher than that of most other genomes of Rhodothermaceae. Strain RA has genes for sulfate permease and arylsulfatase to withstand the high sulfur and sulfate contents of the hot spring. Putative genes encoding proteins involved in adaptation to osmotic stress were identified which encode proteins namely Na+/H+ antiporters, a sodium/solute symporter, a sodium/glutamate symporter, trehalose synthase, malto-oligosyltrehalose synthase, choline-sulfatase, potassium uptake proteins (TrkA and TrkH), osmotically inducible protein C, and the K+ channel histidine kinase KdpD. Furthermore, genome description of strain RA and comparative genome studies in relation to other related genera provide an overview of the uniqueness of this bacterium