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891.
892.
Background
In past, a number of peptides have been reported to possess highly diverse properties ranging from cell penetrating, tumor homing, anticancer, anti-hypertensive, antiviral to antimicrobials. Owing to their excellent specificity, low-toxicity, rich chemical diversity and availability from natural sources, FDA has successfully approved a number of peptide-based drugs and several are in various stages of drug development. Though peptides are proven good drug candidates, their usage is still hindered mainly because of their high susceptibility towards proteases degradation. We have developed an in silico method to predict the half-life of peptides in intestine-like environment and to design better peptides having optimized physicochemical properties and half-life.Results
In this study, we have used 10mer (HL10) and 16mer (HL16) peptides dataset to develop prediction models for peptide half-life in intestine-like environment. First, SVM based models were developed on HL10 dataset which achieved maximum correlation R/R2 of 0.57/0.32, 0.68/0.46, and 0.69/0.47 using amino acid, dipeptide and tripeptide composition, respectively. Secondly, models developed on HL16 dataset showed maximum R/R2 of 0.91/0.82, 0.90/0.39, and 0.90/0.31 using amino acid, dipeptide and tripeptide composition, respectively. Furthermore, models that were developed on selected features, achieved a correlation (R) of 0.70 and 0.98 on HL10 and HL16 dataset, respectively. Preliminary analysis suggests the role of charged residue and amino acid size in peptide half-life/stability. Based on above models, we have developed a web server named HLP (Half Life Prediction), for predicting and designing peptides with desired half-life. The web server provides three facilities; i) half-life prediction, ii) physicochemical properties calculation and iii) designing mutant peptides.Conclusion
In summary, this study describes a web server ‘HLP’ that has been developed for assisting scientific community for predicting intestinal half-life of peptides and to design mutant peptides with better half-life and physicochemical properties. HLP models were trained using a dataset of peptides whose half-lives have been determined experimentally in crude intestinal proteases preparation. Thus, HLP server will help in designing peptides possessing the potential to be administered via oral route (http://www.imtech.res.in/raghava/hlp/).Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-282) contains supplementary material, which is available to authorized users. 相似文献893.
Matthias Schenk Chaitanya A. K. Koppisetty Daniela Costa Santos Euridice Carmona Smita Bhatia Per-Georg Nyholm Nongnuj Tanphaichitr 《Glycoconjugate journal》2009,26(8):1029-1045
Arylsulfatase A (ASA) hydrolyzes sulfate esters with a pH optimum of 5. Interactions between p-nitrocatechol sulfate (NCS, artificial substrate) and active site residues of ASA are revealed from their co-crystal structure.
Since equivalent ASA interactions with its natural substrates, sulfogalactosylceramide (SGC) and sulfogalactosylglycerolipid
(SGG), are not known, we computationally docked SGC/SGG to the ASA crystal structure. Our dockings suggested that Cys69 was
the active site residue, and Lys302 & Lys123 as residues anchoring the sulfate group of SGC/SGG to the active site, as observed
for NCS. We further confirmed these results using 2 recombinant ASA mutants: C69A and CKK (Cys69, Lys302 and Lys123-all mutated
to Ala). Both ASA mutants failed to desulfate SGC/SGG, and CKK showed minimal binding to [14C]SGC, although C69A still had affinity for this sulfoglycolipid. However, our dockings suggested additional intermolecular
hydrogen bonding and hydrophobic interactions between ASA and SGC/SGG, thus contributing to the specificity of SGC/SGG as
natural substrates. 相似文献
894.
895.
Deepak Dibya 《Biophysical journal》2010,99(3):853-861
Reported herein is a method that can be used to study the role of cholesterol in the microclustering of a ubiquitous class of membrane receptors, termed integrins. Integrin microclustering was measured using a fluorescence resonance energy transfer assay that does not require direct attachment of fluorescent donors or acceptors onto the integrins, and thus minimizes unwanted perturbations to integrin clustering. Membrane cholesterol levels were reduced using methyl-β-cyclodextrin (mβCD), as confirmed by Amplex Red assays of total cellular lipid or plasma membrane lipid extract. Subsequent changes in integrin microclustering were measured in cells expressing wild-type (WT) or mutant integrins. Although less integrin microclustering was measured after 27% membrane cholesterol depletion in a cell line expressing WT integrins, there was no statistically significant change for cells expressing α-cytoplasmic integrin mutants after a 45% reduction in plasma membrane cholesterol, and a significant increase in clustering for cells expressing ligand-binding domain integrin mutants after a 57% decrease in membrane cholesterol. These results are explained by differences in WT and mutant integrin partitioning into lipid nanodomains. Restoration of original cholesterol levels was used to confirm that the measured changes in membrane properties were cholesterol-dependent. No correlations between lipid diffusion and integrin microclustering were measured by means of fluorescence recovery after photobleaching using a fluorescent lipid mimetic. Similar lipid diffusion coefficients were measured after cholesterol depletion, irrespective of the integrins being expressed. 相似文献
896.
Singlet oxygen (1O2) scavenging activity of plastoquinol in photosystem II (PSII) of higher plants was studied by electron paramagnetic resonance (EPR) spin-trapping technique. It is demonstrated here that illumination of spinach PSII membranes deprived of intrinsic plastoquinone results in 1O2 formation, as monitored by TEMPONE EPR signal. Interestingly, the addition of exogenous plastoquinol (PQH2-1) to PQ-depleted PSII membranes significantly suppressed TEMPONE EPR signal. The presence of exogenous plastoquinols with a different side-chain length (PQH2-n, n isoprenoid units in the side chain) caused a similar extent of 1O2 scavenging activity. These observations reveal that plastoquinol exogenously added to PQ-depleted PSII membranes serves as efficient scavenger of 1O2. 相似文献
897.
Anuradha Singh Pradeep K. Singh Rakesh Singh Awadhesh Pandit Ajay K. Mahato Deepak K. Gupta Kuldeep Tyagi Ashok K. Singh Nagendra K. Singh Tilak R. Sharma 《Molecular breeding : new strategies in plant improvement》2010,26(2):325-338
Betaine aldehyde dehydrogenase (BADH) is a key enzyme involved in the synthesis of glycinebetaine—a powerful osmoprotectant
against salt and drought stress in a large number of species. Rice is not known to accumulate glycinebetaine but it has two
functional genes coding for the BADH enzyme. A non-functional allele of the BADH2 gene located on chromosome 8 is a major factor associated with rice aroma. However, similar information is not available
regarding the BADH1 gene located on chromosome 4 despite the similar biochemical function of the two genes. Here we report on the discovery and
validation of SNPs in the BADH1 gene by re-sequencing of diverse rice varieties differing in aroma and salt tolerance. There were 17 SNPs in introns with
an average density of one per 171 bp, but only three SNPs in exons at a density of one per 505 bp. Each of the three exonic
SNPs led to changes in amino acids with functional significance. Multiplex SNP assays were used for genotyping of 127 diverse
rice varieties and landraces. In total 15 SNP haplotypes were identified but only four of these, corresponding to two protein
haplotypes, were common, representing more than 85% of the cultivars. Determination of population structure using 54 random
SNPs classified the varieties into two groups broadly corresponding to indica and japonica cultivar groups, aromatic varieties clustering with the japonica group. There was no association between salt tolerance and the common BADH1 haplotypes, but aromatic varieties showed specific
association with a BADH1 protein haplotype (PH2) having lysine144 to asparagine144 and lysine345 to glutamine345 substitutions. Protein modeling and ligand docking studies show that these two substitutions lead to reduction in the substrate
binding capacity of the BADH1 enzyme towards gamma-aminobutyraldehyde (GABald), which is a precursor of the major aroma compound
2-acetyl-1-pyrroline (2-AP). This association requires further validation in segregating populations for potential utilization
in the rice breeding programs. 相似文献
898.
Anju Puri P. Osman Basha Mankesh Kumar Deepak Rajpurohit Gursharn S. Randhawa Shahryar F. Kianian Anantharama Rishi Harcharan S. Dhaliwal 《Functional & integrative genomics》2010,10(3):359-366
T-DNA insertional mutagenesis is one of the most important approaches for gene discovery and cloning. A fertile polyembryo
mutant generated by T-DNA/Ds insertion in Oryza sativa, cv. Basmati 370 showed twin or triple seedlings at a frequency of 15–20%. T-DNA insertion was confirmed by 950 bp hpt gene amplification in the promoter region of the candidate gene. The annotated protein corresponding to the OsPE candidate gene has been reported as a hypothetical protein in O. sativa. OsPE gene lacked functional homologs in other species. No OsPE paralog was found in rice. No conserved domains were found in the protein coded by OsPE. RT-PCR showed the expression of OsPE gene in Basmati 370 shoots. Full-length OsPE gene was cloned in Basmati 370. The combined use of Southern blot, genome walking, TAIL-PCR, RT-PCR techniques, and bioinformatics
led to the identification of a candidate gene controlling the multiple embryos in rice. There is gain of function, i.e., multiple
embryos in the seeds in the knockout mutant OsPE whereas its wild-type allele strictly controls single embryo per seed. The seeds with multiple embryos are distributed at
random in the rice mutant panicle. The origin of multiple embryos, whether apomictic, zygotic or both is under investigation. 相似文献
899.
Perumal D Sakharkar KR Tang TH Chow VT Lim CS Samal A Sugiura N Sakharkar MK 《Journal of molecular microbiology and biotechnology》2010,19(4):169-179
The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public health and emphasizes the need for new antimicrobial targets. The recent development of microbial genomics and the availability of genome sequences allows for the identification of essential genes which could be novel and potential targets for antibacterial drugs. However, these predicted targets need experimental validation to confirm essentiality. Here, we report on experimental validation of a two potential targets in the lipopolysaccharide (LPS) biosynthesis pathway of the pathogen Pseudomonas aeruginosa PAO1 using insertion duplication. Two genes, kdsA and waaG, from LPS encoding proteins 2-dehydro-3-deoxyphosphooctonate aldolase and UDP-glucose (heptosyl) LPS α-1,3-glucosyltransferase were selected as putative target candidates for the gene disruption experiments using plasmid insertion mutagenesis to determine essentiality. The introduction of a selectable ampicillin and kanamycin resistance marker into the chromosome resulted in lack of recovery of antibiotic-resistant colonies suggesting the essentiality of these genes for the survival of P. aeruginosa. Several molecular analyses were carried out in order to confirm the essentiality of these genes. We propose that the above two validated drug targets are essential and can be screened for functional inhibitors for the discovery of novel therapeutic compounds against antibiotic-resistant opportunistic pathogen P. aeruginosa. 相似文献
900.
Bobby Bhatia Arfa Malik Africa Fernandez-L Anna M Kenney 《Cell cycle (Georgetown, Tex.)》2010,9(21):4307-4314
Medulloblastoma, a brain tumor arising in the cerebellum, is the most common solid childhood malignancy. The current standard of care for medulloblastoma leaves survivors with life-long side effects. Gaining insight into mechanisms regulating transformation of medulloblastoma cells-of-origin may lead to development of better treatments for these tumors. Cerebellar granule neuron precursors (CGNPs) are proposed cells of origin for certain classes of medulloblastoma, specifically those marked by aberrant Sonic hedgehog (Shh) signaling pathway activation. CGNPs require signaling by Shh for proliferation during brain development. In mitogen-stimulated cells, nuclear localized cyclin-dependent kinase (Cdk) inhibitor p27Kip1 functions as a checkpoint control at the G1- to S-phase transition by inhibiting Cdk2. Recent studies have suggested that cytoplasmically localized p27Kip1 acquires oncogenic functions. Here, we show that p27Kip1 is cytoplasmically localized in CGNPs and mouse Shh-mediated medulloblastomas. Transgenic mice bearing an activating mutation in the Shh pathway and lacking one or both p27Kip1 alleles have accelerated tumor incidence compared to mice bearing both p27Kip1 alleles. Interestingly, mice heterozygous for p27Kip1 have decreased survival latency compared to p27Kip1-null animals. Our data indicate that this may reflect the requiremen of at least one copy of p27Kip1 for recruiting cyclin D/Cdk4/6 to promote cell cycle progression, yet insufficient expression in the heterozygous or null state to inhibit cyclin E/Cdk2. Finally, we find that mislocalized p27Kip1 may play a positive role in motility in medulloblastoma cells. Together, our data indicate that the dosage of p27Kip1 plays a role in cell cycle progression and tumor suppression in Shh-mediated medulloblastoma expansion.Key words: p27, Kip1, medulloblastoma, cerebellum, cell cycle, Sonic hedgehog, tumor, motility, RhoA 相似文献