Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

<p>Abstract</p> <p>Background</p> <p>Empirical binding models have previously been investigated for the energetics of protein complexation (ΔG models) and for the influence of mutations on complexation (i.e. differences between wild-type and mutant complexes, ΔΔG models). We construct binding models to directly compare these processes, which have generally been studied separately.</p> <p>Results</p> <p>Although reasonable fit models were found for both ΔG and ΔΔG cases, they differ substantially. In a dataset curated for the absence of mainchain rearrangement upon binding, non-polar area burial is a major determinant of ΔG models. However this ΔG model does not fit well to the data for binding differences upon mutation. Burial of non-polar area is weighted down in fitting of ΔΔG models. These calculations were made with no repacking of sidechains upon complexation, and only minimal packing upon mutation. We investigated the consequences of more extensive packing changes with a modified mean-field packing scheme. Rather than emphasising solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with protein. This provides solvent accessible areas for proteins that are much closer to those of experimental structures than the more extended sidechain regime. The new packing scheme increases changes in non-polar burial for mutants compared to wild-type proteins, but does not substantially improve agreement between ΔG and ΔΔG binding models.</p> <p>Conclusion</p> <p>We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation. A simple volume-based, rather than solvent accessibility-based, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour. We discuss the efficacy of volume, as opposed to area, approaches to describe the energetic consequences of mutations at interfaces. This knowledge can be used to develop simple computational screens for binding in comparative modelled interfaces.</p

An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus

Abstract Background: Rapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism. Results: An integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and β-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation. Conclusions: The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3′UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization

Choline transporter: an additional marker of cholinergic nerves in the enteric nervous system

Purpose: The cholinergic circuitry of the enteric nervous system (ENS) is labelled using antibodies against molecules involved in acetylcholine (ACh) synthesis and release. A new component of ACh synthesis, the high affinity choline transporter (CHT), which is essential in the uptake of choline into cholinergic nerves, has been isolated and cloned. Recently, antiserum against CHT has been used in the central nervous system to label cholinergic nerves, but has not been located in the ENS. The aim of this study was to localise CHT immunoreactivity (IR) within rat and human intestine and determine if CHT colocalised with other cholinergic markers in the ENS. Methods: Segments of rat (n = 3) ileum and colon and human paediatric (n = 3) colon were fixed, prepared for sections and wholemounts and incubated with antisera against the full length human CHT sequence, followed by a fluorescent secondary antibody. Tissue was double labelled using antibodies to neuronal nitric oxide synthase (nNOS), common choline acetyltransferase (cChAT), substance P (SP) and vesicular acetylcholine transporter (VAChT). Colocalisation was quantitated in 3 confocal images from each segment. Results: In human and rat intestine, CHT-IR was present in nerve fibres in the circular muscle and myenteric ganglia and in myenteric nerve cell bodies. In human colon, CHT-IR was present in almost all VAChT-IR cholinergic nerve fibres in the circular muscle and myenteric ganglia. In contrast, in the rat only 56% of circular muscle VAChT-IR nerve fibres were CHT-IR, with this accounting for 79% of CHT-IR nerve fibres. In the myenteric ganglia, 48% of VAChT-IR nerve fibres were CHT-IR, accounting for 50% of CHT-IR nerve fibres. Surprisingly, no CHT-IR nerve cell bodies were cChAT-IR. Yet, 40% of CHT-IR nerve cell bodies were SP-IR (tachykinergic), accounting for 12% of SP-IR nerve cell bodies. In both species, there was little localisation of CHT-IR in nitrergic NOSIR inhibitory nerve fibres. Conclusions: In human paediatric colon, there was almost complete colocalisation of CHT-IR and VAChT-IR in nerve fibres in the circular muscle and myenteric ganglia. Therefore the CHT antisera would be useful for studying the enteric cholinergic circuitry in human intestine and complimentary to currently used labels. In rat, CHT-IR identified VAChT-IR positive, VAChT-IR negative nerve fibres and cChAT-IR negative cell bodies. This result suggests the antibody does not bind to all the cholinergic circuitry identified by cChAT-IR or VAChT-IR. Further studies are needed to determine if the CHT antibody is specifically labelling cholinergic nerves in the rat.Andrea M. Harrington, Margaret Lee, Sim-Yee Ong, Eric Yong, Pam Farmer, John M. Hutson and Bridget R. Southwel

Patients with coronary artery disease had high prevalanece of colorectal cancer and adenoma: END-results of metabolic syndrome and smoking

Background: Our previous study showed an association between colorectal neoplasm (CN) and coronary artery disease (CAD), probably due to sharing of common risk factors. Aim: To investigate the prevalence of CN in patients with and without CAD in those aged ≥50 years prospectively and to identify the underlying risk factors. Methods: Patients were recruited for screening colonoscopy after undergoing coronary angiography. They were defined as CAD+ (n=206) if ≥50% diameter stenosis was observed in any one of the major coronary arteries, and CAD- (n=208) if not. A second age and sex matched control group was recruited from the general population (n=207). The prevalence of colonic lesions and underlying risk factors was compared by Pearson chi-square test. A bivariate logistic regression analysis was performed to adjust for age and sex and to identify independent risk factors. Results: The prevalence of the lesions in the CAD+, CAD- and general population group were 40.3%, 28.8%, and 32.9% (p=0.045) for endoscopic polyp, 34.0%, 18.8%, and 20.8% (p<0.0001) for CN, 18.4%, 8.7%, and 5.8% (p<0.00001) for advanced lesion, and 4.4%, 0.5%, and 1.4% (p=0.014) for cancer, respectively. All except one cancers were detected at early stage. After adjusting for age and sex, smoking history (OR: 4.74, CI: 1.38 to 19) and metabolic syndrome (OR: 5.99; CI: 1.43 to 28.0) were independent factors for the coexistence of CAD and advanced lesion. Conclusion: Life style modification is important to prevent the development of both CAD and advanced colonic lesions simultaneously. CAD+ is a surrogate marker for high prevalence of CN, necessitating immediate colonoscopy screening.link_to_subscribed_fulltex