Residue–Residue Contact Can Be a Potential Feature for the Prediction of Lysine Crotonylation Sites

Lysine crotonylation (Kcr) is involved in plenty of activities in the human body. Various technologies have been developed for Kcr prediction. Sequence-based features are typically adopted in existing methods, in which only linearly neighboring amino acid composition was considered. However, modified Kcr sites are neighbored by not only the linear-neighboring amino acid but also those spatially surrounding residues around the target site. In this paper, we have used residue–residue contact as a new feature for Kcr prediction, in which features encoded with not only linearly surrounding residues but also those spatially nearby the target site. Then, the spatial-surrounding residue was used as a new scheme for feature encoding for the first time, named residue–residue composition (RRC) and residue–residue pair composition (RRPC), which were used in supervised learning classification for Kcr prediction. As the result suggests, RRC and RRPC have achieved the best performance of RRC at an accuracy of 0.77 and an area under curve (AUC) value of 0.78, RRPC at an accuracy of 0.74, and an AUC value of 0.80. In order to show that the spatial feature is of a competitively high significance as other sequence-based features, feature selection was carried on those sequence-based features together with feature RRPC. In addition, different ranges of the surrounding amino acid compositions’ radii were used for comparison of the performance. After result assessment, RRC and RRPC features have shown competitively outstanding performance as others or in some cases even around 0.20 higher in accuracy or 0.3 higher in AUC values compared with sequence-based features.

Fine carbohydrate structure governs the structure and function of human gut microbiota independently of variation in glycosyl residue composition

Increased dietary fiber consumption has been shown to increase human gut microbial diversity, but the mechanisms driving this effect remain unclear. One possible explanation is that microbes are able to divide metabolic labor in consumption of complex carbohydrates, which are composed of diverse glycosidic linkages that require specific cognate enzymes for degradation. However, as naturally derived fibers vary in both sugar composition and linkage structure, it is challenging to separate out the impact of each of these variables. We hypothesized that fine differences in carbohydrate linkage structure would govern microbial community structure and function independently of variation in glycosyl residue composition. To test this hypothesis, we fermented commercially available soluble resistant glucans, which are uniformly composed of glucose linked in different structural arrangements, in vitro with fecal inocula from each of three individuals. We measured metabolic outputs (pH, gas, and short-chain fatty acid production) and community structure via 16S rRNA amplicon sequencing. We determined that community metabolic outputs from identical glucans were highly individual, emerging from divergent initial microbiome structures. However, specific operational taxonomic units responded similarly in growth responses across individuals’ microbiota, though in context-dependent ways; these data suggested that certain taxa were more efficient in competing for some structures than others. Together, these data support the hypothesis that variation in linkage structure, independent of sugar composition, governs compositional and functional responses of microbiota.ImportancePrevious studies have reported how physical and chemical structures of carbohydrates influence the gut microbiota, however, variability across dietary fibers in monosaccharide composition and linkage structure obscures the relationship between fine polysaccharide linkage structure and microbial fitness. Revealing connections between subtle differences in glucan structure and microbial composition and metabolic responses, this study suggests much greater attention to substrate structure in the design of experiments to test fiber-microbiome responses in vitro and in vivo. Further, it underscores that, although microbiome responses to distinct fibers are individual and vary among specific glucans, similar carbohydrate structure-microbe relationships occur across individual donor communities. Together, these data may help explain why some individuals may respond (while others do not) to fiber treatments in human feeding trials and support the long-term goal of rational inclusion of specific fibers in dietary patterns to modulate the gut microbiome in support of health.

Effects of the surface polarity of nanomaterials on their interaction with complement protein gC1q

The dependence of the recognition mode of gC1q on the surface polarity of nanomaterials is mainly attributed to its distinct surface residue composition.

Where Natural Protein Sequences Stand out From Randomness

Biological sequences are the product of natural selection, raising the expectation that they differ substantially from random sequences. We test this expectation by analyzing all fragments of a given length derived from either a natural dataset or different random models. For this, we compile all distances in sequence space between fragments within each dataset and compare the resulting distance distributions between sets. Even for 100mers, 95.4% of all distances between natural fragments are in accordance with those of a random model incorporating the natural residue composition. Hence, natural sequences are distributed almost randomly in global sequence space. When further accounting for the specific residue composition of domain-sized fragments, 99.2% of all distances between natural fragments can be modeled. Local residue composition, which might reflect biophysical constraints on protein structure, is thus the predominant feature characterizing distances between natural sequences globally, whereas homologous effects are only barely detectable.

Inter-residue interactions in alpha-helical transmembrane proteins

Motivation The number of available membrane protein structures has markedly increased in the last years and, in parallel, the reliability of the methods to detect transmembrane (TM) segments. In the present report, we characterized inter-residue interactions in α-helical membrane proteins using a dataset of 3462 TM helices from 430 proteins. This is by far the largest analysis published to date. Results Our analysis of residue–residue interactions in TM segments of membrane proteins shows that almost all interactions involve aliphatic residues and Phe. There is lack of polar–polar, polar–charged and charged–charged interactions except for those between Thr or Ser sidechains and the backbone carbonyl of aliphatic and Phe residues. The results are discussed in the context of the preferences of amino acids to be in the protein core or exposed to the lipid bilayer and to occupy specific positions along the TM segment. Comparison to datasets of β-barrel membrane proteins and of α-helical globular proteins unveils the specific patterns of interactions and residue composition characteristic of α-helical membrane proteins that are the clue to understanding their structure. Availability and implementation Results data and datasets used are available at http://lmc.uab.cat/TMalphaDB/interactions.php. Supplementary information Supplementary data are available at Bioinformatics online.

Chemostratigraphy and provenance of clays and other non-carbonate minerals in chalks of Campanian age (Upper Cretaceous) from Sussex, southern England

Geochemical analysis of acid-insoluble residues derived from white chalks and marl seams of Campanian age from Sussex, UK, has been undertaken. All display a broadly similar <2 μm mineralogical composition consisting of smectite or smectite-rich illite-smectite with subordinate illite and minor amounts of talc. Plots of K2O/Al2O3 and TiO2/Al2O3 indicate that most marl seams have an acid-insoluble residue composition which is slightly different to that of the over- and underlying white chalk, implying that marl seams are primary sedimentary features not formed through white chalk dissolution. On the basis of a negative Eu anomaly and trace element geochemistry one marl seam, the Old Nore Marl, is considered to be volcanically derived and best classified as a bentonite; it is considered to correlate with the bentonite M1 of the north German succession.

Soybean Curd Residue: Composition, Utilization, and Related Limiting Factors

The production of soybean products has been increasing throughout the world, and there has been a corresponding increase in the quantity of soybean curd residue (SCR) being thrown out. The dumping of SCR has become a problem to be solved due to its contamination to the environment. SCR is rich in fiber, fat, protein, vitamins, and trace elements. It has potential for value-added processing and utilization; options that simultaneously hold the promise of increased economic benefit as well as decreased pollution potential for the environment. The objective of this study is to fully investigate, review, and summarize the existing literature in order to develop a comprehensive knowledge base for the composition and reuse of SCR. It is evident from the literature survey that SCR shows good potential as a functional food material. However, there are several drawbacks to the use of SCR and corresponding solutions presented in this paper.