Halogenated Benzenes Bound within a Non-polar Cavity in T4 Lysozyme Provide Examples of I?S and I?Se Halogen-bonding

We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume ∼ 150 Å³ that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystallography and related techniques to analyze the binding of halogen-incorporated benzenes typified by C₆F₅X, where X = H, F, Cl, Br or I, and C₆H₅X, where X = H or I was also studied. Because of the increased electron density of fluorine relative to hydrogen, the geometry of binding of the fluoro compounds can often be determined more precisely than their hydrogen-containing analogs. All of the ligands bind in essentially the same plane but the center of the phenyl ring can translate by up to 1.2 Å. In no case does the ligand rotate freely within the cavity. The walls of the cavity consist predominantly of hydrocarbon atoms, and in several cases it appears that van der Waals interactions define the geometry of binding. In comparing the smallest with the largest ligand, the cavity volume increases from 181 Å³ to 245 Å³. This shows that the protein is flexible and adapts to the size and shape of the ligand. There is a remarkably close contact of 3.0 Å between the iodine atom on C₆F₅I and the sulfur or selenium atom of Met or SeMet102. This interaction is 1.0 Å less than the sum of the van der Waals radii and is a clear example of a so-called halogen bond. Notwithstanding this close approach, the increase in binding energy for the halogen bond relative to a van der Waals contact is estimated to be only about 0.5-0.7 kcal/mol.     

Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network

This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.     

Lectinomics II. A highway to biomedical/clinical diagnostics

The review assesses current status and attempts to forecast trends in the development of lectin biorecognition technology. The progressive trend is characterized scientometrically and reflects the current transient situation, when standard low-throughput lectin-based techniques are being replaced by a novel microarray-based techniques offering high-throughput of detection. The technology is still in its infancy (validation phase), but already shows promise as an efficient tool to decipher the enormous complexity of the glycocode that influences physiological status of the cell. Further enhancement in robustness and flexibility of lectin microarrays is predicted by using recombinant and artificial lectins that will render production of lectin microarrays cost-effective and more affordable. Mass spectrometry is expected to play an important role to characterize the binding profile of new lectins. Differences in glycan recognition by lectins and anti-carbohydrate antibodies are given on a molecular basis, and strong and weak points of both biorecognition molecules in diagnosis are briefly discussed.     

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance

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An extraordinary degree of structural specificity is required in neural phospholipids for optimal brain function: n-6 docosapentaenoic acid substitution for docosahexaenoic acid leads to a loss in spatial task performance

This study was conducted to determine whether provision of preformed dietary docosapentaenoic acid (DPAn-6) can replace docosahexaenoic acid (DHA) for brain function as assessed by spatial task performance. A newly modified artificial rearing method was employed to generate n-3 fatty acid-deficient rats. Newborn pups were separated from their mothers at 2 days of age and given artificial rat milk containing linoleic acid (LA), or LA supplemented with 1% DHA (DHA), 1% DPAn-6 (DPA) or 1% DHA plus 0.4% DPAn-6 (DHA/DPA). The animals were then weaned onto similar pelleted diets. At adulthood, behavioural tasks were administered and then the brains were collected for fatty acid analysis. The LA and DPA groups showed a lower (63-65%) brain DHA than the dam-reared, DHA and DHA/DPA groups and this loss was largely compensated for by an increase in brain DPAn-6. The brain fatty acid composition in the DPA group was the same as that in the LA group at adulthood. In the Morris water maze, the LA and DPA groups exhibited a longer escape latency than the dam-reared and DHA groups and had a defect in spatial retention. In conclusion, DPAn-6 could not replace DHA for brain function, indicating a highly specific structural requirement for DHA.     

Artificial leaf aids analysis of chlorophyll fluorescence and P700 absorbance in studies involving microalgae

Measuring chlorophyll fluorescence and P700 absorbance has been widely used to study photosynthesis in both terrestrial plants and algae. However, in order to apply these measurement techniques to study microalgae, a concentrated suspension of algae, which is usually prepared by centrifugation, is required. In this study, instead of using centrifugation, we concentrated microalgae on a nitrocellulose membrane using filtration to create an ‘artificial leaf’ before analysis. Overall, we were able to generate values of the appropriate photosynthetic parameters that were comparable to those obtained when chlorophyll fluorescence and P700 absorbance were measured following centrifugation. There were no statistically significant differences (P > 0.05) between the artificial leaf method and the traditional cuvette method for determining chlorophyll fluorescence or P700 absorbance at appropriate chlorophyll concentrations. We were also able to reduce background noise by using a filter membrane as a carrier. Therefore, an artificial leaf has the potential to be a valuable tool for phycologists interested in studying microalgal photosynthesis by enabling them to eliminate tedious centrifugation steps. In addition, fluorometers commonly used for studying the leaves of higher plants will also be suitable for studying microalgae.     

Phenotype and Micro-array characterization of duplication 11q22.1-q25 and review of the literature

Partial duplication of 11q is related to several malformations like growth retardation, intellectual disability, hypoplasia of corpus callosum, short nose, palate defects, cardiac, urinary tract abnormalities and neural tube defects. We have studied the clinical and molecular characteristics of a patient with severe intellectual disabilities, dysmorphic features, congenital inguinal hernia and congenital cerebral malformation which is referred to as cytogenetic exploration. We have used FISH and array CGH analysis for a better understanding of the double chromosomic aberration involving a 7p microdeletion along with a partial duplication of 11q due to adjacent segregation of a paternal reciprocal translocation t(7;11)(p22;q21) revealed after banding analysis. The patient's karyotype formula was: 46,XY,der(7)t(7;11)(p22;q21)pat. FISH study confirmed these rearrangement and array CGH technique showed precisely the loss of at least 140 Kb on chromosome7p22.3pter and 33.4 Mb on chromosome11q22.1q25. Dysmorphic features, severe intellectual disability and brain malformations could result from the 11q22.1q25 trisomy. Our study provides an additional case for better understanding and delineating the partial duplication 11q.     

固化河岸对长江江豚栖息活动的影响

长江江豚主要栖居在近岸浅水水域,喜好泥沙质类型的河岸。但在长江干流,有很多自然河岸被固化,河岸固化给长江江豚分布和栖息活动造的影响仍不甚清楚。2016年3月—2017年1月,对长江干流2个自然河段江豚的数量和分布做了12次考察,并收集了这2个河段岸型的相关数据,来分析固化河岸对江豚栖息活动的影响。12次考察累计发现江豚215头次,平均每次考察观察到江豚(17.92±7.09)头次。研究区域的固化河岸约占岸线总长的59%,分析发现,仅约13.9%的江豚分布在固化河岸水域,86.1%的江豚均分布在自然河岸水域。江豚在单位河岸长度的分布数量与该段固化河岸长度所占的比例呈显著负相关(r=-0.639,P0.01)。在自然河岸,分布在近岸50 m水域的江豚占31.8%,而在固化河岸,仅观察到2头江豚活动在近岸50 m水域内。由此可见,固化河岸对江豚的近岸分布有明显影响。调查还发现,安庆城区建设带约10 km江段12次考察均未发现江豚分布,城区建设带可能对江豚栖息已造成严重影响。长江干流的固化河岸所占比例非常高,研究结果提示这可能导致长江干流江豚栖息地的丧失和破碎化加剧,在制定长江江豚保护措施必需慎重考虑此因素的影响,并据此提出相应的栖息地保护和恢复方案。     

Odorant binding initially occurring at the central pocket in bovine odorant-binding protein

Why bovine odorant-binding protein (OBPb), among OBP family, assumes a dimeric structure has been unclear. Here we clarified, by measuring the fluorescence of intrinsic tryptophan and tyrosine residues of intact OBPb and OBPb whose C-terminal 10 amino acids were deleted, that odorant enters the central pocket formed by the dimerization when OBPb first encounters odorant, and odorant with high affinity with OBPb subsequently enters the internal cavity (suggested binding site), releasing the pre-bound odorant. The internal cavity-bound odorant can be released by the binding of other odorants at another internal cavity or at the central pocket, depending on the binding odorants. Due to this mechanism enabled by the dimerization, OBPb is more reactive than other monomeric OBPs.