Self‐Assembled BiFeO3‐ε‐Fe2O3 Vertical Heteroepitaxy for Visible Light Photoelectrochemistry

Self‐assembled vertical heterostructure with a high interface‐to‐volume ratio offers tremendous opportunities to realize intriguing properties and advanced modulation of functionalities. Here, a heterostructure composed of two visible‐light photocatalysts, BiFeO₃ (BFO) and ε‐Fe₂O₃ (ε‐FO), is designed to investigate its photoelectrochemical performance. The structural characterization of the BFO‐FO heterostructures confirms the phase separation with BFO nanopillars embedded in the ε‐FO matrix. The investigation of band structure of the heterojunction suggests the assistance of photoexcited carrier separation, leading to an enhanced photoelectrochemical performance. The insights into the charge separation are further revealed by means of ultrafast dynamics and electrochemical impedance spectroscopies. This work shows a delicate design of the self‐assembled vertical heteroepitaxy by taking advantage of the intimate contact between two phases that can lead to a tunable charge interaction, providing a new configuration for the optimization of photoelectrochemical cell.     

Feature selection and classification of protein–protein complexes based on their binding affinities using machine learning approaches

Protein–protein interactions are intrinsic to virtually every cellular process. Predicting the binding affinity of protein–protein complexes is one of the challenging problems in computational and molecular biology. In this work, we related sequence features of protein–protein complexes with their binding affinities using machine learning approaches. We set up a database of 185 protein–protein complexes for which the interacting pairs are heterodimers and their experimental binding affinities are available. On the other hand, we have developed a set of 610 features from the sequences of protein complexes and utilized Ranker search method, which is the combination of Attribute evaluator and Ranker method for selecting specific features. We have analyzed several machine learning algorithms to discriminate protein‐protein complexes into high and low affinity groups based on their K_d values. Our results showed a 10‐fold cross‐validation accuracy of 76.1% with the combination of nine features using support vector machines. Further, we observed accuracy of 83.3% on an independent test set of 30 complexes. We suggest that our method would serve as an effective tool for identifying the interacting partners in protein–protein interaction networks and human–pathogen interactions based on the strength of interactions. Proteins 2014; 82:2088–2096. © 2014 Wiley Periodicals, Inc.     

Novel Pyridinium compound from marine actinomycete, Amycolatopsis alba var. nov. DVR D4 showing antimicrobial and cytotoxic activities in vitro

Marine sediment samples from Visakhapatnam coast of Bay of Bengal, India, were investigated as a source of actinomycetes to screen for the production of antibiotics and cytotoxic compounds. Actinomycete strain DVR D4 with interesting bioactivity profile was isolated during our systematic study of marine actinomycetes. Based on biochemical properties and 16S rDNA analysis the isolate DVR D4 was identified as a strain of Amycolatopsis alba. A solvent extraction followed by a chromatographic purification helped to isolate a cytotoxic compound, which was identified as 1(10-aminodecyl) Pyridinium salt antibiotic, on the basis of spectral data. The compound showed potent cytotoxic activity against cancer cell lines of cervix (HeLa), breast (MCF-7) and brain (U87MG) in vitro and also exhibited antibacterial activities against Gram-positive and Gram-negative bacteria.     

Handcuffing intrinsically disordered regions in Mlh1–Pms1 disrupts mismatch repair

The DNA mismatch repair (MMR) factor Mlh1–Pms1 contains long intrinsically disordered regions (IDRs) whose exact functions remain elusive. We performed cross-linking mass spectrometry to identify interactions within Mlh1–Pms1 and used this information to insert FRB and FKBP dimerization domains into their IDRs. Baker''s yeast strains bearing these constructs were grown with rapamycin to induce dimerization. A strain containing FRB and FKBP domains in the Mlh1 IDR displayed a complete defect in MMR when grown with rapamycin. but removing rapamycin restored MMR functions. Strains in which FRB was inserted into the IDR of one MLH subunit and FKBP into the other subunit were also MMR defective. The MLH complex containing FRB and FKBP domains in the Mlh1 IDR displayed a rapamycin-dependent defect in Mlh1–Pms1 endonuclease activity. In contrast, linking the Mlh1 and Pms1 IDRs through FRB-FKBP dimerization inappropriately activated Mlh1–Pms1 endonuclease activity. We conclude that dynamic and coordinated rearrangements of the MLH IDRs both positively and negatively regulate how the MLH complex acts in MMR. The application of the FRB-FKBP dimerization system to interrogate in vivo functions of a critical repair complex will be useful for probing IDRs in diverse enzymes and to probe transient loss of MMR on demand.     

Haplotype Analyses of DNA Repair Gene Polymorphisms and Their Role in Ulcerative Colitis

Ulcerative colitis (UC) is a major clinical form of inflammatory bowel disease. UC is characterized by mucosal inflammation limited to the colon, always involving the rectum and a variable extent of the more proximal colon in a continuous manner. Genetic variations in DNA repair genes may influence the extent of repair functions, DNA damage, and thus the manifestations of UC. This study thus evaluated the role of polymorphisms of the genes involved in DNA repair mechanisms. A total of 171 patients and 213 controls were included. Genotyping was carried out by ARMS PCR and PCR-RFLP analyses for RAD51, XRCC3 and hMSH2 gene polymorphisms. Allelic and genotypic frequencies were computed in both control & patient groups and data was analyzed using appropriate statistical tests. The frequency of ‘A’ allele of hMSH2 in the UC group caused statistically significant increased risk for UC compared to controls (OR 1.64, 95% CI 1.16–2.31, p = 0.004). Similarly, the CT genotype of XRCC3 gene was predominant in the UC group and increased the risk for UC by 1.75 fold compared to controls (OR 1.75, 95% CI 1.15–2.67, p = 0.03), further confirming the risk of ‘T’ allele in UC. The GC genotype frequency of RAD51 gene was significantly increased (p = 0.02) in the UC group (50.3%) compared to controls (38%). The GC genotype significantly increased the risk for UC compared to GG genotype by 1.73 fold (OR 1.73, 95% CI 1.14–2.62, p = 0.02) confirming the strong association of ‘C’ allele with UC. Among the controls, the SNP loci combination of hMSH2:XRCC3 were in perfect linkage. The GTC and ACC haplotypes were found to be predominant in UC than controls with a 2.28 and 2.93 fold significant increase risk of UC.     

Influence of low phosphorus concentration on leaf photosynthetic characteristics and antioxidant response of rice genotypes

Influence of different phosphorus concentrations was studied in four rice varieties (Akhanphou, MTU1010, RP BIO 226, and Swarna) differing in their tolerance to low phosphorus. There was an increase in shoot and root dry mass with the increase in phosphorus concentration. At the low phosphorus concentration at both tillering and reproductive stages, Swarna, followed by Akhanphou, recorded maximum biomass for both roots and shoots, while the minimum was observed in RP BIO 226. Reduction in photosynthetic rate, stomatal conductance, transpiration rate, and internal CO₂ concentration at low phosphorus concentrations were observed at both tillering and reproductive stages in all the genotypes. In low phosphorus, maximum photosynthetic rate was found in Swarna followed by Akhanphou. Phosphorus deficiency did not alter the maximum efficiency of PSII photochemistry, however, there was a reduction in effective PSII quantum yield, electron transport rate, and coefficient of photochemical quenching, while the coefficient of nonphotochemical quenching was higher in the low phosphorus-treated plants. Prolonged exposure to excessive energy and failure to utilize the energy in carbon-reduction cycle induced the generation of reactive oxygen species, which affected PSII as indicated by the fluorescence traits. The reduction was less severe in case of Swarna and Akhanphou. The activities of superoxide dismutase, peroxidase, and catalase increased in roots under low phosphorus concentration indicating that photoprotective mechanisms have been initiated in rice plants in response to phosphorus deficiency. Comparatively, Swarna and Akhanphou exhibited a higher biomass, higher photosynthetic rate, and better reactive oxygen species-scavenging ability which conferred tolerance under low phosphorus conditions.     

Structural basis of TRAPPIII‐mediated Rab1 activation

The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo‐EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α‐helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.     

In‐depth and 3‐dimensional exploration of the budding yeast phosphoproteome

Phosphorylation is one of the most dynamic and widespread post‐translational modifications regulating virtually every aspect of eukaryotic cell biology. Here, we assemble a dataset from 75 independent phosphoproteomic experiments performed in our laboratory using Saccharomyces cerevisiae. We report 30,902 phosphosites identified from cells cultured in a range of DNA damage conditions and/or arrested in distinct cell cycle stages. To generate a comprehensive resource for the budding yeast community, we aggregate our dataset with the Saccharomyces Genome Database and another recently published study, resulting in over 46,000 budding yeast phosphosites. With the goal of enhancing the identification of functional phosphorylation events, we perform computational positioning of phosphorylation sites on available 3D protein structures and systematically identify events predicted to regulate protein complex architecture. Results reveal hundreds of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic “clashes” predicted to disrupt the interaction. With the advancement of Cryo‐EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.