A novel atomistic motional correlation method combined with thermodynamics to delineate the intricate mechanism of substrate specific catalysis: Enzyme engineering perspective

Enzymes are powerful and highly specific catalysts, both in the reactions that they catalyze and in their choice of reactants. (1) Enzymes show this partiality towards substrate through a precise mechanism. The precision of this mechanism is governed by a well connected network of residues in and around the catalytic site, in terms of their motions and consequential thermodynamics. In this study we have designed a novel atomistic motional (AM) correlation method which measures the distance and direction of the atoms in motion. Discretizing the variable, 41 different combinations (AM alphabets) of displacement and direction of the motion of a single atom was calculated over a wide range of molecular motions derived from MD simulations. This is the maximum reported number of measurements which quantifies high-frequency harmonic oscillations to slow functional conformational transitions with a higher level of sensitivity. The method was tested to delineate the mechanism of the Michaelis complexes of Penicillin G acylase (PGA) & Penicillin-G (native reaction) and PGA & PGSO (slow reaction). Correlation of AM alphabets of a pair of atoms (i,j) was calculated as a normalized mutual information (MI; ), (2) and this was summed to derive the per residue correlation (PRC;CnMI) . The CnMI was used to generate network models and clustering analysis, post 0.25 μs of simulations of the Michaelis complexes. Results show clear difference between the AM alphabets of the fast and the slow hydrolyzing enzymatic reactions (Fig1.A). Networks formed between the amino acids in the slow reaction are very much different from native reaction (Fig1.B & C), especially cluster 1 and 2 which shows close relation with the substrate of the native reaction is completely decomposed in the slow reaction. Further, CnMI was combined with a novel method that quantitatively weights atomic interactions (qWAI) in conjuncture with high throughput binding free energy calculation deposited over every amino acid (PRB). The three methods CnMI, qWAI and PRB in isolation and in combination showed the precise mechanism of PGA pertaining to substrate specificity. To mention CnMI shows decomposition of cluster 1 and 2 in slow reaction. qWAI shows that the amide bond of PenG was stabilized by βSer1, βThr68, βGln23 and βAla69 and the same in PGSO is stabilized only by βSer1 and βAla69. Finally, the combined score (Fig.1.D) shows that βGln23 and βPro22, forming a part of oxyanion hole are extremely modulated in the slow reaction, resulting in the destabilization of tetrahedral intermediate. The presentation will show the precise mechanism of substrate selectivity of PGA revealed by these three methods in conjunction with insights for enzyme engineering. Please click Additional Files below to see the full abstract

Network science based quantification of resilience demonstrated on the Indian Railways Network

The structure, interdependence, and fragility of systems ranging from power grids and transportation to ecology, climate, biology and even human communities and the Internet, have been examined through network science. While the response to perturbations has been quantified, recovery strategies for perturbed networks have usually been either discussed conceptually or through anecdotal case studies. Here we develop a network science-based quantitative methods framework for measuring, comparing and interpreting hazard responses and as well as recovery strategies. The framework, motivated by the recently proposed temporal resilience paradigm, is demonstrated with the Indian Railways Network. The methods are demonstrated through the resilience of the network to natural or human-induced hazards and electric grid failure. Simulations inspired by the 2004 Indian Ocean Tsunami and the 2012 North Indian blackout as well as a cyber-physical attack scenario. Multiple metrics are used to generate various recovery strategies, which are simply sequences in which system components should be recovered after a disruption. Quantitative evaluation of recovery strategies suggests that faster and more resource-effective recovery is possible through network centrality measures. Case studies based on two historical events, specifically the 2004 Indian Ocean tsunami and the 2012 North Indian blackout, and a simulated cyber-physical attack scenario, provides means for interpreting the relative performance of various recovery strategies. Quantitative evaluation of recovery strategies suggests that faster and more resource-effective restoration is possible through network centrality measures, even though the specific strategy may be different for sub-networks or for the partial recovery

PTPerf: On the performance evaluation of Tor Pluggable Transports

Tor, one of the most popular censorship circumvention systems, faces regular blocking attempts by censors. Thus, to facilitate access, it relies on "pluggable transports" (PTs) that disguise Tor's traffic and make it hard for the adversary to block Tor. However, these are not yet well studied and compared for the performance they provide to the users. Thus, we conduct a first comparative performance evaluation of a total of 12 PTs -- the ones currently supported by the Tor project and those that can be integrated in the future. Our results reveal multiple facets of the PT ecosystem. (1) PTs' download time significantly varies even under similar network conditions. (2) All PTs are not equally reliable. Thus, clients who regularly suffer censorship may falsely believe that such PTs are blocked. (3) PT performance depends on the underlying communication primitive. (4) PTs performance significantly depends on the website access method (browser or command-line). Surprisingly, for some PTs, website access time was even less than vanilla Tor. Based on our findings from more than 1.25M measurements, we provide recommendations about selecting PTs and believe that our study can facilitate access for users who face censorship.Comment: 25 pages, 12 figure

Investigating the drying characteristics of Anthocephalus chinensis (Lam.) A. Rich ex Walp wood

Anthocephalus chinensis (Lam.) A. Rich ex Walp is widely used as raw materials in particleboard and match industries in Bangladesh. The current study aimed to identify the drying characteristics of A. Chinensis wood for succeeding industrial usages. A compartment kiln dryer (heat and vent dryer) was used in this study. The drying characteristics and drying quality of A. Chinensis wood were measured. The boards reached 6–10% moisture content in 13 days from their green condition. The total proportions of the check, twist, and collapse in boards were 22.5, 32.5, and 7.3%, respectively. The volumetric shrinkage was 21.67%. Based on this study, further study may help to develop a complete drying schedule of A. Chinensis wood with fewer drying defects for application at industrial level

Impact of FDI and energy consumption on the agricultural productivity of BRICS nations

Agricultural development is essential for world trade and the global economy. This research investigates the relationship between Foreign Direct Investment (FDI) and fossil fuel energy consumption with agricultural productivity (AP). The study used the panel data of BRICS nations from 1991-2019. For data analysis, panel regression analysis along with descriptive statistics was used. The study’s findings are that FDI and FFEC significantly influence the AP of BRICS nations. The FFEC has a positive influence on the AP, while FDI has a negative influence on the AP of BRICS nations. Further, the results revealed that trade openness and gross capital formation have a weak but significant influence on agricultural productivity

Pregnancy in uterus didelphys delivered by caesarean section: a case report

The aim of this study is to report a rare case of pregnancy in uterus didelphys. Mullerian duct anomalies are congenital defects of the female genital system that arise from abnormal embryological development of the Mullerian ducts. A didelphys uterus, also known as double uterus is one of the least common amongst the various Mullerian duct anomalies. It results from complete failure of fusion of Mullerian ducts. There is presence of double uterine bodies with two separate cervices and often double or septate vagina. We report the case in our institute of a pregnancy in the left sided body of a didelphys uterus, delivered by caesarean section. Patients with uterus didelphys belong to high risk group and complications are increased in malformed uterus. Such cases need a meticulous prenatal care. It is a rare Mullerian anomaly and can present with varied obstetrical and gynaecological complications. Prompt and accurate diagnosis of uterine malformations and appropriate surgical intervention are essential to prevent complications

Novel quantum mechanics based engineering approach enables transaminase to convert bulky ketone substrates

Amine transaminases (ATAs) are being used in the production of chiral amines as an alternative to chemical synthesis to reduce cost and inadequate stereoselectivity. Yet, ATAs are enzymes, difficult to engineer because of the unique structural architecture of the active site that limits bulkier substrates, example Sitagliptin. However, in recent yearscombination of computational techniques and protein engineering has evolved enzymesto acceptbulkier substrates as shown for (R) 1 and more recently (S)-selective ATAs2. In this study, we have used the(S)-selective ATA from Chromobacterium violaceum to expand its substrate scope towards bulky ketones using a novel quantum mechanics (QM) based engineering framework. The framework predicts hotspots by analyzing the E-S molecular dynamics (MD) and QM simulations using novel methods developed in-house. To mention a few, path predictor, which predicts the path taken by the substrate to enter the active site, a grid based per residue energy profiling and atomistic motional correlations of the active site residues and QM based alanine scanning method. Please click Additional Files below to see the full abstract