Predicting proteinase specificities from free energy calculations

Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference

To date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.

Systemic Uptake of Oxytetracycline and Streptomycin in Huanglongbing-Affected Citrus Groves after Foliar Application and Trunk Injection

Huanglongbing (HLB), which is caused by the phloem-limited bacterium ‘Candidatus Liberibacter asiaticus,’ is an economically important disease of citrus in many regions of the world. Due to the significant damage caused by the HLB disease in recent years, the use of antibiotics was recommended for the therapy of this destructive disease. Products with active ingredients oxytetracycline and streptomycin have been approved for the control of the HLB via foliar application. However, previous work raised questions about the efficacy of foliar delivery of antibiotics in the field. In this study, we examined the effects of a variety of adjuvants on the uptake of oxytetracycline and streptomycin using the foliar application. We also compared the efficiency of foliar application of oxytetracycline and streptomycin with trunk injection. The ‘Ca. L. asiaticus’ titers in citrus plants were measured using quantitative PCR, and the levels of antibiotics were determined using the ELISA assay. Our results include extremely low levels of oxytetracycline and streptomycin in leaves that were covered during foliar application, indicating that neither streptomycin nor oxytetracycline was successfully systemically delivered by foliar application even after being mixed with adjuvants. Likewise, the ‘Ca. L. asiaticus’ titer0 was not affected by any of the foliar applications. High levels of streptomycin were detected in leaves that were exposed to direct foliar application, indicating that streptomycin was adsorbed or bound to citrus leaves. On the other hand, the trunk injection of oxytetracycline resulted in high levels of this antibiotic in leaves and significantly reduced the level of ‘Ca. L. asiaticus’ titer in citrus trees. Unfortunately, the trunk injection of streptomycin resulted in low levels of streptomycin in citrus leaves and did not affect the ‘Ca. L. asiaticus’ titer, indicating that streptomycin was either bound in the xylem of citrus trees or it was not applied in sufficient quantity required for the inhibition of ‘Ca. L. asiaticus.’ Taken together, our current results demonstrated that foliar application of oxytetracycline and streptomycin did not effectively deliver antibiotics in citrus despite using adjuvants. Our results also suggested that oxytetracycline could be more effective against the HLB pathogen than streptomycin, which is possibly due to differences between the two in systemic movement in citrus trees.

It's all about time: precision and accuracy of Emotiv event-marking for ERP research

Background

The use of consumer-grade electroencephalography (EEG) systems for research purposes has become more prevalent. In event-related potential (ERP) research, it is critical that these systems have precise and accurate timing. The aim of the current study was to investigate the timing reliability of event-marking solutions used with Emotiv commercial EEG systems.

Method

We conducted three experiments. In Experiment 1 we established a jitter threshold (i.e. the point at which jitter made an event-marking method unreliable). To do this, we introduced statistical noise to the temporal position of event-marks of a pre-existing ERP dataset (recorded with a research-grade system, Neuroscan SynAmps² at 1,000 Hz using parallel-port event-marking) and calculated the level at which the waveform peaks differed statistically from the original waveform. In Experiment 2 we established a method to identify ‘true’ events (i.e. when an event should appear in the EEG data). We did this by inserting 1,000 events into Neuroscan data using a custom-built event-marking system, the ‘Airmarker’, which marks events by triggering voltage spikes in two EEG channels. We used the lag between Airmarker events and events generated by Neuroscan as a reference for comparisons in Experiment 3. In Experiment 3 we measured the precision and accuracy of three types of Emotiv event-marking by generating 1,000 events, 1 s apart. We measured precision as the variability (standard deviation in ms) of Emotiv events and accuracy as the mean difference between Emotiv events and true events. The three triggering methods we tested were: (1) Parallel-port-generated TTL triggers; (2) Arduino-generated TTL triggers; and (3) Serial-port triggers. In Methods 1 and 2 we used an auxiliary device, Emotiv Extender, to incorporate triggers into the EEG data. We tested these event-marking methods across three configurations of Emotiv EEG systems: (1) Emotiv EPOC+ sampling at 128 Hz; (2) Emotiv EPOC+ sampling at 256 Hz; and (3) Emotiv EPOC Flex sampling at 128 Hz.

Results

In Experiment 1 we found that the smaller P1 and N1 peaks were attenuated at lower levels of jitter relative to the larger P2 peak (21 ms, 16 ms, and 45 ms for P1, N1, and P2, respectively). In Experiment 2, we found an average lag of 30.96 ms for Airmarker events relative to Neuroscan events. In Experiment 3, we found some lag in all configurations. However, all configurations exhibited precision of less than a single sample, with serial-port-marking the most precise when paired with EPOC+ sampling at 256 Hz.

Conclusion

All Emotiv event-marking methods and configurations that we tested were precise enough for ERP research as the precision of each method would provide ERP waveforms statistically equivalent to a research-standard system. Though all systems exhibited some level of inaccuracy, researchers could easily account for these during data processing.

Smart Farming Introduction in Wine Farms: A Systematic Review and a New Proposal

This study shows a new methodological proposal for wine farm management, as a result of the progressive development of the technological innovations and their adoption. The study was carried out in Italy involving farmers, workers, or owners of wine farms who are progressively introducing or using precision agriculture technologies on their farm. The methodology proposed was divided in four stages (1. understanding the changes in action; 2. identifying the added value of Smart Farming processes; 3. verifying the reliability of new technologies; 4. adjusting production processes) that can be applied at different levels in vine farms to make the adoption of precision agriculture techniques and technologies harmonious and profitable. Data collection was carried out using a participant-observer method in brainstorming sessions, where the authors reflected on the significance of technology adoption means and how to put them in practice, and interviews, questionnaire surveys, diaries, and observations. Moreover, project activities and reports provided auxiliary data. The findings highlighted the issues of a sector which, although with broad investment and finance options, lacks a structure of human, territorial, and organizational resources for the successful adoption of technological innovations. The work represents a basis for the future development of models for strategic scenario planning and risk assessments for farmers, policymakers, and scientists.

Advanced Rhodococcus Biocatalysts for Environmental Biotechnologies

The review is devoted to biocatalysts based on actinobacteria of the genus Rhodococcus, which are promising for environmental biotechnologies. In the review, biotechnological advantages of Rhodococcus bacteria are evaluated, approaches used to develop robust and efficient biocatalysts are discussed, and their relevant applications are given. We focus on Rhodococcus cell immobilization in detail (methods of immobilization, criteria for strains and carriers, and optimization of process parameters) as the most efficient approach for stabilizing biocatalysts. It is shown that advanced Rhodococcus biocatalysts with improved working characteristics, enhanced stress tolerance, high catalytic activities, human and environment friendly, and commercially viable are developed, which are suitable for wastewater treatment, bioremediation, and biofuel production.

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods

Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations.

Recombinant expression of Laceyella sacchari thermitase in Lactococcus lactis

Thermitase (EC 3.4.21.66) is a thermostable endo-protease with the ability to convert various food relevant substrates into low-molecular weight peptides. A thermitase produced by Laceyella sacchari strain DSM43353 was found to have a mature amino acid sequence nearly identical to that of the original thermitase isolated from Thermoactinomyces vulgaris. The DSM43353 thermitase gene sequence contains a pro-peptide including parts of an I9 inhibitor motif. Expression of the thermitase gene in the Lactococcus lactis P170 expression system allowed secretion of stable thermitase in an auto-induced fermentation setup at 30°C. Thermitase accumulated in the culture supernatant during batch fermentations and was easily activated at 50°C or by prolonged dialysis. The activation step resulted in an almost complete degradation of endogenous L. lactis host proteins present in the supernatant. Mature activated product was stable at 50°C and functional at pH values between pH 6 and pH 11, suggesting that substrate hydrolysis can be performed over a broad range of pH values. The L. lactis based P170 expression system is a simple and safe system for obtaining food compatible thermitase in the range of 100 mg/L.

Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues

An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery.