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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) pandemic is tragic, yet we can still learn a great deal about the virus and its effects. The biochemistry of the virus is rather interesting despite its ill effects, and it is important to know how it works in order to understand how to defeat it. In the spring 2020 semester, I was teaching a senior level Biochemistry course that would normally cover topics of DNA replication, RNA replication, protein synthesis, gene regulation, and other biomolecular metabolic pathways. Upon the first call for suspending face-to-face classroom study, my course, with the enthusiastic support of the students in the course, changed our focus to understand these topics in relation to viruses. The course structure was modified to include online quizzes, instead of a written exam, and five minute videos made by each student describing the biochemical nature of a virus of their choosing, instead of a traditional presentation. The class met through synchronous Zoom meetings to discuss topics of virus structure, genomes, replication, and potential treatments and prevention methods such as how vaccines are made. This format allowed both myself and the students in the course to learn a great deal about this current threat and treatments in modern medicine. Concepts and ideas learned here will hopefully plant the seed in the students’ minds so they will be strong advocates for science and education.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) pandemic is tragic, yet we can still learn a great deal about the virus and its effects. The biochemistry of the virus is rather interesting despite its ill effects, and it is important to know how it works in order to understand how to defeat it. In the spring 2020 semester, I was teaching a senior level Biochemistry course that would normally cover topics of DNA replication, RNA replication, protein synthesis, gene regulation, and other biomolecular metabolic pathways. Upon the first call for suspending face-to-face classroom study, my course, with the enthusiastic support of the students in the course, changed our focus to understand these topics in relation to viruses. The course structure was modified to include online quizzes, instead of a written exam, and five minute videos made by each student describing the biochemical nature of a virus of their choosing, instead of a traditional presentation. The class met through synchronous Zoom meetings to discuss topics of virus structure, genomes, replication, and potential treatments and prevention methods such as how vaccines are made. This format allowed both myself and the students in the course to learn a great deal about this current threat and treatments in modern medicine. Concepts and ideas learned here will hopefully plant the seed in the students’ minds so they will be strong advocates for science and education.

Many species of purple photosynthetic bacteria repress synthesis of their photosystem in the presence of molecular oxygen. The bacterium Rhodobacter capsulatus mediates this process by repressing expression of bacteriochlorophyll, carotenoid, and light-harvesting genes via the aerobic repressor, CrtJ. In this study, we demonstrate that CrtJ forms an intramolecular disulfide bond in vitro and in vivo when exposed to oxygen. Mutational and sulfhydryl-specific chemical modification studies indicate that formation of a disulfide bond is critical for CrtJ binding to its target promoters. Analysis of the redox states of aerobically and anaerobically grown cells indicates that they have similar redox states of approximately -200 mV, thereby demonstrating that a change in midpoint potential is not responsible for disulfide bond formation. In vivo and in vitro analyses indicate that disulfide bond formation in CrtJ is insensitive to the addition of hydrogen peroxide but is sensitive to molecular oxygen. These results suggest that disulfide bond formation in CrtJ may differ from the mechanism of disulfide bond formation used by OxyR.

All living organisms alter their physiology in response to changes in oxygen tension. The photosynthetic bacterium uses the RegB–RegA signal transduction cascade to control a wide variety of oxygen‐responding processes such as respiration, photosynthesis, carbon fixation and nitrogen fixation. We demonstrate that a highly conserved cysteine has a role in controlling the activity of the sensor kinase, RegB. In vitro studies indicate that exposure of RegB to oxidizing conditions results in the formation of an intermolecular disulfide bond and that disulfide bond formation is metal‐dependent, with the metal fulfilling a structural role. Formation of a disulfide bond in vitro is also shown to convert the kinase from an active dimer into an inactive tetramer state. Mutational analysis indicates that a cysteine residue flanked by cationic amino acids is involved in redox sensing in vitro and in vivo . These residues appear to constitute a novel ‘redox‐box’ that is present in sensor kinases from diverse species of bacteria.

A system has been developed for expressing a His-tagged form of the ferredoxin-dependent nitrite reductase of spinach in Escherichia coli. The catalytic and spectral properties of the His-tagged, recombinant enzyme are similar, but not identical, to those previously observed for nitrite reductase isolated directly from spinach leaf. A detailed comparison of the spectral, catalytic and fluorescence properties of nitrite reductase variants, in which each of the enzyme's eight tryptophan residues has been replaced using site-directed mutagenesis by either aromatic or non-aromatic amino acids, has been used to examine possible roles for tryptophan residues in the reduction of nitrite to ammonia catalyzed by the enzyme.

Thioredoxins, by reducing disulfide bridges are one of the main participants that regulate cellular redox balance. In plants, the thioredoxin system is particularly complex. The most well-known thioredoxins are the chloroplastic ones, that participate in the regulation of enzymatic activities during the transition between light and dark phases. The mitochondrial system composed of NADPH-dependent thioredoxin reductase and type o thioredoxin has only recently been described. The type h thioredoxin group is better known. Yeast complementation experiments demonstrated that Arabidopsis thaliana thioredoxins h have divergent functions, at least in Saccharomyces cerevisiae. They have diverse affinities for different target proteins, most probably because of structural differences. However, plant thioredoxin h functions still have to be defined.

Experimental data exists for only a vanishingly small fraction of sequenced microbial genes. This community page discusses the progress made by the COMBREX project to address this important issue using both computational and experimental resources.

[...]that DNA sequencing has become orders of magnitude faster and less expensive, focus has shifted to sequencing entire genomes. Since biochemistry and genetics have not, by and large, enjoyed the same improvement of scale, public sequence repositories now predominantly contain putative protein sequences for which there is no direct experimental evidence of function. COMBREX (COMputational BRidges to EXperiments, http://combrex.bu.edu) is an NIH-funded enterprise that has brought computational and experimental biologists together, with the goal of greatly improving our overall understanding of microbial protein function [1],[2]. Since its inception, it has made significant progress toward the following goals: identifying the minority of proteins that have already been experimentally characterized, serving as a public repository of novel protein function predictions made by diverse methods, producing a clear chain of evidence from experiment to prediction, identifying (\"recommending\") those functional predictions whose verification will contribute most to our overall understanding of protein function, and actually funding the experiments to test function. [...]the project issues small monetary awards (COMBREX grants) to biologists to fund the experimental testing of such predictions.

Thioredoxins are redox-active proteins that contain two cysteines separated by two amino acids. These cysteines form an intramolecular disulfide bond which when reduced, can activate or inactivate a number of other redox-sensitive proteins. This dissertation focuses on thiol-containing proteins that are involved in redox-sensitive dithiol/disulfide processes. Escherichia coli thioredoxin is a widely studied protein. However, much remains to be learned about the mechanism by which it reduces target proteins. An investigation of redox properties of the wild-type protein and site-specific mutants has been undertaken. Thioredoxin h from the green alga Chlamydomonas reinhardtii is a structurally similar protein to E. coli thioredoxin and its redox properties have also been investigated. The ligation of the heme group in cytochrome c involves a dithiol/disulfide protein cascade. HelX and Ccl2 are involved in this cascade in Rhodobacter capsulatus, ultimately reducing the disulfide on apo-cytochrome c so that it can bind heme. Disulfide/dithiol systems are also involved in the oxygen sensing mechanism of Rb. capsulatus, where the DNA-binding protein CrtJ contains a redox-active disulfide. Other proteins investigated for their disulfide/dithiol activity include an engineered E. coli malate dehydrogenase, in which a redox-active disulfide was introduced, and APS reductase from Arabidopsis thaliana , which contains a redox-active regulatory disulfide.