Singlet Oxygen, Photodynamic Therapy, and Mechanisms of Cancer Cell Death.

Photodynamic therapy (PDT) can be developed into an important arsenal against cancer; it is a minimally invasive therapy, which is used in the treatment or/and palliation of a variety of cancers and benign diseases. The removal of cancerous tissue is achieved with the use of photosensitizer and a light source, which excites the photosensitizer. This excitation causes the photosensitizer to generate singlet oxygen and other reactive oxygen species. PDT has been used in several types of cancers including nonmelanoma skin cancer, bladder cancer, esophageal cancer, head and neck cancer, and non-small cell lung cancer (NSCLC). Although it is routinely used in nonmelanoma skin cancer, it has not been widely adopted in other solid cancers due to a lack of clinical data showing the superiority of PDT over other forms of treatment. Singlet oxygen used in PDT can alter the activity of the catalase, which induces immunomodulation through HOCl signaling. The singlet oxygen can induce apoptosis through both the extrinsic and intrinsic pathways. The extrinsic pathway of apoptosis starts with the activation of the Fas receptor by singlet oxygen that leads to activation of the caspase-7 and caspase-3. In the case of the intrinsic pathway, disruption caused by singlet oxygen in the mitochondria membrane leads to the release of cytochrome c, which binds with APAF-1 and procaspase-9, forming a complex, which activates caspase-3. Mechanisms of PDT action can vary according to organelles affected. In the plasma membrane, membrane disruption is caused by the oxidative stress leading to the intake of calcium ions, which causes swelling and rupture of cells due to excess intake of water, whereas disruption of lysosome causes the release of the cathepsins B and D, which cleave Bid into tBid, which changes the mitochondrial outer membrane permeability (MOMP). Oxidative stress causes misfolding of protein in the endoplasmic reticulum. When misfolding exceeds the threshold, it triggers unfolding protein response (UPR), which leads to activation of caspase-9 and caspase-3. Finally, the activation of p38 MAPK works as an alternative pathway for the induction of MOMP.

Evolution and origin of sliding clamp in bacteria, archaea and eukarya.

The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.

Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins.

SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host's translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.

Selection of the Optimal L-asparaginase II Against Acute Lymphoblastic Leukemia: An In Silico Approach.

BACKGROUND: L-asparaginase II (asnB), a periplasmic protein commercially extracted from E coli and Erwinia, is often used to treat acute lymphoblastic leukemia. L-asparaginase is an enzyme that converts L-asparagine to aspartic acid and ammonia. Cancer cells are dependent on asparagine from other sources for growth, and when these cells are deprived of asparagine by the action of the enzyme, the cancer cells selectively die. OBJECTIVE: Questions remain as to whether asnB from E coli and Erwinia is the best asparaginase as they have many side effects. asnBs with the lowest Michaelis constant (Km; most potent) and lowest immunogenicity are considered the most optimal enzymes. In this paper, we have attempted the development of a method to screen for optimal enzymes that are better than commercially available enzymes. METHODS: In this paper, the asnB sequence of E coli was used to search for homologous proteins in different bacterial and archaeal phyla, and a maximum likelihood phylogenetic tree was constructed. The sequences that are most distant from E coli and Erwinia were considered the best candidates in terms of immunogenicity and were chosen for further processing. The structures of these proteins were built by homology modeling, and asparagine was docked with these proteins to calculate the binding energy. RESULTS: asnBs from Streptomyces griseus, Streptomyces venezuelae, and Streptomyces collinus were found to have the highest binding energy (-5.3 kcal/mol, -5.2 kcal/mol, and -5.3 kcal/mol, respectively; higher than the E coli and Erwinia asnBs) and were predicted to have the lowest Kms, as we found that there is an inverse relationship between binding energy and Km. Besides predicting the most optimal asparaginase, this technique can also be used to predict the most optimal enzymes where the substrate is known and the structure of one of the homologs is solved. CONCLUSIONS: We have devised an in silico method to predict the enzyme kinetics from a sequence of an enzyme along with being able to screen for optimal alternative asnBs against acute lymphoblastic leukemia.

Vitamin D, Calcium, Parathyroid Hormone, and Sex Steroids in Bone Health and Effects of Aging.

Bone health of the elderly is a major global health concern, since about 1 in 3 women and 1 in 5 men suffer from bone loss and fractures, often called osteoporosis, in old age. Bone health is a complex issue affected by multiple hormones and minerals. Among all the hormones involved in bone health, calcitriol (also vitamin D), parathyroid, and sex hormones (especially estrogen) have been discussed in this review paper. We have discussed the metabolism of these hormones and their effects on bone health. Vitamin D can be obtained from diet or formed from 7-dehydrocholesterol found under the skin in the presence of sunlight. The active form, calcitriol, causes dimerization of vitamin D receptor and acts on the bones, intestine, and kidney to regulate the level of calcium in blood. Similarly, parathyroid hormone is secreted when the serum level of calcium is low. It helps regulate the level of blood calcium through calcitriol. Sex hormones regulate bone modeling at an early age and remodeling later in life. Loss of ovarian function and a decrement in the level of production of estrogen are marked by bone loss in elderly women. In the elderly, various changes in the calcium and vitamin D metabolism, such as decrease in the production of vitamin D, decrease in dietary vitamin D, decreased renal production, increased production of excretory products, decrease in the level of VDR, and decreased calcium absorption by the intestines, can lead to bone loss. When the elderly are diagnosed with osteoporosis, medications that directly target bone such as bisphosphonates, RANK ligand inhibitors, estrogen and estrogen analogues, estrogen receptor modulators, and parathyroid hormone receptor agonists are used. Additionally, calcium and vitamin D supplements are prescribed.

ATP Synthase: Structure, Function and Inhibition.

Oxidative phosphorylation is carried out by five complexes, which are the sites for electron transport and ATP synthesis. Among those, Complex V (also known as the F1F0 ATP Synthase or ATPase) is responsible for the generation of ATP through phosphorylation of ADP by using electrochemical energy generated by proton gradient across the inner membrane of mitochondria. A multi subunit structure that works like a pump functions along the proton gradient across the membranes which not only results in ATP synthesis and breakdown, but also facilitates electron transport. Since ATP is the major energy currency in all living cells, its synthesis and function have widely been studied over the last few decades uncovering several aspects of ATP synthase. This review intends to summarize the structure, function and inhibition of the ATP synthase.