Molecular Dynamics of Thermoenzymes at High Temperature and Pressure: A Review

Lipases are known for their versatility in addition to their ability to digest fat. They can be used for the formulation of detergents, as food ingredients and as biocatalysts in many industrial processes. Because conventional enzymes are frangible at high temperatures, the replacement of conventional chemical routes with biochemical processes that utilize thermostable lipases is vital in the industrial setting. Recent theoretical studies on enzymes have provided numerous fundamental insights into the structures, folding mechanisms and stabilities of these proteins. The studies corroborate the experimental results and provide additional information regarding the structures that were determined experimentally. In this paper, we review the computational studies that have described how temperature affects the structure and dynamics of thermoenzymes, including the thermoalkalophilic L1 lipase derived from Bacillus stearothermophilus. We will also discuss the potential of using pressure for the analysis of the stability of thermoenzymes because high pressure is also important for the processing and preservation of foods.     

Unravelling the stock structure of the Persian brown trout by otolith and scale shape

The simultaneous use of the scale and otolith morphometry was assessed as a potential tool for the identification of Persian brown trout Salmo trutta stocks of the Lar Lake and five rivers from Lar Basin, Iran. Fourier coefficients (FC) and circularity, rectangularity, roundness, ellipticity and form factor shape indices (SI) were calculated for otolith and scale. Several SIs were significantly different among sites for both structures. Permutational multivariate analysis of variance revealed significant differences between several pairwise comparisons for otolith and scale (FCs and indices separately). Discriminant analysis showed otolith FCs (cross-classification rates: 25–86%) and SI (20–45%) appear to be a relatively acceptable tool to discriminate between several locations. Comparatively, the scale morphometry showed lower discriminatory power (FC = 3–65%; SI = 15–34%), with the exception of SI for Elarm River (60%), Kamardasht River (56%) and Lar Lake (75%). Cross-classification rates improved up to 100% when discriminate analysis incorporating all variables for otolith and scale was performed. The results showed a potential segregation between some water bodies, suggesting that the otolith and scale morphometry could be a useful tool to delimit S. trutta populations in relatively close freshwater environments.     

Dual-wavelength plasmonic perfect absorber suitable for refractive index sensing

In this paper, a plasmonic perfect absorber (PPA) based on metal-insulator-metal-insulator-metal (MIMIM) structure has been designed for refractive index sensing of glucose solutions (analyte) and then a new method has been proposed for fast, low-cost, and easy measurement of sensor’s sensitivity. Simulation results show that the absorption spectrum of the proposed sensor has two resonance peaks that with an increase in analyte refractive index, both of them are red-shifted. In our proposed measurement technique, two conventional single-wavelength lasers (with wavelengths of 1050 nm and 1750 nm) are used for vertical plane wave light illumination on the structure. Then, the absorbed powers at 1750 nm (A₂) and 1050 nm (A₁) wavelengths are calculated and variation of the absorption ratio (A₂/A₁) due to change of analyte refractive index would be introduced as the sensitivity of sensor (S = Δ(A₂/A₁)/Δn). Obtained results show that the increase of analyte refractive index from n = 1.312 to n = 1.384 will result in an increase of sensor’s sensitivity from 9.3/RIU to 33.475/RIU.

     

Principal Component Analysis of Time-Related Changes of Some Essential Mineral Contents of Canned Silver Carp (Hypophthalmichthys molitrix) in Different Filling Media

Biological Trace Element Research - The kinetic reaction for changes in some essential mineral contents (iron, zinc, calcium, sodium, and copper) of silver carp canned in sunflower oil, soybean...     

Structural perspectives on HIV‐1 Vif and APOBEC3 restriction factor interactions

Human immunodeficiency virus (HIV) is a retroviral pathogen that targets human immune cells such as CD4⁺ T cells, macrophages, and dendritic cells. The human apo lipoprotein B mRNA‐ e diting c atalytic polypeptide 3 (APOBEC3 or A3) cytidine deaminases are a key class of intrinsic restriction factors that inhibit replication of HIV. When HIV‐1 enters the cell, the immune system responds by inducing the activation of the A3 family proteins, which convert cytosines to uracils in single‐stranded DNA replication intermediates, neutralizing the virus. HIV counteracts this intrinsic immune response by encoding a protein termed viral infectivity factor (Vif). Vif targets A3 to an E3 ubiquitin ligase complex for poly‐ubiquitination and proteasomal degradation. Vif is unique in that it can recognize and counteract multiple A3 restriction factor substrates. Structural biology studies have provided significant insights into the overall architectures and functions of Vif and A3 proteins; however, a structure of the Vif‐A3 complex has remained elusive. In this review, we summarize and reanalyze experimental data from recent structural, biochemical, and functional studies to provide key perspectives on the residues involved in Vif‐A3 protein–protein interactions.     

Synthesis, characterization and cytotoxicity of a series of tetrachloridoplatinum(IV) complexes

Two platinum(IV) complexes, [Pt(4bt)Cl₄] (4) and [Pt(dpyam)Cl₄]·DMF (5) (where 4bt is 4,4′-bithiazole and dpyam is 2,2′-dipyridylamine) were prepared from the reaction of H₂PtCl₆·6H₂O with 4,4′-bithiazole and 2,2′-dipyridylamine, respectively, in methanol. Both complexes were fully characterized and their structures were determined by the X-ray diffraction method. These complexes have a bidentate nitrogenous ligand with four chloride anions attached to a Pt(IV) metal in a distorted octahedral environment. These complexes along with three previously reported analogous complexes were used for in vitro cytotoxicity evaluation against four cultures, NIH-3T3, Caco-2, HT-29 and T47D by MTT assay. The methyl group position in the ligand plays an important role in the cytotoxicity of relevant compounds in different cultures. Interestingly, in some cases, the IC₅₀ values of the new complexes were higher for normal cells but lower against cancer cells in comparison with cisplatin, especially in T47D (breast ductal carcinoma).     

Germline Heterozygous Variants in SEC23B Are Associated with Cowden Syndrome and Enriched in Apparently Sporadic Thyroid Cancer

Cancer-predisposing genes associated with inherited cancer syndromes help explain mechanisms of sporadic carcinogenesis and often inform normal development. Cowden syndrome (CS) is an autosomal-dominant disorder characterized by high lifetime risks of epithelial cancers, such that ∼50% of affected individuals are wild-type for known cancer-predisposing genes. Using whole-exome and Sanger sequencing of a multi-generation CS family affected by thyroid and other cancers, we identified a pathogenic missense heterozygous SEC23B variant (c.1781T>G [p.Val594Gly]) that segregates with the phenotype. We also found germline heterozygous SEC23B variants in 3/96 (3%) unrelated mutation-negative CS probands with thyroid cancer and in The Cancer Genome Atlas (TCGA), representing apparently sporadic cancers. We note that the TCGA thyroid cancer dataset is enriched with unique germline deleterious SEC23B variants associated with a significantly younger age of onset. SEC23B encodes Sec23 homolog B (S. cerevisiae), a component of coat protein complex II (COPII), which transports proteins from the endoplasmic reticulum (ER) to the Golgi apparatus. Interestingly, germline homozygous or compound-heterozygous SEC23B mutations cause an unrelated disorder, congenital dyserythropoietic anemia type II, and SEC23B-deficient mice suffer from secretory organ degeneration due to ER-stress-associated apoptosis. By characterizing the p.Val594Gly variant in a normal thyroid cell line, we show that it is a functional alteration that results in ER-stress-mediated cell-colony formation and survival, growth, and invasion, which reflect aspects of a cancer phenotype. Our findings suggest a different role for SEC23B, whereby germline heterozygous variants associate with cancer predisposition potentially mediated by ER stress “addiction.”