Structure-function studies of prothrombin Amrita, a dysfunctional prothrombin characterized by point mutation at Arg553 → Gln

Development of a model for granule-bound starch synthase I activity using free-energy calculations

Starch is a branched polymer of glucose with two components, both of which have (1 → 4)-α linear links and (1 → 6)-α branch points: amylopectin, of high molecular weight with many short branches, and amylose, of lower molecular weight and only a few long-chain branches. Granule-bound starch synthase I (GBSSI) is one of the main enzymes controlling amylose synthesis and chain-length distribution. As production of different GBSSI mutants is time-consuming and laborious, molecular dynamics (MD) simulations are used here to predict the binding of different GBSSI mutants to a representative amylose fragment. The simulations were atomistic, with explicit solvent and docking, a method successfully used to understand the binding of wild-type GBSSI to amylose fragments. The binding of GBSSI to G5 (a pentasaccharide amylose fragment) is combined with free-energy calculations employing a thermodynamic integration method to predict the effects of mutations on enzyme activity. Ten GBSSI mutants with different enzyme activities were analyzed to find the structural and energy changes among different single amino-acid mutants and their possible relationship to starch characteristics. Comparing the structural changes and the relative binding free energy of G5 to the wild type GBSSI and GBSSI mutants, it was found that mutants with negative binding energy (lower than -2.0 kcal/mol) are more likely to have higher enzyme activity and amylose content compared to the wild type. This theoretical paper used simulations and robust free energy calculations to interpret in planta data with potential predictions as to what mutants might be generated to give desired properties. This study can be used to help develop grains with improved functional properties.

Oyster (Crassostrea gigas) ferritin can efficiently reduce the damage of Pb2+in vivo by electrostatic attraction

Heavy metal ions pollution can cause damage to human body through food, so the development of a new kind of macromolecular that can remove heavy metal ions damage has a good application prospect. The possibilities of removing heavy metal ions from food system with ferritin were studied in this paper. In this study, oyster ferritin (GF1) can resistant to denaturation induced by Pb²⁺, Cd²⁺, Cr³⁺ and still maintains its basic structure. GF1 can bind more Pb²⁺, Cd²⁺, Cr³⁺ than recombinant human H-chain ferritin (rHuHF), especially Pb²⁺, and the findings suggest that each GF1 can capture about 51.42 Pb²⁺ in solution. The hard and soft acids and base also verifies that Pb²⁺ have stronger binding ability to the key amino acids at the outer end of the three-fold symmetry channel. Cells preprotected by ferritin could resistant to heavy metal ions. And GF1 can reduce the high blood lead in mice and may play a role in alleviating lead poisoning in vivo. All findings demonstrated that GF1 can be used as a novel macromolecule to bind heavy metal ions, and the study can broaden the research scope of ferritin in contaminated food systems.

High Prevalence of Plasminogen Activator Inhibitor-1 4G/5G Polymorphism among Patients with Venous Thromboembolism in Kerala, India

Venous thromboembolism (VTE) is a multifactorial clotting disorder in which inherited and environmental factors synergistically contribute to its pathogenesis. The aim of this case-control study was to analyze the prevalence of hereditary thrombophilic risk factors, provoking and non-provoking environmental risk factors in patients with VTE from Kerala, India. We have observed a low prevalence of factor V Leiden (7%), prothrombin G20210A (2%), and prothrombin G20030A (2%) mutations and a high prevalence of plasminogen activator inhibitor-1 (PAI-1) 4G/5G (52%), PAI-1 4G/4G (24%) genotypes in the VTE patients (n = 147). Deficiency of anticoagulants, antithrombin (3.4%), and protein C (4.1%) was relatively low. None of the risk factors were observed in 17% of the patients. Majority of VTE patients were younger than 50 years with a median age of 43 years. In conclusion, our results indicate a high prevalence of PAI-1 4G/5G polymorphism among the VTE patients which is in concordance with previous studies in the Asian population. The PAI-1 4G/5G polymorphism could be a potential biomarker for assessing VTE risk, particularly among the Indian population.

Snake Venoms in Diagnostic Hemostasis and Thrombosis

Snake venoms have evolved primarily to immobilize and kill prey, and consequently, they contain some of the most potent natural toxins. Part of that armory is a range of hemotoxic components that affect every area of hemostasis, which we have harnessed to great effect in the study and diagnosis of hemostatic disorders. The most widely used are those that affect coagulation, such as thrombin-like enzymes unaffected by heparin and direct thrombin inhibitors, which can help confirm or dispute their presence in plasma. The liquid gold of coagulation activators is Russell's viper venom, since it contains activators of factor X and factor V. It is used in a range of clotting-based assays, such as assessment of factor X and factor V deficiencies, protein C and protein S deficiencies, activated protein C resistance, and probably the most important test for lupus anticoagulants, the dilute Russell's viper venom time. Activators of prothrombin, such as oscutarin C from Coastal Taipan venom and ecarin from saw-scaled viper venom, are employed in prothrombin activity assays and lupus anticoagulant detection, and ecarin has a valuable role in quantitative assays of direct thrombin inhibitors. Snake venoms affecting primary hemostasis include botrocetin from the jararaca, which can be used to assay von Willebrand factor activity, and convulxin from the cascavel, which can be used to detect deficiency of the platelet collagen receptor, glycoprotein VI. This article takes the reader to every area of the diagnostic hemostasis laboratory to appreciate the myriad applications of snake venoms available in diagnostic practice.

Improvement of thermal stability of oyster (Crassostrea gigas) ferritin by point mutation

Ferritin can be widely used as functional nanomaterial. But the physiological activity of ferritin can be damaged under excessive temperatures, which affect the self-assembly property. In this study, point mutation was produced in Asp¹²⁰ to Gly¹²⁰ of ferritin amino acid sequence and the heat resistance was improved significantly. The thermal denaturation temperature of mutated ferritin is 89.17 °C and has increased by 13 °C more than the wild-type oyster ferritin. The effect of thermal treatment on the denaturation, aggregation state, particle size and the structure of ferritin was not changed before 90 °C. The computational modeling and analysis indicated that mutated ferritin promotes the overall structural stability assembly via decreasing the interaction energies of 62 percent energies in 3-fold interface. Improving the thermal stability of oyster ferritin by point mutation enhances its applications as a food ingredient.

Identification of blood plasma proteins using heparin-coated magnetic chitosan particles

Heparin was immobilized on magnetic chitosan particles to be used as a tool for human plasma protein identification. Chitosan was magnetized by co-precipitation with Fe²⁺/Fe³⁺ (MAG-CH). Heparin was functionalized with carbodiimide and N-hydroxysuccinimide and covalently linked to MAG-CH (MAG-CH-hep). X-ray diffraction confirmed the presence of chitosan and Fe₃O₄ in MAG-CH. This particle exhibited superparamagnetism and size between 100-300 μm. Human plasma diluted with 10 mM phosphate buffer (pH 5.5) or 50 mM Tris-HCl buffer (pH 8.5) was incubated with MAG-CH-hep, and the proteins fixed were eluted with the same buffers containing increasing concentrations of NaCl. The proteins obtained were investigated by SDS-PAGE, LC/MS, and biological activity tests (PT, aPTT, and enzymatic chromogenic assay). Inhibitors of the serpin family, prothrombin, and human albumin were identified in this study. Therefore, MAG-CH-hep can be used to purify these proteins and presents the following advantages: low-cost synthesis, magnetic separation, ion-exchange purification, and reusability.

Sodium-induced population shift drives activation of thrombin

The equilibrium between active E and inactive E* forms of thrombin is assumed to be governed by the allosteric binding of a Na⁺ ion. Here we use molecular dynamics simulations and Markov state models to sample transitions between active and inactive states. With these calculations we are able to compare thermodynamic and kinetic properties depending on the presence of Na⁺. For the first time, we directly observe sodium-induced conformational changes in long-timescale computer simulations. Thereby, we are able to explain the resulting change in activity. We observe a stabilization of the active form in presence of Na⁺ and a shift towards the inactive form in Na⁺-free simulations. We identify key structural features to quantify and monitor this conformational shift. These include the accessibility of the S1 pocket and the reorientation of W215, of R221a and of the Na⁺ loop. The structural characteristics exhibit dynamics at various timescales: Conformational changes in the Na⁺ binding loop constitute the slowest observed movement. Depending on its orientation, it induces conformational shifts in the nearby substrate binding site. Only after this shift, residue W215 is able to move freely, allowing thrombin to adopt a binding-competent conformation.

Rare bleeding disorders and advances in gene therapy

: Rare bleeding disorders usually begin in childhood and manifest as varying degrees of bleeding, which can be life-threatening in severe cases. With the development of gene editing technology, it is expected that hereditary coagulation factor disorders will someday be fundamentally cured by gene therapy. On account of their rarity, comprehension of these diseases is essential for the application of new treatment strategies. We have compiled the features of some newly discovered mutations of prothrombin, factor VII, and factor X in recent years. In addition, this review introduces the advances and obstacles in gene therapy.