Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions

Protein folding: Then and now

Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases

3D Spheroids of Human Primary Urine-Derived Stem Cells in the Assessment of Drug-Induced Mitochondrial Toxicity

Mitochondrial toxicity (Mito-Tox) risk has increased due to the administration of several classes of drugs, particularly some life-long antiretroviral drugs for HIV+ individuals. However, no suitable in vitro assays are available to test long-term Mito-Tox (≥4 weeks). The goal of this study is to develop a 3D spheroid system of human primary urine-derived stem cells (USC) for the prediction of drug-induced delayed Mito-Tox. The cytotoxicity and Mito-Tox were assessed in 3D USC spheroids 4 weeks after treatment with antiretroviral drugs: zalcitabine (ddC; 0.1, 1 and 10 µM), tenofovir (TFV; 3, 30 and 300 µM) or Raltegravir (RAL; 2, 20 and 200 µM). Rotenone (RTNN, 10 µM) and 0.1% DMSO served as positive and negative controls. Despite only mild cytotoxicity, ddC significantly inhibited the expression of oxidative phosphorylation enzyme Complexes I, III, and IV; and RAL transiently reduced the level of Complex IV. A significant increase in caspase 3 and ROS/RNS level but a decrease in total ATP were observed in USC treated with ddC, TFV, RAL, and RTNN. Levels of mtDNA content and mitochondrial mass were decreased in ddC but minimally or not in TFV- and RAL-treated spheroids. Thus, 3D USC spheroid using antiretroviral drugs as a model offers an alternative platform to assess drug-induced late Mito-Tox

Hospital-acquired invasive pulmonary aspergillosis in patients with hepatic failure

<p>Abstract</p> <p>Background</p> <p>Invasive pulmonary aspergillosis (IPA) is a rapid, progressive, fatal disease that occurs mostly in immunocompromised patients. Patients with severe liver disease are at a heightened risk for infections. Little is known about the clinical presentation including predisposing factors and treatment of IPA in patients with hepatic failure.</p> <p>Methods</p> <p>Medical records of patients with hepatic failure between November 2005 and February 2007 were reviewed for lung infection. Nine medical records of definitive diagnosis of IPA and three of probable IPA were identified.</p> <p>Results</p> <p>The main predisposing factors were found to be prolonged antibiotic therapy and steroid exposure. Clinical signs and radiological findings were non-specific and atypical. Timely use of caspofungin was found to reduce the mortality due to the disease.</p> <p>Conclusion</p> <p>A high index of suspicion is required for early IPA diagnosis in patients with hepatic failure.</p

Recombinant proteins A29L, M1R, A35R, and B6R vaccination protects mice from mpox virus challenge

Since May 2022, mutant strains of mpox (formerly monkeypox) virus (MPXV) have been rapidly spreading among individuals who have not traveled to endemic areas in multiple locations, including Europe and the United States. Both intracellular and extracellular forms of mpox virus have multiple outer membrane proteins that can stimulate immune response. Here, we investigated the immunogenicity of MPXV structural proteins such as A29L, M1R, A35R, and B6R as a combination vaccine, and the protective effect against the 2022 mpox mutant strain was also evaluated in BALB/c mice. After mixed 15 μg QS-21 adjuvant, all four virus structural proteins were administered subcutaneously to mice. Antibody titers in mouse sera rose sharply after the initial boost, along with an increased capacity of immune cells to produce IFN-γ alongside an elevated level of cellular immunity mediated by Th1 cells. The vaccine-induced neutralizing antibodies significantly inhibited the replication of MPXV in mice and reduced the pathological damage of organs. This study demonstrates the feasibility of a multiple recombinant vaccine for MPXV variant strains

Research on Formation Identification Based on Drilling Shock and Vibration Parameters and Energy Principle

In geotechnical engineering and geological survey, the stratum structure and its corresponding physical and mechanical properties are the most concerned. The stratum structure not only affects the safety of the project but also plays a decisive role in the construction method and construction sequence. In this paper, a new type of stratum geological interface recognition system is adopted, and an R-20 rotary drilling rig is used to conduct on-site drilling experiments for a granite site with no ventilation. The research results show that the system can monitor and record the main parameters (axial pressure, drilling rate, rotation speed, flushing fluid pressure, and torque) of the drilling rig during the drilling process. The comparative analysis of monitoring data and on-site survey results shows that different drilling parameters have different sensitivities to changes in the formation structure. According to the prediction accuracy, the ranking from high to low is drilling rate, axial pressure, torque, rotation speed, and flushing fluid pressure. In drilling engineering, by observing the change law of drilling rig parameters, not only can the position of the special rock mass interlayer be predicted, but also the stratum structure and strength can be identified, and the prediction formula is also given. Based on the established drilling specific energy formula, the energy analysis method is used to predict the formation structure and compressive strength, and the corresponding prediction formula is given. The research results show that, compared with the single drilling parameter prediction method, the rock-soil structure and strength identification method based on energy theory has higher prediction accuracy and can meet engineering needs

Modifying of mechanical properties in the deposited metal prepared by welding wire containing nanosized oxide particles

Fine oxide particles can play a role in refining grains and promoting nucleation in steel. In this research, a solid welding wire containing nanosized oxides was obtained by preparing a ‘master alloy’. The oxide size was studied by optical microscopy, scanning electron microscopy and transmission electron microscopy. The results show that micron-sized oxides were crushed into nanosized particles under thermal shock in the welding wire steel smelting process. The mechanical properties of deposited metals were studied by tensile and Charpy impact tests. The results demonstrate that the low-temperature impact toughness of deposited metal is effectively improved by adding oxides to wires. When the oxide content was 1%, the impact absorbed energy was 59 J at −40 °C. Compared with that of the deposited metal without oxides, the impact absorbed energy increased by 22.92%. The addition of oxides refines the original austenite grains and promotes acicular ferrite nucleation so that the deposited metal has better mechanical properties. To obtain good strength toughness matching, the welding wire with 1% oxides has the best comprehensive properties

Genome-Wide Analysis of <i>ZAT</i> Gene Family in <i>Osmanthus fragrans</i> and the Function Exploration of <i>OfZAT35</i> in Cold Stress

Osmanthus fragrans is a popular ornamental and odorant plant with high commercial value, but its cultivation and exploitation are limited by low temperature. The ZAT (zinc finger of Arabidopsis thaliana) genes as a subclass of the C2H2-type zinc finger proteins (C2H2-ZFP) family play essential roles in various abiotic stresses. However, their roles in cold stress response in O. fragrans remain unclear. This study identified 38 OfZATs, which could be divided into 5 subgroups based on the phylogenetic tree, with OfZATs in the same subgroup harboring similar gene structures and motif patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZAT genes, while some OfZAT genes exhibited specific expression patterns in different tissues. Furthermore, two OfZATs were induced in salt stress and eight OfZATs responded to cold stress. Interestingly, OfZAT35 showed a continuously increasing expression trend under cold stress, while its protein showed nucleus localization with no transcriptional activation activity. Transiently transformed tobacco overexpressing OfZAT35 exhibited a significantly higher relative electrolyte leakage (REL) level and increased activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX), while there was significantly decreased activity of catalase (CAT). Moreover, CAT, DREB3, and LEA5, which are associated with cold stress, were dramatically decreased after cold treatment in transiently transformed tobacco, suggesting that overexpression of OfZAT35 negatively regulated cold stress. This study provides a basis for exploring the roles of ZAT genes and contributes to uncovering the mechanism of ZAT-mediated cold stress response in O. fragrans