A5029697012- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- HIV Research and Treatment
- HIV/AIDS drug development and treatment
- SARS-CoV-2 and COVID-19 Research
- Computational Drug Discovery Methods
- Entomopathogenic Microorganisms in Pest Control
- Enzyme Production and Characterization
- Nematode management and characterization studies
- Crystallography and molecular interactions
- Insect Resistance and Genetics
- Monoclonal and Polyclonal Antibodies Research
- Insect symbiosis and bacterial influences
- Lipid Membrane Structure and Behavior
- Plant-Microbe Interactions and Immunity
- Mass Spectrometry Techniques and Applications
- Catalysis and Hydrodesulfurization Studies
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Glycosylation and Glycoproteins Research
- Supramolecular Chemistry and Complexes
- Hemoglobin structure and function
Yunnan University
2016-2025
Kunming University
2017-2020
Wenzhou City People's Hospital
2019
Lanzhou University of Technology
2007-2018
First Affiliated Hospital of Kunming Medical University
2016-2017
Kunming Medical University
2016-2017
Huaibei Normal University
2012-2015
Chinese Academy of Sciences
2001-2013
Academe of Grassland And Animal Science
2013
Tsinghua University
2003-2012
Nematode-trapping fungi are "carnivorous" and attack their hosts using specialized trapping devices. The morphological development of these traps is the key indicator switch from saprophytic to predacious lifestyles. Here, genome nematode-trapping fungus Arthrobotrys oligospora Fres. (ATCC24927) was reported. contains 40.07 Mb assembled sequence with 11,479 predicted genes. Comparative analysis showed that A. shared many more genes pathogenic than non-pathogenic fungi. Specifically, compared...
Abstract Because of the significant industrial, agricultural and biotechnological importance serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis kinetic measurement. However, detailed aspects enzymatic mechanism substrate binding, release relevant regulation remain unstudied. Molecular dynamics (MD) simulations K alone in complex with peptide AAPA were performed to investigate effect binding...
Proteins are dynamic entities in cellular solution with functions governed essentially by their personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating behaviors molecular motions for a complete understanding structure–function relationships. Using computer simulations essential (ED) analysis approaches, data obtained revealed that: (i) has highly flexible substrate-binding site,...
Abstract In their natural habitat, bacteria are consumed by bacterivorous nematodes; however, they not simply passive preys. Here we report a defensive mechanism used certain to mobilize nematode-trapping fungi kill nematodes. These release urea, which triggers lifestyle switch in the fungus Arthrobotrys oligospora from saprophytic nematode–predatory form; this predacious form is characterized formation of specialized cellular structures or ‘traps’. The significantly promote elimination...
Abstract Chemical cross-linking of proteins coupled with mass spectrometry is widely used in protein structural analysis. In this study we develop a class non-hydrolyzable amine-selective di- ortho -phthalaldehyde (DOPA) cross-linkers, one which called DOPA2. Cross-linking DOPA2 60–120 times faster than that the N-hydroxysuccinimide ester cross-linker DSS. Compared DSS cross-links, cross-links show better agreement crystal structures tested proteins. More importantly, has unique advantages...
Understanding how fungi interact with other organisms has significant medical, environmental, and agricultural implications. Nematode-trapping (NTF) can switch to pathogens by producing various trapping devices capture nematodes. Here we perform comparative genomic analysis of the NTF four representative devices. Phylogenomic reconstruction these suggested an evolutionary trend device simplification in morphology. Interestingly, was accompanied expansion gene families encoding adhesion...
The human transmembrane protease, serine 2 (TMPRSS2), essential for SARS-CoV-2 entry, is a key antiviral target. Here, we computationally profiled the TMPRSS2-binding affinities of 15 compounds. Molecular dynamics (MD) simulations docked complexes revealed that three compounds exited substrate-binding cavity (SBC), suggesting noncompetitive inhibition. Of remaining compounds, five charged ones exhibited reduced binding stability due to competing electrostatic interactions and increased...
Cuticle-degrading proteases are involved in the breakdown of cuticle/eggshells nematodes or insects, a hard physical barrier against fungal infections. Understanding 3-dimensional structures these proteins can provide crucial information for improving effectiveness fungi biocontrol applications, e.g., by targeted protein engineering. However, remain unknown. Here, we report two cuticledegrading from species nematophagous fungi. The were solved with X-ray crystallography to resolutions 1.65 Å...
In high-temperature environments, thermophilic proteins must possess enhanced thermal stability in order to maintain their normal biological functions. However, the physicochemical basis of structural at high temperatures remains elusive. this study, we performed comparative molecular dynamics simulations on serine protease (THM) and its homologous mesophilic counterpart (PRK). The analyses dynamic geometrical properties suggested that THM adopted a more compact conformation exhibited...
The disease caused by SARS-CoV-2 infection threatens human health. In this study, we used high-pressure homogenization technology not only to efficiently drive the bacterial membrane produce artificial vesicles but also force fusion protein ClyA-receptor binding domain (RBD) pass through gaps in increase contact between ClyA-RBD and membrane. Therefore, load of on is substantially increased. Using technology, constructed a "ring-like" biomimetic vesicle (BBV) loaded with polymerized RBD...
The physicochemical bases for enzyme cold-adaptation remain elusive.
Cuticle-degrading serine proteases secreted by nematophagous fungi can degrade the nematode cuticle during infection processes.
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (RBDCoV2) has a higher binding affinity to human receptor angiotensin-converting enzyme 2 (ACE2) than SARS-CoV RBD (RBDCoV). Here, we performed molecular dynamics (MD) simulations, free energy (BFE) calculations, and interface residue contact network (IRCN) analysis explore mechanistic origin different ACE2-binding affinities two RBDs. results demonstrate that, when compared RBDCoV2-ACE2 complex, RBDCoV-ACE2 features enhanced...
Cuticle-degrading proteases secreted by nematophagous fungi can degrade nematode cuticle during infection. Alkaline from nematode-parasitic show stronger nematicidal activity in vitro than neutral nematode-trapping fungi. Sequence alignment of these revealed that the active-site residues were much conserved. Disulfide bridges alkaline not only contribute to thermal stability enzyme structure but also increase flexibility S1 and S4 pockets located at substrate-binding site. Molecular...
To investigate the role of electrostatics in different temperature adaptations, we performed a comparative study on subtilisin-like serine proteases from psychrophilic Vibrio sp. PA-44 (VPR), mesophilic Engyodontium album (Tritirachium album) (PRK), and thermophilic Thermus aquaticus (AQN) using multiple-replica molecular dynamics (MD) simulations combined with continuum calculations. The results reveal that although salt bridges are not crucial factor determining overall thermostability...
Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, 573 K). The comparative analyses MD trajectories reveal that almost all temperatures, exhibits greater structural fluctuations/deviations, more unstable regular secondary elements, higher global flexibility than PRK. Although these two...