A5083093251- Protein Structure and Dynamics
- Circadian rhythm and melatonin
- Cytokine Signaling Pathways and Interactions
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Microtubule and mitosis dynamics
- RNA Research and Splicing
- Hydrocarbon exploration and reservoir analysis
- Methane Hydrates and Related Phenomena
- DNA and Nucleic Acid Chemistry
- SARS-CoV-2 and COVID-19 Research
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Protein Kinase Regulation and GTPase Signaling
- Machine Learning in Bioinformatics
- Atmospheric and Environmental Gas Dynamics
- Histone Deacetylase Inhibitors Research
- Insect behavior and control techniques
- Genomics and Chromatin Dynamics
- Bacterial Genetics and Biotechnology
- Insect symbiosis and bacterial influences
- Cellular Mechanics and Interactions
- HIV Research and Treatment
- Cancer therapeutics and mechanisms
- Silk-based biomaterials and applications
- Cardiovascular Effects of Exercise
Central South University
2023-2025
The University of Texas at El Paso
2019-2024
Second Xiangya Hospital of Central South University
2024
Tianjin Agricultural University
2024
China Agricultural University
2020
Abstract The short-chain gaseous alkanes (ethane, propane, and butane; SCGAs) are important components of natural gas, yet their fate in environmental systems is poorly understood. Microbially mediated anaerobic oxidation SCGAs coupled to nitrate reduction has been demonstrated for but be shown ethane or butane—despite being energetically feasible. Here we report two independent bacterial enrichments performing butane oxidation, respectively, dinitrogen gas ammonium. Isotopic 13C-...
Circadian clock perturbation frequently occurs in cancer and facilitates tumor progression by regulating malignant growth shaping the immune microenvironment. Emerging evidence has indicated that genes are disrupted melanoma linked to escape. Herein, we found expression of retinoic acid receptor-related orphan receptor-α (RORA) is downregulated patients with higher RORA have a better prognosis after immunotherapy. Additionally, was significantly positively correlated T-cell infiltration...
Grapholita molesta, the oriental fruit moth, is a serious global pest of many Rosaceae trees. Gut microorganisms play important roles in host nutrition, digestion, detoxification, and resistance to pathogens. However, there are few studies on microbiota G. particularly during metamorphosis. Here, diversity gut across holometabolous life cycle molesta was investigated comprehensively by Illumina high-throughput sequencing technology. The results showed that associated with eggs had high...
Abstract The family of Janus Kinases (JAKs) associated with the JAK–signal transducers and activators transcription signaling pathway plays a vital role in regulation various cellular processes. conformational change JAKs is fundamental steps for activation, affecting multiple intracellular pathways. However, transitional process from inactive to active kinase still mystery. This study aimed at investigating electrostatic properties states JAK1 fully activation catalytically enzyme. To...
Microtubules are key players in several stages of the cell cycle and also involved transportation cellular organelles. polymerized by α/β tubulin dimers with a highly dynamic feature, especially at plus ends microtubules. Therefore, understanding interactions among tubulins is crucial for characterizing microtubule dynamics. Studying dynamics can help researchers make advances treatment neurodegenerative diseases cancer. In this study, we utilize series computational approaches to study...
A large population in the world has been infected by COVID-19. Understanding mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is important for management and treatment When it comes to infection process, one most proteins SARS-CoV-2 spike (S) protein, which able bind human Angiotensin-Converting Enzyme (ACE2) initializes entry host cell. In this study, we implemented multiscale computational approaches study electrostatic features interfaces S protein receptor...
SARS-CoV-2 that caused COVID-19 has spread since the end of 2019. Its major effects resulted in over four million deaths around whole world by August 2021. Therefore, understanding virulence mechanisms is important to prevent future outbreaks and for drug development. The envelope (E) protein an structural protein, affecting virus assembly budding. E pentamer a viroporin, serving as ion transferring channel cells. In this work, we applied molecular dynamic simulations topological...
Overactive Janus kinases (JAKs) are known to drive leukemia, making them well-suited targets for treatment. We sought identify new JAK-activating mutations and instead found a JAK1-inactivating pseudokinase mutation, V666G. In contrast other that canonically lead an active kinase, the JAK1 V666G mutation led under-activation seen by reduced phosphorylation. To understand functional role of in modifying kinase activity we investigated its influence on JAK within Interleukin-2 pathway. not...
<abstract> <p>COVID-19 is increasingly affecting human health and global economy. Understanding the fundamental mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) highly demanded to develop treatments for COVID-19. SARS-CoV SARS-CoV-2 share 92.06% identity in their N protein RBDs' sequences, which results very similar structures. However, more easily spread. Utilizing multi-scale computational approaches, this work studied nucleocapsid (N) proteins...
Kinesins are microtubule-based motor proteins that play important roles ranging from intracellular transport to cell division. Human Kinesin-5 (Eg5) is essential for mitotic spindle assembly during By combining molecular dynamics (MD) simulations with other multi-scale computational approaches, we systematically studied the interaction between Eg5 and microtubule. We find electrostatic feature on domains of provides attractive interactions Additionally, folding binding energy analysis...
Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They vital in sustaining ecological services, especially maintaining essential biogeochemical cycles. Recent years have seen a substantial increase surplus nitrogenous pollutants ecosystems heightened occurrence anthropogenic activities. Elevated levels free ammonia (FA, NH
One quarter of the world's population are infected by Mycobacterium tuberculosis (Mtb), which is a leading death-causing bacterial pathogen. Recent evidence has demonstrated that two virulence factors, ESAT-6 and CFP-10, play crucial roles in Mtb's cytosolic translocation. Many efforts have been made to study CFP-10 proteins. Some studies shown an essential role rupturing phagosome. However, mechanisms how interacts with membrane not yet fully understood. indicate disassociates upon their...
Janus Kinase 3 (JAK3) plays a key role in the development, proliferation, and differentiation of various immune cells. It regulates gene expression by phosphorylation Signal Transducers Activators Transcriptions (STATs) via JAK/STAT pathway. Recently, we found new JAK3 site, tyrosine 841 (Y841). The results showed that pY841 helps kinase domain flip around pseudo domain, which may cause conformational changes. also reduces size cleft between N-lobe C-lobe domain. However, was to enlarge when...
Drosophila Ncd proteins are motor that play important roles in spindle organization. and the tubulin dimer highly charged. Thus, it is crucial to investigate Ncd-tubulin interactions presence of ions, especially ions bound or restricted at binding interfaces. To consider ion effects, widely used implicit solvent models treat implicitly continuous environment without focusing on individual ions' effects. But charged biomolecules such as may capture some regions ions. Such their sites; thus,...
Abstract Dengue viral capsid plays a significant role in life cycle of dengue, especially vial genome protection and virus-cell fusion. Revealing mechanisms the protein assembly may lead to discovery anti-viral drugs that inhibit capsid. The E M-proteins are arranged into heterotetramers, which consists two copies M-protein. heterotetramers assembled highly ordered While many investigations interactions between have been performed, there very few studies on their roles assembly. Utilizing...
Electrostatic features are fundamental to protein functions and protein-protein interactions. Studying highly charged biomolecules is challenging given the heterogeneous distribution of ionic cloud around such biomolecules. Here we report a new computational method, Hybridizing Ions Treatment-2 (HIT-2), which used model biomolecule-bound ions using implicit solvation model. By modeling ions, HIT-2 allows user calculate important electrostatic applies an efficient algorithm position bound...
Janus tyrosine kinase (JAK) variants are known drivers for hematological disorders. With the full-length structure of mouse JAK1 being recently resolved, new observations on localization within closed, open, and dimerized JAK structures possible. Full-length homology models human wild-type family members were developed using Glassman et al. reported containing V658F as a template. Many mutational sites related to proliferative disorders reside in JH2 pseudokinase domains facing region...
Solid stress, originating from rigid and elastic components of extracellular matrix cells, is a typical physical hallmark tumors. Mounting evidence indicates that elevated solid stress drives metastasis affects prognosis. However, the molecular mechanism how cancer cells sense thereby exacerbating malignancy, remains elusive. In this study, our clinical data suggest in metastatic tumors highly associated with expression cytoskeleton-associated protein 4 (CKAP4). Intriguingly, CKAP4, as...
Fast and accurate calculations of the electrostatic features highly charged biomolecules such as DNA, RNA, proteins are crucial challenging tasks. Traditional implicit solvent methods calculate quickly, but these not able to balance high net biomolecular charges effectively. Explicit add unbalanced ions neutralize in molecular dynamic simulations, which require more expensive computing resources. Here we report developing a novel method, Hybridizing Ions Treatment (HIT), hybridizes method...
The electrostatic features of highly charged biomolecules are crucial and challenging tasks in computational biophysics. calculations by traditional implicit solvent methods efficient but have difficulties on biomolecules. We developed a Hybridizing Ion Treatment (HIT) tool, which successfully hybridizes the explicit ions solvation model to accurately calculate potential for Here we implemented HIT tool into web server. In this study, training set was prepared optimize number frames results...
Janus tyrosine kinase 3 (JAK3) is primarily expressed in immune cells and needed for signaling by the common gamma chain (γc) family of cytokines. Abnormal JAK3 signal transduction can manifest as hematological disorders, e.g., leukemia, severe combined immunodeficiency (SCID) autoimmune disease states. While regulatory phosphosites have been well studied, here a functional proteomics approach coupling autokinase assay to mass spectrometry revealed ten previously unreported...