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  1. Article ; Online: SARS-CoV-2 Spike Protein Post-Translational Modification Landscape and Its Impact on Protein Structure and Function via Computational Prediction

    Buwen Liang / Yiying Zhu / Wenhao Shi / Can Ni / Bowen Tan / Shaojun Tang

    Research, Vol

    2023  Volume 6

    Abstract: To elucidate the role of post-translational modifications (PTMs) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein’s structure and virulence, we generated a high-resolution map of 87 PTMs using liquid chromatography with ... ...

    Abstract To elucidate the role of post-translational modifications (PTMs) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein’s structure and virulence, we generated a high-resolution map of 87 PTMs using liquid chromatography with tandem mass spectrometry data on the extracted spike protein from SARS-CoV-2 virions and then reconstituted its structure heterogeneity caused by PTMs. Nonetheless, Alphafold2, a high-accuracy artificial intelligence tool to perform protein structure prediction, relies solely on primary amino acid sequence, whereas the impact of PTM, which often modulates critical protein structure and function, is much ignored. To overcome this challenge, we proposed the mutagenesis approach—an in silico, site-directed amino acid substitution to mimic the influence of PTMs on protein structure due to altered physicochemical properties in the post-translationally modified amino acids—and then reconstituted the spike protein’s structure from the substituted sequences by Alphafold2. For the first time, the proposed method revealed predicted protein structures resulting from PTMs, a problem that Alphafold2 has yet to address. As an example, we performed computational analyses of the interaction of the post-translationally modified spike protein with its host factors such as angiotensin-converting enzyme 2 to illuminate binding affinity. Mechanistically, this study suggested the structural analysis of post-translationally modified protein via mutagenesis and deep learning. To summarize, the reconstructed spike protein structures showed that specific PTMs can be used to modulate host factor binding, guide antibody design, and pave the way for new therapeutic targets. The code and Supplementary Materials are freely available at https://github.com/LTZHKUSTGZ/SARS-CoV-2-spike-protein-PTM.
    Keywords Science ; Q
    Subject code 612
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher American Association for the Advancement of Science
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Association of regular glucosamine use with incident dementia

    Jiazhen Zheng / Can Ni / Yingchai Zhang / Jinghan Huang / Daniel Nyarko Hukportie / Buwen Liang / Shaojun Tang

    BMC Medicine, Vol 21, Iss 1, Pp 1-

    evidence from a longitudinal cohort and Mendelian randomization study

    2023  Volume 13

    Abstract: Abstract Background Emerging data suggests the neuroprotective and anti-neuroinflammatory effects of glucosamine. We aimed to examine the association between regular glucosamine use and risk of incident dementia, including dementia subtypes. Methods We ... ...

    Abstract Abstract Background Emerging data suggests the neuroprotective and anti-neuroinflammatory effects of glucosamine. We aimed to examine the association between regular glucosamine use and risk of incident dementia, including dementia subtypes. Methods We conducted large-scale observational and two-sample Mendelian randomization (MR) analyses. Participants in UK Biobank having accessible data for dementia incidence and who did not have dementia at baseline were included in the prospective cohort. Through the Cox proportional hazard model, we examined the risks of incident all-cause dementia, Alzheimer’s disease (AD), and vascular dementia among glucosamine users and non-users. To further test the causal association between glucosamine use and dementia, we conducted a 2-sample MR utilizing summary statistics from genome-wide association studies (GWAS). The GWAS data were obtained from observational cohort participants of mostly European ancestry. Results During a median follow-up of 8.9 years, there were 2458 cases of all-cause dementia, 924 cases of AD, and 491 cases of vascular dementia. In multivariable analysis, the hazard ratios (HR) of glucosamine users for all-cause dementia, AD, and vascular dementia were 0.84 (95% CI 0.75–0.93), 0.83 (95% CI 0.71–0.98), and 0.74 (95% CI 0.58–0.95), respectively. The inverse associations between glucosamine use and AD appeared to be stronger among participants aged below 60 years than those aged above 60 years (p = 0.04 for interaction). The APOE genotype did not modify this association (p > 0.05 for interaction). Single-variable MR suggested a causal relationship between glucosamine use and lower dementia risk. Multivariable MR showed that taking glucosamine continued to protect against dementia after controlling for vitamin, chondroitin supplement use and osteoarthritis (all-cause dementia HR 0.88, 95% CI 0.81–0.95; AD HR 0.78, 95% CI 0.72–0.85; vascular dementia HR 0.73, 95% CI 0.57–0.94). Single and multivariable inverse variance weighted (MV-IVW) and MR-Egger ...
    Keywords Glucosamine ; Dementia ; Alzheimer’s disease ; APOE ; Medicine ; R
    Subject code 360
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Correction

    Jiazhen Zheng / Can Ni / Yingchai Zhang / Jinghan Huang / Daniel Nyarko Hukportie / Buwen Liang / Shaojun Tang

    BMC Medicine, Vol 21, Iss 1, Pp 1-

    Association of regular glucosamine use with incident dementia: evidence from a longitudinal cohort and Mendelian randomization study

    2023  Volume 1

    Keywords Medicine ; R
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  4. Article ; Online: Integrated Traditional Chinese Medicine Improves Functional Outcome in Acute Ischemic Stroke

    Qian Guo / Can Ni / Linjing Li / Mo Li / Xiaoqing Jiang / Li Gao / Huaiqiu Zhu / Juexian Song

    Frontiers in Cellular and Infection Microbiology, Vol

    From Clinic to Mechanism Exploration With Gut Microbiota

    2022  Volume 12

    Abstract: As a life-threatening disease, stroke is the leading cause of death and also induces adult disability worldwide. To investigate the efficacy of the integrated traditional Chinese medicine (ITCM) on the therapeutic effects of acute ischemic stroke (AIS) ... ...

    Abstract As a life-threatening disease, stroke is the leading cause of death and also induces adult disability worldwide. To investigate the efficacy of the integrated traditional Chinese medicine (ITCM) on the therapeutic effects of acute ischemic stroke (AIS) patients, we enrolled 26 patients in the ITCM [Tanhuo decoction (THD) + Western medicine (WM)] group and 23 in the WM group. Thirty healthy people were also included in the healthy control (HC) group. ITCM achieved better functional outcomes than WM, including significant reduction of the phlegm-heat syndrome and neurological impairment, and improvement of ability. These facts were observed in different pretreatment gut enterotypes. In this paper, we collected the stool samples of all participants and analyzed the 16S rRNA sequence data of the gut microbiota. We identified two enterotypes (Type-A and Type-B) of the gut microbial community in AIS samples before treatment. Compared to Type-B, Type-A was characterized by a high proportion of Bacteroides, relatively high diversity, and severe functional damage. In the ITCM treatment group, we observed better clinical efficacy and positive alterations in microbial diversity and beneficial bacterial abundance, and the effect of approaching healthy people’s gut microbiota, regardless of gut enterotypes identified in pretreatment. Furthermore, we detected several gut microbiota as potential therapeutic targets of ITCM treatment by analyzing the correlations between bacterial abundance alterations and functional outcomes, where Dorea with the strongest correlation was known to produce anti-inflammatory metabolite and negatively linked to trimethylamine-N-oxide (TMAO), a biomarker of AIS. This study analyzed clinical and gut microbial data and revealed the possibility of a broad application independent of the enterotypes, as well as the therapeutic targets of the ITCM in treating AIS patients with phlegm-heat syndrome.
    Keywords acute ischemic stroke ; integrated traditional Chinese medicine ; therapeutic efficacy ; gut microbiota ; enterotype ; Microbiology ; QR1-502
    Subject code 616 ; 610
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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