The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein on the viral envelope mediates human angiotensin-converting enzyme 2 (ACE2) binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein models described in our previous work, and performed all-atom molecular dynamics simulations to get insight into the structural dynamics and interactions between S protein and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes, and the influences of antibody on the motion of S protein receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy.
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http://dx.doi.org/10.1101/2021.05.10.443519 | DOI Listing |
Int J Surg
December 2024
Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
Background: RPN1, also known as ribophorin I (RPN1), is a type I transmembrane protein that plays an important role in glycosylation. However, the effects of RPN1 on cancer progression and immune evasion in breast cancer (BC) have not been identified.
Materials And Methods: The expression of RPN1 was evaluated using RT-qPCR and immunohistochemistry (IHC).
Bioinform Biol Insights
December 2024
Department of Biology, Faculty of Science, Burapha University, Chonburi, Thailand.
Clinical and experimental studies have demonstrated that type 2 diabetes mellitus (T2DM) affects the brain structure and function, in particular the hippocampus, leading to cognitive impairments. However, the molecular mechanisms underlying cognitive deficits induced by T2DM are not fully understood. In this study, we aimed to investigate the effects of T2DM on behavior, the proteome profile in the hippocampus, and the potential molecular pathways involved in the development of cognitive dysfunction in T2DM mice.
View Article and Find Full Text PDFBMC Genom Data
December 2024
School of Science, Constructor University, 28759, Bremen, Germany.
Objectives: SARS-CoV-2 spike (S) glycoprotein furin cleavage site is a key determinant of SARS-CoV-2 virulence and COVID-19 pathogencity. Located at the S1/S2 junction, it is unique among sarbecoviruses but frequently found among betacoronaviruses. Recent evidence suggests that this site includes two additional functional motifs: a pat7 nuclear localization signal and two flanking O-glycosites.
View Article and Find Full Text PDFBiochim Biophys Acta Mol Cell Biol Lipids
December 2024
Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe 658-8558, Japan. Electronic address:
Serum amyloid A (SAA) is a family of apolipoproteins predominantly synthesized and secreted by the liver. Human SAA4 is constitutively expressed and contains an N-glycosylation site that is not present in other SAA subtypes. SAA4 proteins are not fully glycosylated, resulting in the presence of both glycosylated and non-glycosylated forms in human plasma.
View Article and Find Full Text PDFJ Sep Sci
December 2024
Department of Laboratory Medicine, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, P. R. China.
Sweroside, a natural secoiridoid glycoside derived from various medicinal plants, is known for its anti-tumor, anti-inflammatory, and hepatoprotective properties. However, its pharmacological significance is not fully supported by its low systemic exposure. In this study, a de novo strategy was proposed to investigate the metabolism of sweroside in rats, including drug administration, sample pretreatment, ultra-high-performance liquid chromatography/Quadrupole-Exactive mass spectrometry data acquisition, data processing, and semi-quantitative analysis.
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