The impacts of 13 novel mutations of SARS-CoV-2 on protein dynamics: In silico analysis from Turkey

Unlu, Sezin; Güçlü, Aylin Üsküdar; Cela, I.

doi:10.1016/j.humgen.2022.201040

Cited by 2 publications

(4 citation statements)

References 27 publications

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“…During 100 ns MD simulation, the SASA values of all peptides QNDF, QGGDF, EPVTLT, and EVNYDFGGK showed a decreasing trend, and the SASA values of peptide EVNYDFGGK decreased the most (Figure C). In general, the decrease of SASA value indicates that the hydrophobic interaction between nonpolar residues is increasing and the structure of the protein is more stable . Therefore, the aforementioned results indicated that the binding of all four peptides to receptor T1R1/T1R3 made the structure of the receptor protein more stable, especially the peptide EVNYDFGGK.…”

Section: Resultsmentioning

confidence: 89%

“…In general, the decrease of SASA value indicates that the hydrophobic interaction between nonpolar residues is increasing and the structure of the protein is more stable. 42 Therefore, the aforementioned results indicated that the binding of all four peptides to receptor T1R1/T1R3 made the structure of the receptor protein more stable, especially the peptide EVNYDFGGK.…”

Section: ■ Results and Discussionmentioning

confidence: 93%

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Identification of Novel Umami Peptides in Termitornyces albuminosus (Berk) Heim Soup by In Silico Analyses Combined with Sensory Evaluation: Discovering Potential Mechanism of Umami Taste Formation with Molecular Perspective

Yu,

Zhao,

et al. 2023

J. Agric. Food Chem.

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In this study, 24 peptides were identified in Termitornyces albuminosus (Berk) Heim soup, 12 of which were predicted to possess an umami taste based on the BIOPEP-UWM or Umami-MRNN databases. Among these 12 peptides, four peptides (i.e., QNDF, QGGDF, EPVTLT, and EVNYDFGGK) exhibited the lowest affinity energy with the umami receptor type 1 member 1 (T1R1) subunit. Molecular docking and molecular dynamics simulation further confirmed the strong binding of these four umami peptides to the umami receptor T1R1/T1R3, with the EVNYDFGGK forming the most stable complex. After synthesizing the four peptides, their umami taste was validated through sensory and electronic tongue analyses with recognition thresholds ranging from 0.0938 to 0.3750 mmol/L. Notably, the EVNYDFGGK peptide displayed the strongest umami taste (recognition threshold, 0.0938 mmol/L). This study may contribute to the industrial development of T. albuminosus by providing a new understanding of the mechanism of its umami formation.

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Section: Resultsmentioning

confidence: 89%

Section: ■ Results and Discussionmentioning

confidence: 93%

Identification of Novel Umami Peptides in Termitornyces albuminosus (Berk) Heim Soup by In Silico Analyses Combined with Sensory Evaluation: Discovering Potential Mechanism of Umami Taste Formation with Molecular Perspective

Yu,

Zhao,

et al. 2023

J. Agric. Food Chem.

View full text Add to dashboard Cite

show abstract

“…In the AA region 339-505, some lineage-defining mutations decreased in prevalence in XM and increased in prevalence in XQ and XZ indicating a potential host editing for a fitness advantage. A mutation like T732I has been observed in BA.3 for the first time that with the neighboring two amino acids favoring β-sheet formation vis a vis coil formation 40 . This would potentially have an impact on the conformation and functions of the spike protein.…”

Section: The Heatmap (Fig 4c) Further Highlights the Differential Dis...mentioning

confidence: 96%

“…Prevalence of the lineage-defining mutations in Pune showcased reversedprevalence of G142-and G142D amongst BA.1 and BA.2. In silico analysis of the G142D mutation suggests a disturbance of the surface topography of the 'super site' epitope that binds NTD-directed neutralizing antibodies (NAbs)[38][39][40] . The changing pattern for G142 to D142 or G142-and V213 to G213 or G213-observed at multiple time points and across Delta VOC sub-lineages indicates the rapid generation of multiple variants for selection.…”

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confidence: 99%

A Tale of Two Waves: Diverse Genomic and Transmission Landscapes Over 15 Months of the COVID-19 Pandemic in Pune, India

Niveditha

Khan

Khilari

et al. 2022

Preprint

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The modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Genomic surveillance has come to the forefront during the coronavirus disease 2019 (COVID-19) pandemic at both local and global scales to identify variants of concern. Tracking variants of concern (VOC) is integral to understanding the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in space and time. Combining phylogenetics with epidemiological data like case incidence, spatial spread, and transmission dynamics generates actionable information. Here we discuss the genome surveillance done in Pune, India, through sequencing 10,496 samples from infected individuals and integrating them with multiple heterogeneous outbreak data. The rise and fall of VOCs along with shifting transmission dynamics in the time interval of December 2020 to March 2022 was identified. Population-based estimates of the proportion of circulating variants indicated the second and third peak of infection in Pune to be driven by VOCs Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) respectively. Integrating single nucleotide polymorphism changes across all sequenced genomes identified C (Cytosine) > T (Thymine) and G (Guanine) > T (Thymine) substitutions to dominate with higher rates of adaptive evolution in Spike (S), RNA-dependent RNA polymerase (RdRp), and Nucleocapsid (N) genes. Spike Protein mutational profiling during and pre-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified specific recombinant X lineages, XZ, XQ, and XM. BA.1 from Pune was found to be highly divergent by global sequence alignment and hierarchical clustering. Our ″band of five″ outbreak data analytics which includes the integration of five heterogeneous data types indicates that a strong surveillance system with comprehensive high-quality metadata was critical to understand the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. We anticipate the use of such integrated workflows to be critical for pandemic preparedness in the future.

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The impacts of 13 novel mutations of SARS-CoV-2 on protein dynamics: In silico analysis from Turkey

Cited by 2 publications

References 27 publications

Identification of Novel Umami Peptides in Termitornyces albuminosus (Berk) Heim Soup by In Silico Analyses Combined with Sensory Evaluation: Discovering Potential Mechanism of Umami Taste Formation with Molecular Perspective

Identification of Novel Umami Peptides in Termitornyces albuminosus (Berk) Heim Soup by In Silico Analyses Combined with Sensory Evaluation: Discovering Potential Mechanism of Umami Taste Formation with Molecular Perspective

A Tale of Two Waves: Diverse Genomic and Transmission Landscapes Over 15 Months of the COVID-19 Pandemic in Pune, India

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