3β-Corner Stability by Comparative Molecular Dynamics Simulations

Rudnev, Vladimir R.; Nikolsky, Kirill S.; Petrovsky, Denis V.; Kulikova, Liudmila I.; Kargatov, A. M.; Malsagova, Kristina A.; Stepanov, Alexander A.; Kopylov, Arthur T.; Kaysheva, Anna L.; Ефимов, А. В.

doi:10.3390/ijms231911674

Cited by 7 publications

(4 citation statements)

References 25 publications

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“…The larger protein structures can be obtained by the stepwise addition of other β-strands to the 3β-corner, taking into account a restricted set of rules inferred from the known principles of protein structure [14]. Molecular dynamics simulations also support these ideas [19].…”

Section: Discussionmentioning

confidence: 92%

Biological Role of the 3β-Corner Structural Motif in Proteins

et al. 2022

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In this study, we analyze the occurrence of the unique structural motif, the 3β-corner, belonging to the Structural Classification of Proteins (SCOP) folds, in proteins of various origins. We further assess the structural and functional role of this motif as well as the clustering of the biological functions of proteins in which it occurs. It has been shown previously that the 3β-corner occurs with different probabilities in all beta proteins, alpha and beta proteins (α + β and α/β), and alpha classes occur most often in the composition of β-proteins. The 3β-corner is often found as a building block in protein structures, such as β-barrels, -sandwiches, and -sheets/-layers.

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Section: Discussionmentioning

confidence: 92%

Biological Role of the 3β-Corner Structural Motif in Proteins

et al. 2022

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“…If the RMSD value is below 5 Å (Angstrom), it can be said to be a relatively stable value in molecular dynamics simulations. In contrast, if it is above 5 Å, it indicates significant conformational changes and large structural changes and means low stability (Rudnev et al, 2022). The flexibility of the structure of each compound can influence conformational changes over time.…”

Section: Analysis Of Molecular Dynamics Simulation Resultsmentioning

confidence: 99%

Analysis of Molecular Docking and Dynamics Simulation of Mahogany (Swietenia macrophylla King) Compounds Against the PLpro Enzyme SARS-COV-2

Lalu Sanik Wahyu Fadil Amrulloh,

Nuraini Harmastuti,

Andri Prasetiyo

et al. 2023

JFIKI

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Background: Using natural ingredients as antivirals can be considered a treatment for SARS-CoV-2. One of the potential plants, mahogany (Swietenia macrophylla King), is widely used in various countries as an antiviral treatment. Paparin-like protease (PLpro) is an essential cysteine protease that regulates viral replication and interferes with the regulation of immune sensing. Objective: This study aims to predict which compounds in the mahogany plant have good affinity, patterns, and stability interaction against the target protein of SARS-CoV-2. Methods: The drug-likeness parameter using SwissADME was used to screen compounds that will be docked against PLpro using the Autodock program. The parameters observed in molecular docking analysis are the value of bond energy and interaction model to amino acid residues. The compounds in mahogany plants that have the best interactions were then analyzed using molecular dynamics simulation methods to determine the stability of their bonds based on the values of Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). Results: Twenty-two compounds met the drug-likeness requirements. Molecular docking analysis showed that the compounds predicted to have the best binding affinity and have an interaction pattern similar to natural ligands towards the molecular target of PLpro are 7-deacetoxy-7-oxogedunin and 3β-hydroxy-stigmast-5-en-7-one. The molecular dynamics simulation results revealed that based on the RMSD and RMSF values, the compound 3β-hydroxy-stigmast-5-en-7-one showed higher stability than 7-deacetoxy-7-oxogedunin. Conclusion: 3β-hydroxy-stigmast-5-en-7-one and 7-deacetoxy-7-oxogedunin were predicted to have good interaction with PLPro; however, 3β-hydroxy-stigmast-5-en-7-one showed the higher interaction stability.

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“…These non-canonical amino acid residues that are located in the border zone can be misrecognized with STRIDE, DSSP, etc. [40,41]. The occurrence of modification sites in β-strands and α-helices is also quite high: ~21% and 6%, respectively (Figure 2b).…”

Section: Phosphorylated Proteins In Pdbmentioning

confidence: 96%

Analysis of Structural Changes in the Protein near the Phosphorylation Site

Nikolsky,

Kulikova,

Petrovskiy

et al. 2023

Biomolecules

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Modification of the protein after synthesis (PTM) often affects protein function as supported by numerous studies. However, there is no consensus about the degree of structural protein changes after modification. For phosphorylation of serine, threonine, and tyrosine, which is a common PTM in the biology of living organisms, we consider topical issues related to changes in the geometric parameters of a protein (Rg, RMSD, Cα displacement, SASA). The effect of phosphorylation on protein geometry was studied both for the whole protein and at the local level (i.e., in different neighborhoods of the modification site). Heterogeneity in the degree of protein structural changes after phosphorylation was revealed, which allowed for us to isolate a group of proteins having pronounced local structural changes in the neighborhoods of up to 15 amino acid residues from the modification site. This is a comparative study of protein structural changes in neighborhoods of 3–15 amino acid residues from the modified site. Amino acid phosphorylation in proteins with pronounced local changes caused switching from the inactive functional state to the active one.

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3β-Corner Stability by Comparative Molecular Dynamics Simulations

Cited by 7 publications

References 25 publications

Biological Role of the 3β-Corner Structural Motif in Proteins

Biological Role of the 3β-Corner Structural Motif in Proteins

Analysis of Molecular Docking and Dynamics Simulation of Mahogany (Swietenia macrophylla King) Compounds Against the PLpro Enzyme SARS-COV-2

Analysis of Structural Changes in the Protein near the Phosphorylation Site

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