Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions

Agamennone, Mariangela; Nicoli, Alessandro; Bayer, Sebastian; Weber, Verena; Borro, Luca; Gupta, Satish; Fantacuzzi, Marialuigia; Pizio, Antonella Di

doi:10.1016/bs.mcb.2021.06.012

“…As introduced above, to visualize MD analysis results, VMD has been widely used. In their very complete review on the visualization of biomolecular interactions [ 103 ], Agamennone et al show how Visual Molecular Dynamics (VMD) [ 95 ] can be used to retrieve dynamic interface information from an MD trajectory of the spike RBD-ACE2 complex. More specifically, in this example, the stability of the contacts is measured by monitoring the occupancy of hydrogen bonds along time.…”

Section: Tools For Calculating Ppi Dynamicsmentioning

confidence: 99%

Modeling the Dynamics of Protein–Protein Interfaces, How and Why?

Karaca

¹

,

Prévost

²

,

Sacquin-Mora

³

2022

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Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface.

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“…One is the usual protein-protein interactions (PPI) and the other is the protein-glycan interactions (PGI). The PPI ensures the formation of a stable complex of spike protein with angiotensin converting enzyme 2 (ACE2) by electrostatic forces, hydrogen bonding, and hydrophobic effect (Agamennone et al, 2021;Jones & Thornton, 1995) whereas PGI serves as the preliminary point of contact for priming the interactions (Gimeno et al, 2020;Raman et al, 2016). In the case of the recent variant of SARS-CoV-2 (Omicron), the 452-498 loop in the receptor-binding domain (RBD) of spike protein plays a significant role in PPI (Baral et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern

Madasu

¹

,

Maity

²

,

Ghosh

³

et al. 2022

Journal of Biomolecular Structure and Dynamics

3

0

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The prefatory protein-glycan interaction and stabilizing protein-protein interaction of severe acute respiratory syndrome viruses with angiotensin-converting enzyme 2 play a significant role in complex formation thereby promoting endocytosis. The microevolution of SARS-CoV-2 over a period of time has a significant role in increasing the affinity of receptor-binding domain against angiotensin converting-enzyme 2. In the current study, we have corroborated the vitality of acquired SNPs over a period of time with increased affinity by using docking studies. The results indicate that the virus modulates the undesirable glycosylation sites by a series of substitution and deletion mutations. It uses bulky residues such as Tyr/Phe for dynamic arrest for quick stabilization of the complex, and Lys residues for stabilizing via hydrogen bond formation besides increasing the binding affinity to ease the cell entry.

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Insights into the microevolution of SARS-ACE2 Interactions: In-silico analysis of glycosylation and SNP pattern

Madasu

¹

,

Maity

²

,

Ghosh

³

et al. 2022

Preprint

0

View full text Add to dashboard Cite

The prefatory protein-glycan interaction and stabilizing protein-protein interaction of severe acute respiratory syndrome viruses with angiotensin-converting enzyme 2 play a significant role in complex formation thereby promoting endocytosis. The microevolution of SARS-CoV-2 over a period of time has a significant role in increasing the affinity of receptor-binding domain against angiotensin converting-enzyme 2. In the current study, we have corroborated the vitality of acquired SNPs over a period of time with increased affinity by using docking studies. The results indicate that the virus modulates the undesirable glycosylation sites by a series of substitution and deletion mutations. It uses bulky residues such as Tyr/Phe for dynamic arrest for quick stabilization of the complex, and Lys residues for stabilizing via hydrogen bond formation besides increasing the binding affinity to ease the cell entry.

show abstract

Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions

Cited by 3 publications

References 150 publications

Modeling the Dynamics of Protein–Protein Interfaces, How and Why?

Modeling the Dynamics of Protein–Protein Interfaces, How and Why?

Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern

Insights into the microevolution of SARS-ACE2 Interactions: In-silico analysis of glycosylation and SNP pattern

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