Time dependent dihedral angle oscillations of the spike protein of SARS-CoV-2 reveal favored frequencies of dihedral angle rotations.

Publication date: Feb 09, 2024

The spike protein of SARS-CoV-2 is critical to viral infection of human host cells which ultimately results in COVID-19. In this study we analyzed the behavior of dihedral angles (phi and psi) of the wild-type spike protein over time from molecular dynamics and identified that their oscillations are dominated by a few discrete, relatively low frequencies in the 23-63 MHz range with 42. 969 MHz being the most prevalent frequency sampled by the oscillations. We thus observed the spike protein to favor certain frequencies more than others. Gaps in the tally of all observed frequencies for low-abundance amino acids also suggests that the frequency components of dihedral angle oscillations may be a function of position in the primary structure since relatively more abundant amino acids lacked gaps. Lastly, certain residues identified in the literature as constituting the inside of a druggable pocket, as well as others identified as allosteric sites, are observed in our data to have distinctive time domain profiles. This motivated us to propose additional residues with similar time domain profiles, which may be of potential interest to the vaccine and drug design communities for further investigation. Thus these findings indicate that there is a particular frequency domain profile for the spike protein hidden within the time domain data and this information, perhaps with the suggested residues, might provide additional insight into therapeutic development strategies for COVID-19 and beyond.

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Concepts Keywords
969mhz COVID-19
Abundant Dihedral angles
Host Spike protein
Molecular Therapeutics
Vaccine

Semantics

Type Source Name
disease VO time
disease MESH viral infection
disease IDO host
disease MESH COVID-19
disease VO frequency
drug DRUGBANK Amino acids
disease VO vaccine
drug DRUGBANK Coenzyme M
disease VO organization
disease IDO pathogen
drug DRUGBANK Angiotensin II
disease MESH death
disease MESH infections
disease IDO infection
disease VO USA
drug DRUGBANK Water
disease VO volume
drug DRUGBANK L-Lysine
drug DRUGBANK L-Arginine
disease IDO algorithm
disease VO population
drug DRUGBANK Methionine
drug DRUGBANK L-Tryptophan
drug DRUGBANK Esomeprazole
drug DRUGBANK Glycine
drug DRUGBANK Serine
drug DRUGBANK L-Threonine
drug DRUGBANK L-Phenylalanine
drug DRUGBANK L-Valine
drug DRUGBANK L-Asparagine
drug DRUGBANK Alpha-Linolenic Acid
drug DRUGBANK L-Leucine
drug DRUGBANK L-Aspartic Acid
drug DRUGBANK Glutamic Acid
drug DRUGBANK L-Isoleucine
drug DRUGBANK L-Tyrosine
disease VO Glycoprotein
disease IDO cell
disease VO dose
disease VO effectiveness
disease MESH emergency
drug DRUGBANK Diethylstilbestrol
disease IDO infectivity

Original Article

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