Evolution of the SARS-CoV-2 Omicron spike

RJ Parsons, P Acharya - Cell reports, 2023 - cell.com
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of
concern, first identified in November 2021, rapidly spread worldwide and diversified into …

Mechanical communication within the microtubule through network-based analysis of tubulin dynamics

M Cannariato, EA Zizzi, L Pallante, M Miceli… - … and Modeling in …, 2024 - Springer
The identification of the mechanisms underlying the transfer of mechanical vibrations in
protein complexes is crucial to understand how these super-assemblies are stabilized to …

Exploring TAS2R46 biomechanics through molecular dynamics and network analysis

M Cannariato, R Fanunza, EA Zizzi, M Miceli… - Frontiers in Molecular …, 2024 - frontiersin.org
Understanding the intricate interplay between structural features and signal-processing
events is crucial for unravelling the mechanisms of biomolecular systems. G protein-coupled …

Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of the influenza A virus

JE Gonzales, I Kim, A Bastiray, W Hwang… - Proceedings of the …, 2025 - pnas.org
Viral proteins frequently mutate to evade host innate immune responses, yet the impact of
these mutations on the molecular energy landscape remains unclear. Epistasis, the …

Multiscale Computational Analysis of the Effect of Taxol on Microtubule Mechanics

M Cannariato, EA Zizzi, JA Tuszynski… - … Biomaterials Science & …, 2024 - ACS Publications
Microtubules (MTs) are widely recognized as targets for cancer therapies. They are directly
related to unique mechanical properties, closely dependent on MT architecture and tubulin …

Complementary Pocket and Network-Based Approach to Search for Spike Protein Allosteric Pocket Sites

RL Cheng, JC Quirante, LEZ Vargas, AF Gatchalian… - ACS …, 2023 - ACS Publications
COVID-19 is a persistent public health concern due to the emergence of more virulent and
contagious variants resulting from mutations in the spike protein. The spike protein in newer …

Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors

PD Manrique, IV Leus, CA López, J Mehla… - Communications …, 2024 - nature.com
The ability Gram-negative pathogens have at adapting and protecting themselves against
antibiotics has increasingly become a public health threat. Data-driven models identifying …

Molecular Biomechanics of the TAS2R46 Bitter Taste Receptor through Network-based Investigation

M Cannariato, R Fanunza, EA Zizzi, M Miceli… - bioRxiv, 2023 - biorxiv.org
The intricate relationship between structural characteristics and the resultant signal-
processing events is fundamental in comprehending the functions and mechanisms inherent …

Paired associated SARS-CoV-2 spike variable positions: a network analysis approach to emerging variants

Y Manoussopoulos, C Anastassopoulou… - Msystems, 2023 - journals.asm.org
Amino acids in variable positions of proteins may be correlated, with potential structural and
functional implications. Here, we apply exact tests of independence in R× C contingency …