New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …

[HTML][HTML] Integrating cellular electron microscopy with multimodal data to explore biology across space and time

CL McCafferty, S Klumpe, RE Amaro, W Kukulski… - Cell, 2024 - cell.com
Biology spans a continuum of length and time scales. Individual experimental methods only
glimpse discrete pieces of this spectrum but can be combined to construct a more holistic …

Molecular dynamics simulation of an entire cell

JA Stevens, F Grünewald, PAM van Tilburg… - Frontiers in …, 2023 - frontiersin.org
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's
components with atomic resolution. In contrast to their real-world counterparts …

Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses

EL Shrock, RT Timms, T Kula, EL Mena, AP West Jr… - Science, 2023 - science.org
Despite the vast diversity of the antibody repertoire, infected individuals often mount
antibody responses to precisely the same epitopes within antigens. The immunological …

Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities

L Casalino, C Seitz, J Lederhofer… - ACS Central …, 2022 - ACS Publications
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-
19 pandemic, raising serious concerns about the nature and magnitude of future epidemics …

Informing geometric deep learning with electronic interactions to accelerate quantum chemistry

Z Qiao, AS Christensen, M Welborn… - Proceedings of the …, 2022 - National Acad Sciences
Predicting electronic energies, densities, and related chemical properties can facilitate the
discovery of novel catalysts, medicines, and battery materials. However, existing machine …

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort

D Beltrán, A Hospital, JL Gelpí… - Nucleic Acids …, 2024 - academic.oup.com
Molecular dynamics (MD) simulations are keeping computers busy around the world,
generating a huge amount of data that is typically not open to the scientific community …

Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation

X Bogetti, A Bogetti, J Casto, G Rule, L Chong… - Protein …, 2023 - Wiley Online Library
The catalytic activity of human glutathione S‐transferase A1‐1 (hGSTA1‐1), a homodimeric
detoxification enzyme, is dependent on the conformational dynamics of a key C‐terminal …

Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors

K Kapoor, T Chen… - Proceedings of the …, 2022 - National Acad Sciences
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein is the
prime target for vaccines, diagnostics, and therapeutic antibodies against the virus. While …

[HTML][HTML] Molecular simulations of complex carbohydrates and glycoconjugates

E Fadda - Current Opinion in Chemical Biology, 2022 - Elsevier
Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in
nature. The broad diversity of biochemical functions that carbohydrates cover is a direct …