Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens

X Nuqui, L Casalino, L Zhou, M Shehata… - Nature …, 2024 - nature.com
The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-
19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that …

Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents

F Waibl, F Casagrande, F Dey… - Journal of Chemical …, 2024 - ACS Publications
Macrocycles are a promising class of compounds as therapeutics for difficult drug targets
due to a favorable combination of properties: They often exhibit improved binding affinity …

Engineering of pH-dependent antigen binding properties for toxin-targeting IgG1 antibodies using light-chain shuffling

T Tulika, F Ruso-Julve, S Ahmadi, A Ljungars… - Structure, 2024 - cell.com
Immunoglobulin G (IgG) antibodies that bind their cognate antigen in a pH-dependent
manner (acid-switched antibodies) can release their bound antigen for degradation in the …

GRACE: Generative Redesign in Artificial Computational Enzymology

RE Hu, CH Yu, IS Ng - ACS Synthetic Biology, 2024 - ACS Publications
Designing de novo enzymes is complex and challenging, especially to maintain the activity.
This research focused on motif design to identify the crucial domain in the enzyme and …

[HTML][HTML] On the specificity of the recognition of m6A-RNA by YTH reader domains

J Widmer, A Vitalis, A Caflisch - Journal of Biological Chemistry, 2024 - Elsevier
Most processes of life are the result of polyvalent interactions between macromolecules,
often of heterogeneous types and sizes. Frequently, the times associated with these …

Thermostability Enhancement of Tagatose 4-Epimerase through Protein Engineering and Whole-Cell Immobilization

Z Liu, X Guo, Y Xu, J Wu - Journal of Agricultural and Food …, 2025 - ACS Publications
d-Tagatose, a rare sugar endowed with a low-calorie property, superior taste quality, and
probiotic functionality, has garnered significant research attention. However, the prevailing …

Partition analysis of dipole moments in solution applied to functional groups in polypeptide motifs

DG Fedorov - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
A partition analysis based on segments is developed for density functional theory defining
solute dipole moments of functional groups, and the corresponding induced solvent dipoles …

In silico evolution of globular protein folds from random sequences

H Sahakyan, S Babajanyan, YI Wolf, EV Koonin - bioRxiv, 2024 - biorxiv.org
The origin and evolution of protein folds are among the most challenging, long-standing
problems in biology 1, 2. Although many plausible scenarios of early protein evolution …

Structural basis of broad protection against influenza virus by a human antibody targeting the neuraminidase active site via a recurring motif in CDR H3

G Jo, S Yamayoshi, KM Ma, O Swanson, JL Torres… - bioRxiv, 2024 - biorxiv.org
Influenza viruses evolve rapidly, driving seasonal epidemics and posing global pandemic
threats. While neuraminidase (NA) has emerged as a vaccine target, shared molecular …

De novo designed pMHC binders facilitate T cell induced killing of cancer cells

KH Johansen, D Wolff, B Scapolo… - bioRxiv, 2024 - biorxiv.org
The recognition of intracellular antigens by CD8+ T cells through T cell receptors (TCRs) is
central to adaptive immunity, enabling responses against infections and cancer. The recent …