Mass spectrometry-complemented molecular modeling predicts the interaction interface for a camelid single-domain antibody targeting the Plasmodium falciparum circumsporozoite protein’s C-terminal domain

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 3300 - 3314

Published: Aug. 28, 2024

Bioanalytical methods that enable rapid and high-detail characterization of binding specificities strengths protein complexes with low sample consumption are highly desired. The interaction between a camelid single domain antibody (sdAbCSP1) its target antigen (PfCSP-Cext) was selected as model system to provide proof-of-principle for the here described methodology.

Language: Английский

---

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

Published: Nov. 10, 2024

Abstract The simultaneous identification of proteins as well their conformations in a biological system would greatly enhance our understanding cellular mechanisms and disease. As an emerging technique, native proteomics analyzes states, facilitating the acquisition protein stoichiometry, post-translational modifications (PTMs), interactions with ligands. However, revealing at proteome scale remains significant challenge. In this study, we propose AI-assisted method that integrates structure prediction (PSP) module top-down (TDP) mass spectrometry (nMS) to acquire both identity conformations. First, sequences PTMs are obtained using TDP method, while solvent-accessible surface area (SASA) is measured parallel by nMS. These data then input into PSP most probable conformation under nMS experimental conditions. We validate feasibility accuracy through analysis globular intrinsically disordered protein. Additionally, apply approach delineate ribosomal pre- post-assembly. Interactions drug molecules also explored. By enabling characterization from relatively small amounts endogenous proteins, bridge gap between structural biology conventional technologies.

Language: Английский

---

Investigation on topology-dependent adsorption and aggregation of protein on nanoparticle surface enabled by integrating time-limited proteolysis with cross-linking mass spectrometry

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: unknown, P. 138511 - 138511

Published: Dec. 1, 2024

Language: Английский

---

Rational design of¹⁹F NMR labelling sites to probe protein structure and interactions

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 12, 2024

Abstract Proteins are investigated in increasingly more complex biological systems, where 19 F NMR is proving highly advantageous due to its high gyromagnetic ratio and background-free spectra. Its application has, however, been hindered by limited chemical shift dispersions an incomprehensive relationship between shifts protein structure. We exploit the sensitivity of ring currents designing labels with direct contact a native or engineered aromatic ring. Fifty variants predicted AlphaFold molecular dynamics simulations show 80-90% success rates correlations their experimental magnitude current. Our method consequently improves dispersion through simple 1D experiments enables structural analyses alternative conformational states, including ribosome-bound folding intermediates, in-cell measurements thermodynamics protein-protein interactions. strategy thus provides sensitive tool extract residue restraints from for previously intractable systems.

Language: Английский

---