Speaker

Ricky B. Nellas, PhD
Professor, Institute of Chemistry, College of Science, University of the Philippines Diliman
Visiting Professor at IPR

Date&Time

July 2, 2026 (Thu) 10:00-11:30

Venue

IPR 1F Auditorium

Title

Revealing Hidden Protein Communication: From Allosteric Pockets to Glycan Shielding in Spike Protein Dynamics

Abstract

Proteins are dynamic molecular systems whose functions emerge from an ensemble of conformational states rather than from a single static structure. These motions influence molecular recognition, allosteric regulation, and the accessibility of potential therapeutic targets, yet many of the underlying mechanisms remain difficult to capture using experimental structures alone. In this seminar, I will discuss how computational approaches can be used to uncover hidden functional behavior in proteins and provide insights relevant to drug discovery. Using the SARS-CoV-2 spike protein as a model system, I will present case studies that explore how transient allosteric pockets, long-range communication networks, and glycan-mediated shielding collectively shape protein behavior and regulate the accessibility of potential binding sites. Through molecular simulations and contact- and network-based analyses, we identify cryptic pockets beneath the receptor-binding domains, map communication pathways connecting distant functional regions, and examine how glycans dynamically modulate pocket exposure across different conformational states. These case studies illustrate how computational approaches can uncover mechanistic insights beyond static structures and demonstrate the value of computational biology in complementing experimental approaches to understand protein function and guide the discovery of novel therapeutic strategies.

Contact

Taeko Yanagimoto
t-yanagimoto[at]protein.osaka-u.ac.jp (Please replace [at] with @.)