Elucidating the pH-Dependent Conformational Dynamics in Coronavirus Spike Proteins

We need a postdoctoral researcher to investigate the pH-dependent structural dynamics and receptor-binding behaviour of coronavirus spike proteins across multiple variants. The project will focus on understanding how environmental conditions, such as pH, influence spike protein conformational states, ACE2 binding, and viral infectivity.

The research will integrate all-atom molecular dynamics simulations, structural modelling, and quantitative analysis of biomolecular interactions to characterise how spike proteins from SARS-CoV-2 variants (e.g. wild-type, Omicron and emerging strains) respond to physiologically relevant pH conditions. Particular emphasis will be placed on how protonation states and environmental factors drive conformational transitions, structural stability, and compaction or aggregation behaviour, and how these changes modulate receptor recognition and immune evasion.

Building on prior work in pH-dependent protein dynamics and biomolecular interactions, the project will extend these principles to complex viral systems, enabling mechanistic understanding of how environmental conditions regulate virus–host interactions. The work will include comparative analysis across variants and may integrate experimental collaborations to validate predicted structural and functional changes.

The overall aim is to generate mechanistic insights that can inform variant-adapted vaccine design, improved diagnostics, and preparedness for future coronavirus outbreaks.

The position will join the Multiscale Simulation, Modelling & Design (MSMD) group at the Bioinformatics Institute (BII), A*STAR (https://www.a-star.edu.sg/bii/research/bsmd/msmd).

Requirements

The role requires a PhD in computational chemistry, computational biophysics, computational biology, or a related discipline, with strong expertise in molecular dynamics simulations and biomolecular modelling.

Essential experience includes:

• Extensive experience in all-atom molecular dynamics simulations of biomolecular systems
• Analysis of protein structural dynamics, conformational transitions, and stability under varying environmental conditions (e.g. pH, ionic strength)
• Experience in studying biomolecular binding interactions, including protein–protein, protein–receptor, or protein–ligand systems
• Ability to analyse and interpret binding modes, interaction networks, and structural determinants of molecular recognition
• Strong ability to interpret simulation results in a biological and mechanistic context

Desirable skills include:

• Experience with simulation packages (e.g. GROMACS, AMBER, CHARMM) and associated analysis tools
• Familiarity with enhanced sampling methods or binding free energy approaches (e.g. MM/PBSA or related techniques)
• Experience in trajectory analysis and handling large-scale simulation datasets
• Scripting/programming skills (e.g. Python, Bash) for data analysis and workflow automation
• Experience collaborating on interdisciplinary or experimental-led projects

A strong publication record in computational biomolecular research or molecular simulation studies is advantageous.