NAISS
SUPR
NAISS Projects
SUPR
Water inside the ring: interior hydration effects on gas-phase annular proteins for single-particle imaging
Dnr:

NAISS 2026/4-1442

Type:

NAISS Small

Principal Investigator:

Xinyue Gao

Affiliation:

Uppsala universitet

Start Date:

2026-09-14

End Date:

2027-10-01

Primary Classification:

10408: Biochemistry

Webpage:

Allocation

Abstract

Single-particle imaging (SPI) at intense X-ray free-electron lasers is a promising approach to determine the structure of biological molecules without crystallization. A key challenge is understanding how the hydration layer proteins carry into the gas phase affects their structure and the resulting diffraction patterns. Our group has performed molecular dynamics (MD) simulations of the 12-subunit erythrocruorin complex (PDB: 2GTL, ~3.6 MDa) in the gas phase with varying hydration shell thicknesses (0–2.0 nm), using GROMACS with the CHARMM27 force field and TIP3P water. Theoretically a protein's backbone will constract lack of hydrogen bonds. A central finding is that the optimal shell thickness for preserving the protein radius of gyration is approximately 1.5 nm, while thicker shells (~2 nm) produce significant outward dilation. This dilation is partly attributed to hydrostatic pressure from water enclosed in 2GTL's large central pore at the beginning of simulation. This project extends that work to proteins with a topological hole through their center that retains a confined population of water regardless of the external shell thickness. The key question is whether this interior water acts as an internal pressure source coupling to the outer protein scaffold, producing structural effects additional to those from the external shell. This is relevant for a whole class of biologically important ring-shaped complexes that are natural targets for SPI. We will run gas-phase MD simulations of three target systems: PCNA (PDB: 1AXC), TRAP (PDB: 1C9S), and GroEL (PDB: 1GRL). GroEL is particularly relevant as it is the first isolated protein complex observed at an XFEL-SPI. For each system we simulate: pure protein, thin water shell, thick water shell. Primary observables are radius of gyration, per-subunit RMSD, interior water density profiles, and simulated X-ray diffraction patterns.