SUPR
Molecular Dynamics Simulations of Metal-Binding Domains and Functional Intermediates in Membrane Proteins: Insights into CadA and LMCA1 Mechanisms
Dnr:

NAISS 2024/22-1265

Type:

NAISS Small Compute

Principal Investigator:

Fatemeh Sabzian Molaei

Affiliation:

Umeå universitet

Start Date:

2024-10-02

End Date:

2025-11-01

Primary Classification:

10402: Physical Chemistry

Webpage:

Allocation

Abstract

I am a PhD student in the Department of Chemistry at Umeå University, working on understanding how membrane proteins function using molecular dynamics (MD) simulations. My research focuses on two key projects: studying the metal-binding domains of the MMCadA protein, which is involved in metal ion transport, using GROMACS; and exploring the intermediate states of the calcium-transporting LMCA1 protein using both Targeted and Basic MD simulations. These studies aim to reveal important structural changes that occur during the proteins' functional cycles. To carry out these projects, I require significant computational power due to the complexity of the proteins and the long simulation times needed to capture their behavior. Access to HPC2N’s resources will allow me to efficiently perform the necessary simulations, leading to valuable insights into the mechanisms of ion transport and protein function. These results will contribute to a better understanding of the role of these proteins in biological systems.