Molecular Dynamics-Driven Engineering in Non-ribosomal Peptide Synthetase 5N9X

Molecular Dynamics-Driven Engineering in Non-ribosomal Peptide Synthetase 5N9X

This project involved applying Molecular Dynamics (MD) simulations to study the Streptomyces adenylation–thiolation domain (PDB 5N9X) in non-ribosomal peptide synthetase (NRPS) pathways. Developed and implemented full MD workflows using the AMBER software suite on high-performance computing clusters, including parameterisation of ligands, system minimisation, equilibration, and production runs. Investigated substrate adenylation and thiolation steps, analysing conformational dynamics and catalytic geometries using Chimera and cpptraj.

Naim Ahmed

Protein dynamics, Computer simulations, Enzyme research, Drug discovery, Antibiotics, Protein flexibility, Molecular modelling, Catalysis, Protein design, Structural modelling, Bioinformatics, Computational chemistry, Protein function, Enzyme flexibility, Biotechnology, Synthetic biology, Protein structures, Protein–ligand interactions, Enzyme engineering, Molecular biology, Molecular Dynamics, AMBER, Protein Simulation, Computational Biochemistry, Structural Biology, NRPS, Nonribosomal Peptide Synthetase, Adenylation, Thiolation, ATP, Magnesium coordination, PPant arm, Enzyme Mechanism, Conformational Dynamics, High Performance Computing, ChimeraX, cpptraj, Parameterisation, Force Fields, Protein Engineering