2M30

Solution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods

Summary for 2M30

• Entry DOI: 10.2210/pdb2m30/pdb
• Related: 1R1U 1R1V 2KJB 2KJC
• NMR Information: BMRB: 7376
• Descriptor: Repressor protein, ZINC ION (2 entities in total)
• Functional Keywords: metal ion refinement, transcription repressor
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 2
• Total formula weight: 24146.23

Authors

Chakravorty, D.K.,Wang, B.I.,Lee, C.I.,Guerra, A.J.,Giedroc, D.P.,Merz Jr., K.M.,Arunkumar, A.I.,Pennella, M.,Kong, X. (deposition date: 2013-01-04, release date: 2013-05-08, Last modification date: 2024-05-01)

Primary citation

Chakravorty, D.K.,Wang, B.,Lee, C.W.,Guerra, A.J.,Giedroc, D.P.,Merz, K.M.
Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.
J.Biomol.Nmr, 56:125-137, 2013

PubMed Abstract: Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.

PubMed: 23609042
DOI: 10.1007/s10858-013-9729-7

Experimental method

SOLUTION NMR