University of Notre Dame

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Computational Studies on HMG-CoA Reductases and Other Biomolecular Systems

posted on 2024-03-25, 02:17 authored by Himani N. Patel

HMG-CoA reductases are four electron oxidoreductases that process three substrates in the same active site. The computational studies performed using theozyme (DFT) and QM/MM models show that the thiohemiacetal decomposition reaction, that occurs between the two hydride transfer reactions, has an energy barrier of ~ 7 kcal/mol in presence of cofactor NADH. MD simulations performed using a transition state force field (TSFF) for this reaction show that two hydrogen bonds of the nicotinamide and ribose moieties of NADH are necessary for maintaining the TS geometry.

Experimental studies of PmHMGR with different intermediates are challenging because the optimum activity for the reductive reaction occurs at the crystallization pH. pH-jump experiments have been used to obtain time-dependent crystal structures for the oxidative reaction, whose optimum activity is at pH 9. All-atom MD simulations were used to probe all possible protonation states of catalytic residues to investigate the variations in the optimum pH for the reductive and oxidative reactions. The favorable protonation states system, in presence of mevaldehyde and NADH, had a positively charged His381, a neutral Glu83, and an HIE-neutral His385. A photocaged substrate (pHP-HMG-CoA) would also facilitate time-dependent crystallography by restoring the substrate activity after the cleavage of the covalently bound photoprotecting group (pHP). MD simulations performed on select binding poses of the photocaged HMG-CoA in PmHMGR, in the presence and absence of the flap domain, show that the proximity of the photocaged substrate to the binding site is maintained in presence of the flap domain. This suggests soaking the PmHMGR crystals in photocaged substrate and cofactor since the flap domain only closes over the active site in presence of both ligands.

To crystallize Staphylococcus aureus HMGR, its surface residues were mutated guided by the crystal structure of EfHMGR. The initial 25 aa mutant was challenging to purify but a single shortened loop mutant was easier to purify and was used in crystallization screening experiments. Two other regional mutants were suggested and are currently being investigated in the Stauffacher lab at Purdue University.

Stabilized helices have been used to target protein-protein interactions in biomolecular systems. Classical MD simulations of N-aminated peptides at the eVP40 dimeric interface show conservation of helicity in ~4 hydrophobic residues at the center of the stabilized helix.

Engineering large proteins such as SpCas9 in order to add functionality through domain insertions is of great interest albeit a labor-intensive process. RMSF analysis from long timescale (1 μs) all-atom MD simulations shows a good correlation to the experimental domain insertion hotspots. This indicates that MD simulations can be used to guide protein engineering.


Date Modified


Defense Date


CIP Code

  • 40.0501

Research Director(s)

Olaf G. Wiest


  • Doctor of Philosophy

Degree Level

  • Doctoral Dissertation

Alternate Identifier


OCLC Number


Program Name

  • Chemistry and Biochemistry

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