Theoretical assessment of global and local motions in carbonmonoxy myoglobin and their functional significance

Date of Award




Degree Name

Doctor of Philosophy (Ph.D.)

First Committee Member

Jeffrey D. Evanseck - Committee Chair


The structural, dynamic and electronic origins of the spectroscopic A-states in carbonmonoxy myoglobin have been investigated using molecular dynamics to sample conformational space, principal component analysis (PCA) to aid in structural interpretations and quantum mechanics (restricted Hartree-Fock theory with the 6-31G* basis set) to compute ligand stretch frequencies. In vacuum, twenty one short (each of 95 ps duration) and one long (1 ns duration) trajectories were computed. In solvent, fifteen trajectories (400 ps) were created of which two were extended to 1200 ps. PCA provided between 25 and 65% of all structural variation of these high-dimensional ensembles for visualization in two dimensions and proved that multiple short-time trajectories provide a better sampling of conformational space than one long-time trajectory.The combination of two side chain movements involving His64 and Arg45 was found as the principal determinant of the spectroscopic A-states in carbonmonoxy myoglobin. Conformations with His64 more than 5A away from the CO ligand were defined as the A0-state with negligible electrostatic effect on nCO . The A1,2-state was assigned to conformations where His64 had rotated and formed a weak hydrogen bond with CO (difference between nCO (A0) and nCO (A1,2): -10 cm-1). The strongest red-shifted ligand frequency (A3-state) was computed with His64 hydrogen bonded to CO and in addition, Arg45 interacting with His64 at distances ≤ 5A (computed DnCO (A0,A3): -19 cm-1). Simulations with a His64 isomer protonated at the Ne atom showed an extremely strong hydrogen bond between His64 and CO and small structural fluctuations. Thus, this isomer could be ruled out as contributor to the A-states since it would not allow substate interconversion.Large-scale motions and transitions between substates in carbonmonoxy rnyoglobin were studied using conformational flooding. With this method slow conformational transitions are accelerated by energetically destabilizing the initial substate. Accordingly, transitions as slow as microseconds are expected to become observable in molecular dynamics simulations. Indeed, flooding simulations revealed a high flexibility in regions containing residues 35 to 50 (short helices C, D and CD loop, affecting distal heme pocket), residues 80 to 100 (F helix, EF and FG loops, affecting proximal pocket) and residues 120 to 140 (GH loop, H helix). The motions in residues 35 to 50 are directly relevant for the heme's accessibility to ligands or solvent. Movement of residues 80 to 100 opens the cleft formed by helices E and F and indirectly influences the solvent exposure of the heme.


Chemistry, Physical

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