CO migration in native and mutant myoglobin: Atomistic simulations for the understanding of protein function

Abstract

Molecular dynamics simulations of the events after the photodissociation of CO in the myoglobin mutant L29F in which leucine is replaced by phenylalanine are reported. Using both classical and mixed quantum-classical molecular dynamics calculations, we observed the rapid motion of CO away from the distal heme pocket to other regions of the protein, in agreement with recent experimental results. The experimentally observed and calculated infrared spectra of CO after dissociation are also in good agreement. We compared the results with data from simulations of WT myoglobin. As the time resolution of experimental techniques is increased, theoretical methods and models can be validated at the atomic scale by direct comparison with experiment. R ecently, the time-resolved infrared spectrum and x-ray diffraction of photodissociated 13 CO in myoglobin (Mb) have been reported for a particular mutant, L29F (1). In this mutant the leucine (L) residue at position 29 is replaced by a phenylalanine (F) (see Fig. 1). This mutation introduces a bulky phenyl side chain into the distal heme pocket that can be expected to have an impact on the dynamics after photodissociation. It was previously found that the equilibrium constants for O 2 binding are larger by a factor of 15 in L29F compared to native Mb (2). This difference was interpreted as due to stabilizing interactions between the bound dioxygen and atoms of the phenyl ring. The infrared experiments, carried out at 283 K, found that the characteristic infrared absorption band for CO in the native Mb changes profoundly in the case of the L29F mutant (1). The well known bimodal distribution, indicative of the population of different binding sites [conformational substates B1 and B2, which differ in the orientation of the CO (3, 4), and possibly B3, which can only be populated by extended illumination in native MbCO (5)] is fundamentally altered. For L29F, the bimodal structure of the infrared spectrum disappears after Ϸ100 ps, whereas for native Mb it persists for 100 ns. This effect was explained by the escape of CO from the primary docking site within the distal heme pocket (Fig. 1) to neighboring sites within the protein on a time scale three orders of magnitude faster than in the case of native Mb (1).Previous theoretical investigations of the ligand dynamics of CO in myoglobin focused mostly on the short time scale and have considered effects after dissociation of the ligand from the iron on the picosecond time scale (6, 7). Some of the investigations used a three-site model for the CO ligand (8). This model correctly describes the static dipole and quadrupole moment of CO. Recently, we developed a refined model that uses fluctuating charges on the C and O atom sites and at the center of mass (9). This model reproduces high-level ab initio calculations of the dipole and quadrupole moment over a wide range of intermolecular separations (10, 11) and allows the calculation of the infrared spectrum associated with the CO vibration. The model correctly describes the experimen...

The Position 68(E11) Side Chain in Myoglobin Regulates Ligand Capture, Bond Formation with Heme Iron, and Internal Movement into the Xenon Cavities

“…Several simulations (23,24,26) and time-resolved x-ray crystallography studies (17,18) have shown that ligand trajectories from the distal pocket to Xe4 are the most probable route of ligand movement into the protein interior after photodissociation. For the H64L/V68F double mutant, the combination of reduced steric hindrance at the iron and partial filling of the Xe4 cavity combine to cause ϳ100% geminate recombination from the initial B state, and the observed kinetic phase can be assigned with certainty to geminate recombination from the initial docking site labeled as "B" in the structure of wild-type MbCO shown in Fig.…”

Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations

“…The photosensitive Fe-ligand bond has allowed transient intermediates to be studied by flash photolysis methods ranging from spectroscopy (1, 5-7) to x-ray crystallography (9)(10)(11)(12)(13)(14)(15)(16). Since the seminal work of Case and Karplus (17), Mb has also been the target of molecular dynamics (MD) simulations (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). This combination of experimental and theoretical investigations has made Mb one of the most thoroughly studied proteins.…”

Determination of Ligand Pathways in Globins

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