Analysis of intermolecular coupling in heme compound dynamics using nuclear resonance vibrational spectroscopy
Abstract
Understanding the dynamics of heme proteins begins with analysis of the heme molecule, which is modeled by a wide array of Fe porphyrin/ligand complexes. We measure experimental Fe densities of state using nuclear resonance vibrational spectroscopy (NRVS). Normal mode analysis (NMA) is done by refining force constants to the experimental data. The resulting force field gives important information regarding heme dynamics. Single molecule NMA was done previously to refine the vibrational density of states (VDOS) for several porphyrin compounds. To simplify, speed up, and remove some of the randomness in the refining process a systematic algorithm was developed. Fe(II)octaethylporphyrin, Fe(OEP), the simplest possible heme compound was used to test the algorithm. A good quality fit was achieved for Fe(OEP), allowing the character of the modes to be identified. The results were in good agreement with both experimental data (Raman and Infrared spectroscopies) and theoretical calculations (Density Functional Theory). Single molecule NMA was also performed for a sequence of very similar porphyrins: (nitrosyl) iron (II) protoporphyrin, PPIX(NO), (nitrosyl) iron (II) mesoporphyrin, MPIX(NO), and (nitrosyl) iron (II) deuteroporphyrin, DPIX(NO). These three compounds demonstrated the value of the systematic refinement algorithm as convergence was achieved much faster. The results of this sequence of similar molecules suggested the importance of intermolecular coupling, i.e. going beyond the single molecule model of NMA. NMA was therefore modified to calculate the VDOS for an infinite crystal, not a single molecule. As a result, first of all, a better fit (especially in low frequency region) was obtained, which provides a more accurate picture of iron dynamics. Secondly, intermolecular coupling has replaced widely used before force constant coupling, which was widely used but is without physical justification. Thirdly, detailed mode analysis revealed that dispersion affects a number of the modes and some broadening in these modes has been seen as a result. This broadening was comparable or exceeded the instrumental resolution only for a few modes, but these modes were found to be mostly in the low frequency region, which is very important biologically. Lastly, introducing intermolecular interaction made possible investigating elastic properties of heme compounds and proteins. It was shown that the number of intermolecular bonds affects elastic parameters, such as speed of sound or elastic moduli. A good fit to the speed of sound in Fe(OEP) was achieved with a reasonable number of intermolecular bonds in this crystalline model. Thus, intermolecular coupling was proved to play an important role in Fe atom dynamics and crystal NMA was shown to be an excellent tool in its study.
Degree
Ph.D.
Advisors
Durbin, Purdue University.
Subject Area
Biophysics
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