Structural Characterization of Synthetic and Protein-Bound Porphyrins in Terms of the Lowest-Frequency Normal Coordinates of the Macrocycle

Abstract

The X-ray crystal structures of synthetic and protein-bound metalloporphyrins are analyzed using a new normal structural decomposition method for classifying and quantifying their out-of-plane and in-plane distortions. These distortions are characterized in terms of equivalent displacements along the normal coordinates of the D 4h -symmetric porphyrin macrocycle (normal deformations) by using a computational procedure developed for this purpose. Often it turns out that the macrocyclic structure is, even in highly distorted porphyrins, accurately represented by displacements along only the lowest-frequency normal coordinates. Accordingly, the macrocyclic structure obtained from just the out-of-plane normal deformations of the saddling (sad, B 2u )-, ruffling (ruf, B 1u )-, doming (dom, A 2u )-, waving [waV(x), waV(y); E g ]-, and propellering (pro, A 1u )-type essentially simulates the out-of-plane distortion of the X-ray crystal structure. Similarly, the observed inplane distortions are decomposed into in-plane normal deformations corresponding to the lowest-frequency vibrational modes including macrocycle stretching in the direction of the meso-carbon atoms (meso-str, B 2g ), stretching in the direction of the nitrogen atoms (N-str, B 1g ), x and y pyrrole translations [trn(x), trn(y); E u ], macrocycle breathing (bre, A 1g ), and pyrrole rotation (rot, A 2g ). The finding that the displacements of the 24 atoms of the macrocycle primarily occur along the lowest-frequency normal coordinates is expected on physical grounds and is verified by structural decomposition of more than 100 synthetic and 150 protein-bound metalloporphyrin X-ray crystal structures. Because of the high resolution of the X-ray crystal structures of synthetic metalloporphyrins, the small displacements for other normal coordinates are also able to be discerned. However, for the heme groups in proteins, only the displacements along the lowest-frequency modes are detectable because of the large uncertainties in the atomic positions. The heme groups in the four X-ray crystal structures of deoxyhemoglobin are used to evaluate the structural decomposition method. We find that the corresponding heme groups in different X-ray crystal structures are similar. Furthermore, the outof-plane distortions for the heme groups in the R-and -chains are found to be inequivalent, that is, the two

Structural evidence for substrate strain in antibody catalysis

“…The porphyrin conformation observed in the crystal structure of Fab-MP complex agrees with prior resonance Raman spectroscopy data, which indicate an up-anddown tilting of the pyrrole rings, based on the observation of specific out-of-plane vibration mode (20). A normal mode decomposition analysis (21), which deconstructs porphyrin deformations into low-frequency normal coordinate displacements, shows a moderate doming (A2u) deformation, as well as strong saddling (B2u) and ruffling (B1u) deformations for the antibody-bound MP.…”

Electronic properties of the highly ruffled heme bound to the heme degrading enzyme IsdI

“…A total of 252 water molecules and 2 Mg 2þ ions were modeled around the protein. The extent of heme ruffling in the final IsdIFe 3þ CN structure was analyzed using the NSD) program (20). Graphic renderings of the structure were created with PyMOL (Schrödinger).…”

“…Normal-coordinate structural decomposition (NSD) analysis (20) reveals that the heme at the active sites of these enzymes is distorted 2.1 Å out of plane, far more than has been observed for any other heme-binding protein. This distinctive structural characteristic has been suggested to be a major factor in the mechanism by which these enzymes oxidize heme (4,5,19).…”

Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c

“…Systematic analysis of X-ray crystal structures of heme proteins has shown that the proteins belonging to the same functional class share similar out-of-plane (OOP) heme distortions (4)(5)(6). These protein-induced OOP distortions are energetically unfavorable for the heme, and their evolutionary conservation implies that they have biological significance.…”