PDBsum entry 2g0z

Transport protein

PDB id: 2g0z

Contents

Protein chain

154 a.a.

Ligands

SO4

HEM-CMO

Waters ×147

References listed in PDB file

Key reference

Title

Time-Dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin.

Authors

R.Aranda, E.J.Levin, F.Schotte, P.A.Anfinrud, G.N.Phillips.

Ref.

Acta Crystallogr D Biol Crystallogr, 2006, 62, 776-783. [DOI no: 10.1107/S0907444906017318]

PubMed id

16790933

Abstract

Picosecond time-resolved crystallography was used to follow the dissociation of carbon monoxide from the heme pocket of a mutant sperm whale myoglobin and the resultant conformational changes. Electron-density maps have previously been created at various time points and used to describe amino-acid side-chain and carbon monoxide movements. In this work, difference refinement was employed to generate atomic coordinates at each time point in order to create a more explicit quantitative representation of the photo-dissociation process. After photolysis the carbon monoxide moves to a docking site, causing rearrangements in the heme-pocket residues, the coordinate changes of which can be plotted as a function of time. These include rotations of the heme-pocket phenylalanine concomitant with movement of the distal histidine toward the solvent, potentially allowing carbon monoxide movement in and out of the protein and proximal displacement of the heme iron. The degree of relaxation toward the intermediate and deoxy states was probed by analysis of the coordinate movements in the time-resolved models, revealing a non-linear progression toward the unbound state with coordinate movements that begin in the heme-pocket area and then propagate throughout the rest of the protein.

Figure 2.
Figure 2 -Carbon difference distance matrices comparing the CO-bound `laser off' and 3.16 µs time-point models with deoxy-Mb. -Carbon difference distance matrices were made by comparing the CO-bound `laser off' and 3.16 µs model C^ atoms to deoxy-Mb C^ atoms (PDB code [207]1moa ). The gray boxes correspond to the eight Mb helices and values are -1 Å (brightest red) to 0 Å (white) to +1 Å (brightest blue). (a) is the C^ [208][alpha] difference distance matrix of (deoxy-Mb) - (CO-bound `laser off' Mb). (b) is the C^ [209][alpha] difference distance matrix of (deoxy-Mb) - (3.16 µs Mb).

Figure 4.
Figure 4 Electron-density maps of the various CO cavities. Electron-density maps were made by removing residues affected by CO photolysis and/or CO from the model and then calculating the [A]-weighted F[o] - F[c] maps. The labelled photolyzed residues and/or CO were reinserted to show that their placements fit with the F[o] - F[c] density at 3 . The CO-bound `laser off' model is represented by the purple coordinates, the photolyzed time points are represented by the green coordinates and the photolyzed CO in blue. Positive density in the F[o] - F[c] map is displayed in red and negative density is displayed in black at 3 . (a) shows the 100 ps F[o] - F[c] map with Phe29 and His64 from the photolyzed model and the primary docking site CO deleted. (b) shows the 316 ps F[o] - F[c] map with only the photolyzed COs removed and (c) shows the 316 ns F[o] - F[c] map with the CO removed from the proximal Xe1 site.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 776-783) copyright 2006.