Kinetic proofreading by the cavity system of myoglobin: protection from poisoning

Radding, Wilson; Phillips, George N.

doi:10.1002/bies.20010

Cited by 17 publications

(19 citation statements)

References 103 publications

(125 reference statements)

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“…b Relative CO occupancy (in percent) of each site calculated from the sum of occurrences in all trajectories at 200, 300, or 320 K. their distribution and localization inside proteins, as well as their hydration. Both crystallographic studies and MD simulations performed on wild-type or mutant myoglobins (Elber and Karplus 1990;Carlson et al 1996;Hummer et al 2004;Radding and Phillips 2004;Bossa et al 2005), hemoglobin , and truncated Hb (Milani et al 2004) suggested that internal cavities play a functional role and partly determine the protein reactivity by defining preferred diffusion pathways and providing transient docking sites for ligands.…”

Section: Internal Cavitiesmentioning

confidence: 99%

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

Mouawad¹,

Tétreau²,

Abdel‐Azeim³

et al. 2007

Protein Science

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Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450 cam (camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450 cam (cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics. (Srajer et al. 2001;Bourgeois et al. 2003;Schotte et al. 2003;Hummer et al. 2004), cryocrystallography (Brunori et al. 2000Chu et al. 2000;Ostermann et al. 2000;Schlichting 2000), spectroscopy (Engler et al. 2000;Lamb et al. 2002;Nienhaus et al. 2002;Kriegl et al. 2003), kinetic competition experiments with xenon (Scott and Gibson 1997;Scott et al. 2001; Nienhaus et al. 2003a,b;Tetreau et al. 2004, and molecular dynamics (MD) simulations (Elber and Karplus 1990;Carlson et al. 1996;Meller and Elber 1998;Amara et al. 2001;Mouawad et al. 2005). Article published online ahead of print. Article and publication date are at

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Section: Internal Cavitiesmentioning

confidence: 99%

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

Mouawad¹,

Tétreau²,

Abdel‐Azeim³

et al. 2007

Protein Science

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“…Mb is a small globular protein that functions as an oxygen transport, storage, and mobile buffer protein in muscle 24. Mb folds as a compact monomer and does not undergo large conformational changes in comparison with multidomain proteins, but localized changes are observed17 as it reversibly binds various ligands,11, 25 and with pH variation 26.…”

Section: Introductionmentioning

confidence: 99%

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments

et al. 2007

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Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a range of crystallization conditions, often resulting in different space groups and changes in the packing arrangements. Three high resolution structures of myoglobin (Mb) in different crystal space groups are presented, including one in a new space group P6(1)22 and two structures in space groups P2(1)2(1)2(1) and P6. We compare coordinates and anisotropic displacement parameters (ADPs) from these three structures plus an existing structure in space group P2(1). While the overall changes are small, there is substantial variation in several external regions with varying patterns of crystal contacts across the space group packing arrangements. The structural ensemble containing four different crystal forms displays greater conformational variance (Calpha rmsd of 0.54-0.79 A) in comparison to a collection of four Mb structures with different ligands and mutations in the same crystal form (Calpha rmsd values of 0.28-0.37 A). The high resolution of the data enables comparison of both the magnitudes and directions of ADPs, which are found to be suppressed by crystal contacts. A composite dynamic profile of Mb structural variation from the four structures was compared with an independent structural ensemble developed from NMR refinement. Despite the limitations and biases of each method, the ADPs of the crystallographic ensemble closely match the positional variance from the solution NMR ensemble with linear correlation of 0.8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure.

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“…Myoglobin (Mb) is a heme protein that reversibly binds diatomic oxygen and other small gaseous ligands such as carbon monoxide (CO) and nitric oxide and serves as a mobile oxygen buffer in muscle (Radding & Phillips, 2004;Springer et al, 1994). Owing to its simple well characterized structure, the presence of a photolabile bond between the ligand and the heme iron (Gibson & Ainsworth, 1957) and the availability of a large number of mutants with altered functional and kinetic properties, Mb is an appealing model for protein dynamics and has been thoroughly studied by various biophysical techniques (Brunori et al, 2004;Bourgeois et al, 2003;Nienhaus et al, 2003;Srajer et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

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

Aranda¹,

Levin²,

Schotte³

et al. 2006

Acta Crystallogr D Biol Cryst

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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.

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Kinetic proofreading by the cavity system of myoglobin: protection from poisoning

Cited by 17 publications

References 103 publications

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments

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

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Kinetic proofreading by the cavity system of myoglobin: protection from poisoning

Cited by 17 publications

References 103 publications

CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations

CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments

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

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CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations

CO migration pathways in cytochrome P450_cam studied by molecular dynamics simulations