Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. I. Carbon monoxide and dioxygen binding to four heme systems

Lopez, Marco A.; Kollman, Peter A.

doi:10.1021/ja00198a036

Cited by 32 publications

(20 citation statements)

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“…The distortion of the heme planarity suggests that there may be a significant amplitude to the oscillation of the atoms within the heme. A similar oscillation was also observed in the simulation of model iron porphyrin-ligand systems (Lopez & Kollman 1989). …”

supporting

confidence: 79%

“…The corresponding free energy change is = -RT In( 500) = -3.62 kcal. As reported previously (Lopez & Kollman, 1989), the value of AAG (expt1) This comparison assumes that the solubility of O2 and CO is the same in water and in the 2% aqueous soap solution, and that the difference between the Fe-02 and Fe-CO bond strengths are the same in the two aqueous systems. It further neglects the differences in histidine tautomers for the two bound Mb systems.…”

Section: Free Energy Resultsmentioning

confidence: 93%

“…In order to compare the calculated values with experimental values, we compared experimentaI and caIculated values for the difference in free energy between a test system and a control system in a previous study (Lopez& Kollman, 1989). The control system used in the experimental study is monochelated protoheme (mcph) (Traylor & Berziniz, 1980;Mims et al, 1983).…”

Section: Free Energy Resultsmentioning

confidence: 99%

“…Unlike previous work (Lopez & Kollman 1989) where the solvent effects were modeled with a constant dielectric, the present calculations model the solvent with a distance-dependent dielectric constant. The control system was also run through the perturbation calculation using a distance-dependent dielectric constant.…”

Section: Free Energy Resultsmentioning

confidence: 99%

“…The features of this model are as follows: (1) explicit water was not included; (2) a distance-dependent dielectric constant was employed; and (3) only those residues within 9 A of the binding site were allowed to move during the MD calculations. For comparison purposes with our earlier simulation (Lopez & Kollman, 1989), we also carried out simulations with E = 1, which led to a significant exaggeration of long-range effects. Thus, the distance-dependent dielectric model appears to be a reasonable and simple compromise to use for computational efficiency in lieu of explicit incorporation of solvent.…”

Section: Discussionmentioning

confidence: 99%

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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin‐ligand systems ii: Co and dioxygen binding to myoglobin

Lopez

Kollman

1993

Protein Science

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The protein contribution to the relative binding affinity of the ligands CO and O2 toward myoglobin (Mb) has been simulated using free energy perturbation calculations. The tautomers of the His E7 residue are different for the oxymyoglobin (MbO2) and carboxymyoglobin (MbCO) systems. This was modeled by performing two‐step calculations that mutate the ligand and mutate the His E7 tautomers in separate steps. Differences in hydrogen bonding to the O2 and CO ligands were incorporated into the model. The O2 complex was calculated to be 2–3 kcal/mol more stable than the corresponding CO complex when compared to the same difference in an isolated heme control. This value agrees well with the experimental value of 2.0 kcal/mol. In qualitative agreement with experiments, the Fe‐C‐O bond is found to be bent (θ = 159.8°) with a small tilt (ϕ = 6.2°). The contributions made by each of the 29 residues — within the 9.0‐Å radius of the iron atom — to the free energy difference are separated into van der Waals and electrostatic contributions; the latter contributions are dominant. Aside from the proximal histidine and the heme group, the residues having the largest difference in free energy in mutating MbO2 → MbCO are His E7, Phe CD1, Phe CD4, Val E11, and Thr E10.

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supporting

confidence: 79%

Section: Free Energy Resultsmentioning

confidence: 93%

Section: Free Energy Resultsmentioning

confidence: 99%

Section: Free Energy Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin‐ligand systems ii: Co and dioxygen binding to myoglobin

Lopez

Kollman

1993

Protein Science

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Iron Porphyrin Chemistry

Walker¹,

Simonis²

2005

Encyclopedia of Inorganic Chemistry

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This article reviews most aspects of the chemistry of iron porphyrins, from Fe(0) to Fe(V), including occurrence and roles of natural iron porphyrins (hemes) and their synthetic analogs, structures and electron configurations of iron porphyrins of all oxidation and spin states, π electron configuration of the porphyrin ring, synthesis of metal‐free porphyrins and other related macrocycles, insertion of iron into free‐base porphyrins and related macrocycles, the properties, reactions, uses and biological relevance of iron(0), ‐(I), ‐(II) porphyrins (the latter with S = 0, 1, and 2 spin state possibilities), of iron(II) porphyrin π‐cation radicals, of iron(III) porphyrins (with S = 1/2, 3/2, and 5/2 spin state possibilities), of iron(III) porphyrin and corrole π‐cation radicals, of iron(IV) porphyrins (including five‐ and six‐coordinate ferryl (FeO) 2+ , iron(IV) phenyl, carbene and hydrazine complexes, and the bis‐methoxide complex) and a comparison of iron(IV) porphyrins to iron(III) porphyrin π‐cation radicals, of iron(IV) porphyrin π‐cation radicals, and of the possible existence of iron(V) porphyrins. Included in the Fe(II) part are sections on addition of ligands to four‐coordinate iron(II) porphyrins, including equilibrium binding constants, photodissociation of ligands from PFeL 2 complexes, binding of small molecules (O 2 , CO, NO, HNO) to 5‐coordinate iron(II) porphyrins and design of porphyrin ligands that will mimic the active sites of heme proteins such as myoglobin and hemoglobin, the cytochromes P450 and nitric oxide synthases, and the nitrophorins and guanylyl cyclases. Included in the iron(III) part are sections on both 5‐ and 6‐coordinate high‐spin complexes and their similarities and differences, bridged or through‐space magnetically coupled complexes of high‐spin iron(III) porphyrins with other metal complexes as possible models for cytochrome oxidase and the assimilatory sulfite reductases, coupled oxidation of hemes by hydrogen peroxide or its equivalent, and the relationship of this reactivity to the reactions of heme oxygenase, iron(III) porphyrins as reduction catalysts, and photochemistry of iron(III) porphyrins, possible electron configurations of low‐spin iron(III) porphyrins, the phenomenon and possible electronic consequences of ruffling of the porphinato core in iron(III) porphyrins, the preferred orientation of planar axial ligands bound to low‐spin iron(III) porphyrins, NO complexes of iron(III) porphyrins, reduction potentials, equilibrium constants and rates of axial‐ligand addition and exchange, kinetics of axial‐ligand rotation and porphyrin ring inversion, kinetics of reduction and autoreduction of iron(III) porphyrins, electron self‐exchange between low‐spin iron(III) and iron(II) porphyrins, synthetic ferriheme proteins, and synthesis of five‐coordinate low‐spin iron(III) porphyrins having σ‐alkyl or σ‐aryl groups as axial ligands. The iron(IV) and iron(IV) cation radical sections discuss the high‐valent states of cytochromes P450 and related enzymes.

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