Spin-forbidden CO ligand recombination in myoglobin

Harvey, Jeremy N.

doi:10.1039/b314768a

Cited by 139 publications

(171 citation statements)

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“…QoMMMa [28], an in-house interface between QM packages such Jaguar The B3LYP method has several well-known limitations, including the lack of dispersion, and it often (but not always) underestimates reaction barriers [5]. To further investigate the energetic of the reaction further (and to test the performance of B3LYP for this system), single point energy calculations on the structures generated by B3LYP/6-31G(d)/CHARMM27 were carried out at the MP2/aVDZ and SCS-MP2/aVDZ levels (i.e.…”

Section: Methodsmentioning

confidence: 99%

Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

Lawan

Ranaghan

Manby

et al. 2014

Chemical Physics Letters

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Section: Methodsmentioning

confidence: 99%

Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

Lawan

Ranaghan

Manby

et al. 2014

Chemical Physics Letters

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“…1), and how this influence is expressed in the transition from the T to the R state. Quantumchemical methods have already been successfully used to study members of the globin family (18)(19)(20). In this article we employ a quantum mechanics/molecular mechanics (QM/MM) method to look at this coupling of conformation and spin change.…”

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confidence: 99%

A quantum-chemical picture of hemoglobin affinity

Alcantara

Spiro

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Understanding the molecular mechanism of hemoglobin cooperativity remains an enduring challenge. Protein forces that control ligand affinity are not directly accessible by experiment. We demonstrate that computational quantum mechanics/molecular mechanics methods can provide reasonable values of ligand binding energies in Hb, and of their dependence on allostery. About 40% of the binding energy differences between the relaxed state and tense state quaternary structures result from strain induced in the heme and its ligands, especially in one of the pyrrole rings. The proximal histidine also contributes significantly, in particular, in the ␣-chains. The remaining energy difference resides in protein contacts, involving residues responsible for locking the quaternary changes. In the ␣-chains, the most important contacts involve the FG corner, at the ''hinge'' region of the ␣1␤2 quaternary interface. The energy differences are spread more evenly among the ␤-chain residues, suggesting greater flexibility for the ␤-than for the ␣-chains along the quaternary transition. Despite this chain differentiation, the chains contribute equally to the relaxed substitute state energy difference. Thus, nature has evolved a symmetric response to the quaternary structure change, which is a requirement for maximum cooperativity, via different mechanisms for the two kinds of chains.allostery ͉ cooperativity ͉ heme ͉ quantum mechanics/molecular mechanics H emoglobin has been a paradigm for our understanding of multisubunit proteins, beginning with the pioneering work of Adair (1) and then with the elucidation of the oxygenated and deoxygenated crystal structures of Hb by Perutz (2), some four decades ago. Interest in Hb continues to the present, with new experimental and theoretical methods aimed at characterizing intermediate ligation states of the molecule (3-5) and at gaining a deeper understanding of its allosteric transition (6-11).The Hb molecule is composed of four chains that contain a heme group capable of reversibly binding CO or O 2 . The molecule is arranged as a dimer of dimers, where each dimer is made up of an ␣-and a ␤-chain (denoted as ␣ 1 ␤ 1 or ␣ 2 ␤ 2 ) with a hydrophobic intradimer interface. Adair observed that Hb binds oxygen in a cooperative manner, successive ligation events occurring with higher affinity. For some time it was believed that such cooperativity could be explained by direct interaction of the closely packed heme groups. However the 1960s saw the appearance of the first allosteric models for Hb cooperativity. In particular, the Monod-Wyman-Changeux (12) model postulated the existence of two states of the molecule: the relaxed (R) state with high ligand affinity and the tense (T) state with low affinity. Ligand binding preferentially stabilized the R form and led to cooperativity. Early Hb crystallization attempts revealed that deoxy crystals would shatter when exposed to oxygen, which suggested that a quaternary rearrangement was associated with the T-R transition of the molecule.Crystal structure...

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“…The study of SCO compounds is being actively pursued for potential applications in magnetic data storage and as a basis for bistable devices [3]. In biology, SCO plays an important role in the binding of ligands in heme proteins [4]. Finally, ultrafast spin changes (like the case presented here) may offer a route for data processing at the nanoscale [5].…”

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confidence: 99%

Structural Determination of a Short-Lived Excited Iron(II) Complex by Picosecond X-Ray Absorption Spectroscopy

et al. 2007

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Structural changes of the iron(II)-tris-bipyridine ( Fe II bpy 3 2 ) complex induced by ultrashort pulse excitation and population of its short-lived ( 0:6 ns) quintet high spin state have been detected by picosecond x-ray absorption spectroscopy. The structural relaxation from the high spin to the low spin state was followed over the entire lifetime of the excited state. A combined analysis of the x-rayabsorption near-edge structure and extended x-ray-absorption fine structure spectroscopy features delivers an Fe-N bond elongation of 0.2 Å in the quintet state compared to the singlet ground state.

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Spin-forbidden CO ligand recombination in myoglobin

Cited by 139 publications

References 67 publications

Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

A quantum-chemical picture of hemoglobin affinity

Structural Determination of a Short-Lived Excited Iron(II) Complex by Picosecond X-Ray Absorption Spectroscopy

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