Literature DB >> 12121767

Theoretical study of the discrimination between O(2) and CO by myoglobin.

Emma Sigfridsson1, Ulf Ryde.   

Abstract

Combined quantum chemical and molecular mechanics geometry optimisations have been performed on myoglobin without or with O(2) or CO bound to the haem group. The results show that the distal histidine residue is protonated on the N(epsilon 2) atom and forms a hydrogen bond to the haem ligand both in the O(2) and the CO complexes. We have also re-refined the crystal structure of CO[bond]myoglobin by a combined quantum chemical and crystallographic refinement. Thereby, we probably obtain the most accurate available structure of the active site of this complex, showing a Fe[bond]C[bond]O angle of 171 degrees, and Fe[bond]C and C[bond]O bond lengths of 170-171 and 116-117 pm. The resulting structures have been used to calculate the strength of the hydrogen bond between the distal histidine residue and O(2) or CO in the protein. This amounts to 31-33 kJ/mol for O(2) and 2-3 kJ/mol for CO. The difference in hydrogen-bond strength is 21-22 kJ/mol when corrected for entropy effects. This is slightly larger than the observed discrimination between O(2) or CO by myoglobin, 17 kJ/mol. We have also estimated the strain of the active site inside the protein. It is 2-4 kJ/mol larger for the O(2) complex than for the CO complex, independent of which crystal structure the calculations are based on. Together, these results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.

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Year:  2002        PMID: 12121767     DOI: 10.1016/s0162-0134(02)00426-9

Source DB:  PubMed          Journal:  J Inorg Biochem        ISSN: 0162-0134            Impact factor:   4.155


  16 in total

1.  The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure.

Authors:  Nikki Strickland; Adrian J Mulholland; Jeremy N Harvey
Journal:  Biophys J       Date:  2005-12-30       Impact factor: 4.033

2.  Vibrational Dynamics of Biological Molecules: Multi-quantum Contributions.

Authors:  Bogdan M Leu; J Timothy Sage; Marek Z Zgierski; Graeme R A Wyllie; Mary K Ellison; W Robert Scheidt; Wolfgang Sturhahn; E Ercan Alp; Stephen M Durbin
Journal:  J Phys Chem Solids       Date:  2005-12       Impact factor: 3.995

3.  New light on NO bonding in Fe(III) heme proteins from resonance Raman spectroscopy and DFT modeling.

Authors:  Alexandra V Soldatova; Mohammed Ibrahim; John S Olson; Roman S Czernuszewicz; Thomas G Spiro
Journal:  J Am Chem Soc       Date:  2010-04-07       Impact factor: 15.419

Review 4.  Ambidentate H-bonding of NO and O2 in heme proteins.

Authors:  Thomas G Spiro; Alexandra V Soldatova
Journal:  J Inorg Biochem       Date:  2012-06-01       Impact factor: 4.155

5.  Renormalization of myoglobin-ligand binding energetics by quantum many-body effects.

Authors:  Cédric Weber; Daniel J Cole; David D O'Regan; Mike C Payne
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-09       Impact factor: 11.205

6.  CO, NO and O2 as Vibrational Probes of Heme Protein Interactions.

Authors:  Thomas G Spiro; Alexandra V Soldatova; Gurusamy Balakrishnan
Journal:  Coord Chem Rev       Date:  2012-06-06       Impact factor: 22.315

7.  Quantitative vibrational dynamics of iron in nitrosyl porphyrins.

Authors:  Bogdan M Leu; Marek Z Zgierski; Graeme R A Wyllie; W Robert Scheidt; Wolfgang Sturhahn; E Ercan Alp; Stephen M Durbin; J Timothy Sage
Journal:  J Am Chem Soc       Date:  2004-04-07       Impact factor: 15.419

8.  Electronic structure and ligand vibrations in FeNO, CoNO, and FeOO porphyrin adducts.

Authors:  Alexandra V Soldatova; Mohammed Ibrahim; Thomas G Spiro
Journal:  Inorg Chem       Date:  2013-06-13       Impact factor: 5.165

9.  Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.

Authors:  Meng-Sheng Liao; Ming-Ju Huang; John D Watts
Journal:  J Mol Model       Date:  2013-05-10       Impact factor: 1.810

Review 10.  Binding and docking interactions of NO, CO and O₂in heme proteins as probed by density functional theory.

Authors:  Vangelis Daskalakis; Constantinos Varotsis
Journal:  Int J Mol Sci       Date:  2009-09-22       Impact factor: 6.208

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