Literature DB >> 24717844

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

Cédric Weber1, Daniel J Cole, David D O'Regan, Mike C Payne.   

Abstract

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe-O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of the many-body effects induced by the Hund's coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.

Entities:  

Keywords:  metalloprotein; natural bond orbitals; optical absorption; quantum-mechanical simulation; strong correlation

Mesh:

Substances:

Year:  2014        PMID: 24717844      PMCID: PMC4000798          DOI: 10.1073/pnas.1322966111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  26 in total

1.  Generalized Gradient Approximation Made Simple.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  NATURE OF THE IRON-OXYGEN BOND IN OXYHAEMOGLOBIN.

Authors:  J J WEISS
Journal:  Nature       Date:  1964-07-11       Impact factor: 49.962

3.  NATURE OF THE IRON-OXYGEN BOND IN OXYHAEMOGLOBIN.

Authors:  J J WEISS
Journal:  Nature       Date:  1964-04-04       Impact factor: 49.962

4.  Signatures of electronic correlations in iron silicide.

Authors:  Jan M Tomczak; Kristjan Haule; Gabriel Kotliar
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-10       Impact factor: 11.205

5.  Quantum chemical evaluation of protein control over heme ligation: CO/O2 discrimination in myoglobin.

Authors:  Filippo De Angelis; Andrzej A Jarzecki; Roberto Car; Thomas G Spiro
Journal:  J Phys Chem B       Date:  2005-02-24       Impact factor: 2.991

6.  Linear-scaling density-functional simulations of charged point defects in Al2O3 using hierarchical sparse matrix algebra.

Authors:  N D M Hine; P D Haynes; A A Mostofi; M C Payne
Journal:  J Chem Phys       Date:  2010-09-21       Impact factor: 3.488

7.  Infrared magnetic circular dichroism of myoglobin derivatives.

Authors:  T Nozawa; T Yamamoto; M Hatano
Journal:  Biochim Biophys Acta       Date:  1976-03-18

Review 8.  Design and fabrication of magnetic nanoparticles for targeted drug delivery and imaging.

Authors:  Omid Veiseh; Jonathan W Gunn; Miqin Zhang
Journal:  Adv Drug Deliv Rev       Date:  2009-11-10       Impact factor: 15.470

9.  Fe-O2 bonding and oxyheme structure in myoglobin.

Authors:  M W Makinen; A K Churg; H A Glick
Journal:  Proc Natl Acad Sci U S A       Date:  1978-05       Impact factor: 11.205

10.  Ozone model for bonding of an O2 to heme in oxyhemoglobin.

Authors:  W A Goddard; B D Olafson
Journal:  Proc Natl Acad Sci U S A       Date:  1975-06       Impact factor: 11.205

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Review 5.  From Rust to Quantum Biology: The Role of Iron in Retina Physiopathology.

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