Literature DB >> 20666384

Electronic structure and dynamics of nitrosyl porphyrins.

W Robert Scheidt1, Alexander Barabanschikov, Jeffrey W Pavlik, Nathan J Silvernail, J Timothy Sage.   

Abstract

Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT functionals are not fully successful at capturing the trans interaction between the axial NO and imidazole ligands. This supports previous conclusions that heme-NO complexes exhibit an unusual degree of variability with respect to the computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune its reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity.

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Year:  2010        PMID: 20666384      PMCID: PMC2919577          DOI: 10.1021/ic100261b

Source DB:  PubMed          Journal:  Inorg Chem        ISSN: 0020-1669            Impact factor:   5.165


  77 in total

1.  A steric mechanism for inhibition of CO binding to heme proteins.

Authors:  G S Kachalova; A N Popov; H D Bartunik
Journal:  Science       Date:  1999-04-16       Impact factor: 47.728

Review 2.  Nitric oxide signaling: no longer simply on or off.

Authors:  Stephen P L Cary; Jonathan A Winger; Emily R Derbyshire; Michael A Marletta
Journal:  Trends Biochem Sci       Date:  2006-03-10       Impact factor: 13.807

3.  Spin density distribution in five- and six-coordinate iron(II)-porphyrin NO complexes evidenced by magnetic circular dichroism spectroscopy.

Authors:  V K K Praneeth; Frank Neese; Nicolai Lehnert
Journal:  Inorg Chem       Date:  2005-04-18       Impact factor: 5.165

4.  Structural characterization of the myoglobin active site using infrared crystallography.

Authors:  J T Sage; W Jee
Journal:  J Mol Biol       Date:  1997-11-21       Impact factor: 5.469

5.  Direct probe of iron vibrations elucidates NO activation of heme proteins.

Authors:  Weiqiao Zeng; Nathan J Silvernail; David C Wharton; Georgi Y Georgiev; Bogdan M Leu; W Robert Scheidt; Jiyong Zhao; Wolfgang Sturhahn; E Ercan Alp; J Timothy Sage
Journal:  J Am Chem Soc       Date:  2005-08-17       Impact factor: 15.419

6.  Toward modeling H-NOX domains: a DFT study of heme-NO complexes as hydrogen bond acceptors.

Authors:  Espen Tangen; Anders Svadberg; Abhik Ghosh
Journal:  Inorg Chem       Date:  2005-10-31       Impact factor: 5.165

7.  Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane.

Authors:  Daniel M Copeland; Ann H West; George B Richter-Addo
Journal:  Proteins       Date:  2003-11-01

8.  Broken-symmetry DFT spin densities of iron nitrosyls, including Roussin's red and black salts: striking differences between pure and hybrid functionals.

Authors:  Kathrin H Hopmann; Jeanet Conradie; Abhik Ghosh
Journal:  J Phys Chem B       Date:  2009-07-30       Impact factor: 2.991

9.  Resonance Raman investigation of dioxygen bonding in oxycobaltmyoglobin and oxycobalthemoglobin: structural implication of splittings of the bound O--O stretching vibration.

Authors:  M Tsubaki; N T Yu
Journal:  Proc Natl Acad Sci U S A       Date:  1981-06       Impact factor: 11.205

Review 10.  What is the real physiological NO concentration in vivo?

Authors:  Catherine N Hall; John Garthwaite
Journal:  Nitric Oxide       Date:  2009-07-12       Impact factor: 4.427

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  9 in total

1.  Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.

Authors:  B Ross Belvin; Faik N Musayev; John Burgner; J Neel Scarsdale; Carlos R Escalante; Janina P Lewis
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-04-05       Impact factor: 7.652

2.  New perspectives on iron-ligand vibrations of oxyheme complexes.

Authors:  Jianfeng Li; Qian Peng; Alexander Barabanschikov; Jeffrey W Pavlik; E Ercan Alp; Wolfgang Sturhahn; Jiyong Zhao; Charles E Schulz; J Timothy Sage; W Robert Scheidt
Journal:  Chemistry       Date:  2011-08-29       Impact factor: 5.236

3.  Spectroscopic identification of reactive porphyrin motions.

Authors:  Alexander Barabanschikov; Alexander Demidov; Minoru Kubo; Paul M Champion; J Timothy Sage; Jiyong Zhao; Wolfgang Sturhahn; E Ercan Alp
Journal:  J Chem Phys       Date:  2011-07-07       Impact factor: 3.488

Review 4.  What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes.

Authors:  W Robert Scheidt; Jianfeng Li; J Timothy Sage
Journal:  Chem Rev       Date:  2017-09-18       Impact factor: 60.622

5.  Lessons on O2 and NO bonding to heme from ab initio multireference/multiconfiguration and DFT calculations.

Authors:  Sason Shaik; Hui Chen
Journal:  J Biol Inorg Chem       Date:  2011-03-04       Impact factor: 3.358

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.  Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)].

Authors:  Qian Peng; Jeffrey W Pavlik; W Robert Scheidt; Olaf Wiest
Journal:  J Chem Theory Comput       Date:  2011-11-29       Impact factor: 6.006

8.  Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies.

Authors:  Saumen Chakraborty; Julian Reed; J Timothy Sage; Nicole C Branagan; Igor D Petrik; Kyle D Miner; Michael Y Hu; Jiyong Zhao; E Ercan Alp; Yi Lu
Journal:  Inorg Chem       Date:  2015-08-14       Impact factor: 5.165

9.  Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes.

Authors:  Jianfeng Li; Qian Peng; Allen G Oliver; E Ercan Alp; Michael Y Hu; Jiyong Zhao; J Timothy Sage; W Robert Scheidt
Journal:  J Am Chem Soc       Date:  2014-12-18       Impact factor: 15.419

  9 in total

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