Literature DB >> 18597456

Low-frequency mode activity of heme: femtosecond coherence spectroscopy of iron porphine halides and nitrophorin.

Minoru Kubo1, Flaviu Gruia, Abdelkrim Benabbas, Alexander Barabanschikov, William R Montfort, Estelle M Maes, Paul M Champion.   

Abstract

The low-frequency mode activity of metalloporphyrins has been studied for n class="Chemical">iron porphine-halides (Fe(P)(X), X = Cl, Br) and nitrophorin 4 (NP4) using femtosecond coherence spectroscopy (FCS) in combination with polarized resonance Raman spectroscopy and density functional theory (DFT). It is confirmed that the mode symmetry selection rules for FCS are the same as for Raman scattering and that both Franck-Condon and Jahn-Teller mode activities are observed for Fe(P)(X) under Soret resonance conditions. The DFT-calculated low-frequency (20-400 cm (-1)) modes, and their frequency shifts upon halide substitution, are in good agreement with experimental Raman and coherence data, so that mode assignments can be made. The doming mode is located at approximately 80 cm (-1) for Fe(P)(Cl) and at approximately 60 cm (-1) for Fe(P)(Br). NP4 is also studied with coherence techniques, and the NO-bound species of ferric and ferrous NP4 display a mode at approximately 30-40 cm (-1) that is associated with transient heme doming motion following NO photolysis. The coherence spectra of three ferric derivatives of NP4 with different degrees of heme ruffling distortion are also investigated. We find a mode at approximately 60 cm (-1) whose relative intensity in the coherence spectra depends quadratically on the magnitude of the ruffling distortion. To quantitatively account for this correlation, a new "distortion-induced" Raman enhancement mechanism is presented. This mechanism is unique to low-frequency "soft modes" of the molecular framework that can be distorted by environmental forces. These results demonstrate the potential of FCS as a sensitive probe of dynamic and functionally important nonplanar heme vibrational excitations that are induced by the protein environmental forces or by the chemical reactions in the aqueous phase.

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Year:  2008        PMID: 18597456      PMCID: PMC2765994          DOI: 10.1021/ja800916d

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  45 in total

Review 1.  Femtosecond processes in proteins.

Authors:  M H Vos; J L Martin
Journal:  Biochim Biophys Acta       Date:  1999-04-21

2.  Coherence spectroscopy investigations of the low-frequency vibrations of heme: effects of protein-specific perturbations.

Authors:  Flaviu Gruia; Minoru Kubo; Xiong Ye; Dan Ionascu; Changyuan Lu; Robert K Poole; Syun-Ru Yeh; Paul M Champion
Journal:  J Am Chem Soc       Date:  2008-03-20       Impact factor: 15.419

3.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

4.  Nitric oxide binding to nitrophorin 4 induces complete distal pocket burial.

Authors:  A Weichsel; J F Andersen; S A Roberts; W R Montfort
Journal:  Nat Struct Biol       Date:  2000-07

Review 5.  Regulation of oxygen affinity of hemoglobin: influence of structure of the globin on the heme iron.

Authors:  M F Perutz
Journal:  Annu Rev Biochem       Date:  1979       Impact factor: 23.643

6.  Axial ligand complexes of the Rhodnius nitrophorins: reduction potentials, binding constants, EPR spectra, and structures of the 4-iodopyrazole and imidazole complexes of NP4.

Authors:  Robert E Berry; Xiao D Ding; Tatjana Kh Shokhireva; Andrzej Weichsel; William R Montfort; F Ann Walker
Journal:  J Biol Inorg Chem       Date:  2003-12-13       Impact factor: 3.358

7.  Investigations of vibrational coherence in the low-frequency region of ferric heme proteins.

Authors:  Flaviu Gruia; Minoru Kubo; Xiong Ye; Paul M Champion
Journal:  Biophys J       Date:  2007-12-07       Impact factor: 4.033

8.  The crystal structure of nitrophorin 4 at 1.5 A resolution: transport of nitric oxide by a lipocalin-based heme protein.

Authors:  J F Andersen; A Weichsel; C A Balfour; D E Champagne; W R Montfort
Journal:  Structure       Date:  1998-10-15       Impact factor: 5.006

9.  Detailed assignment of the magnetic circular dichroism and UV-vis spectra of five-coordinate high-spin ferric [Fe(TPP)(Cl)].

Authors:  Florian Paulat; Nicolai Lehnert
Journal:  Inorg Chem       Date:  2008-04-25       Impact factor: 5.165

10.  Structural and functional properties of a single domain hemoglobin from the food-borne pathogen Campylobactor jejuni.

Authors:  Changyuan Lu; Masahiro Mukai; Yu Lin; Guanghui Wu; Robert K Poole; Syun-Ru Yeh
Journal:  J Biol Chem       Date:  2007-07-02       Impact factor: 5.157

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  18 in total

1.  NMR studies of the dynamics of nitrophorin 2 bound to nitric oxide.

Authors:  Dhanasekaran Muthu; Robert E Berry; Hongjun Zhang; F Ann Walker
Journal:  Biochemistry       Date:  2013-10-30       Impact factor: 3.162

2.  Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding.

Authors:  Hao Ren; Zaizhi Lai; Jason D Biggs; Jin Wang; Shaul Mukamel
Journal:  Phys Chem Chem Phys       Date:  2013-11-28       Impact factor: 3.676

3.  Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c.

Authors:  Yuhan Sun; Abdelkrim Benabbas; Weiqiao Zeng; Jesse G Kleingardner; Kara L Bren; Paul M Champion
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-21       Impact factor: 11.205

4.  NMR and DFT investigation of heme ruffling: functional implications for cytochrome c.

Authors:  Matthew D Liptak; Xin Wen; Kara L Bren
Journal:  J Am Chem Soc       Date:  2010-07-21       Impact factor: 15.419

5.  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

6.  Vibrational coherence spectroscopy of the heme domain in the CO-sensing transcriptional activator CooA.

Authors:  Venugopal Karunakaran; Abdelkrim Benabbas; Hwan Youn; Paul M Champion
Journal:  J Am Chem Soc       Date:  2011-10-28       Impact factor: 15.419

7.  Investigations of low-frequency vibrational dynamics and ligand binding kinetics of cystathionine beta-synthase.

Authors:  Venugopal Karunakaran; Abdelkrim Benabbas; Yuhan Sun; Zhenyu Zhang; Sangita Singh; Ruma Banerjee; Paul M Champion
Journal:  J Phys Chem B       Date:  2010-03-11       Impact factor: 2.991

8.  Two-Dimensional Stimulated Ultraviolet Resonance Raman Spectra of Tyrosine and Tryptophan; A Simulation Study.

Authors:  Hao Ren; Jason D Biggs; Shaul Mukamel
Journal:  J Raman Spectrosc       Date:  2013-04       Impact factor: 3.133

9.  Investigations of the low-frequency spectral density of cytochrome c upon equilibrium unfolding.

Authors:  Yuhan Sun; Venugopal Karunakaran; Paul M Champion
Journal:  J Phys Chem B       Date:  2013-08-07       Impact factor: 2.991

10.  1H and 13C NMR spectroscopic studies of the ferriheme resonances of three low-spin complexes of wild-type nitrophorin 2 and nitrophorin 2(V24E) as a function of pH.

Authors:  Fei Yang; Markus Knipp; Tatiana K Shokhireva; Robert E Berry; Hongjun Zhang; F Ann Walker
Journal:  J Biol Inorg Chem       Date:  2009-06-11       Impact factor: 3.358

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