Literature DB >> 21391540

Investigation of the low frequency dynamics of heme proteins: native and mutant cytochrome P450(cam) and redox partner complexes.

Venugopal Karunakaran1, Ilia Denisov, Stephen G Sligar, Paul M Champion.   

Abstract

Vibrational coherence spectroscopy (VCS) is used to investigate the low-frequency dynamics of camphor-free and camphor-bound cytochrome P450(cam) (CYP 101) and its L358P mutant. The low-frequency heme vibrations are found to be perturbed upon binding to the electron transfer partner putidaredoxin (Pdx). A strong correlation between the "detuned" vibrational coherence spectrum, which monitors frequencies between 100 and 400 cm(-1), and the lower frequency part of the Raman spectrum is also demonstrated. The very low frequency region ≤200 cm(-1), uniquely accessed by open-band VCS measurements, reveals a mode near 103 cm(-1) in P450(cam) when camphor is not present in the distal pocket. This reflects the presence of a specific heme distortion, such as saddling or ruffling, in the substrate-free state where water is coordinated to the low-spin iron atom. Such distortions are likely to retard the rate of electron transfer to the substrate-free protein. The presence of strong mode near ∼33 cm(-1) in the camphor-bound form suggests a significant heme-doming distortion, which is supported by analysis using normal coordinate structural decomposition. Pdx also displays a strong coherent vibration near 30 cm(-1) that in principle could be involved in vibrational resonance with its electron transfer target. A splitting of the 33 cm(-1) feature and intensification of a mode near 78 cm(-1) appear when the P450(cam)/Pdx complex is formed. These observations are consistent with vibrational mixing and heme geometric distortions upon Pdx binding that are coincident with the increased thiolate electron donation to the heme. The appearance of a mode near 65 cm(-1) in the coherence spectra of the L358P mutant is comparable to the mode at 78 cm(-1) seen in the P450(cam)/Pdx complex and is consistent with the view that the heme and its environment in the L358P mutant are similar to the Pdx-bound native protein. Resonance Raman spectra are presented for both P450(cam) and the L358P mutant and the changes are correlated with an increased amount of thiolate electron donation to the heme in the mutant sample.

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Year:  2011        PMID: 21391540      PMCID: PMC3088772          DOI: 10.1021/jp112298y

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  45 in total

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Journal:  Phys Rev Lett       Date:  1994-01-10       Impact factor: 9.161

2.  Spectral broadening in biomolecules.

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Journal:  Phys Rev Lett       Date:  1986-09-08       Impact factor: 9.161

3.  A thermodynamic model of regulation: modulation of redox equilibria in camphor monoxygenase.

Authors:  S G Sligar; I C Gunsalus
Journal:  Proc Natl Acad Sci U S A       Date:  1976-04       Impact factor: 11.205

4.  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

5.  A structure-based model for cytochrome P450cam-putidaredoxin interactions.

Authors:  T C Pochapsky; T A Lyons; S Kazanis; T Arakaki; G Ratnaswamy
Journal:  Biochimie       Date:  1996       Impact factor: 4.079

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Authors:  T L Poulos; B C Finzel; A J Howard
Journal:  J Mol Biol       Date:  1987-06-05       Impact factor: 5.469

7.  Modulating heme redox potential through protein-induced porphyrin distortion.

Authors:  Charles Olea; John Kuriyan; Michael A Marletta
Journal:  J Am Chem Soc       Date:  2010-09-22       Impact factor: 15.419

8.  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

9.  Solution NMR structure of putidaredoxin-cytochrome P450cam complex via a combined residual dipolar coupling-spin labeling approach suggests a role for Trp106 of putidaredoxin in complex formation.

Authors:  Wei Zhang; Susan S Pochapsky; Thomas C Pochapsky; Nitin U Jain
Journal:  J Mol Biol       Date:  2008-09-20       Impact factor: 5.469

10.  Phe393 mutants of cytochrome P450 BM3 with modified heme redox potentials have altered heme vinyl and propionate conformations.

Authors:  Zhucheng Chen; Tobias W B Ost; Johannes P M Schelvis
Journal:  Biochemistry       Date:  2004-02-24       Impact factor: 3.162

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  8 in total

Review 1.  Spectroscopic studies of the cytochrome P450 reaction mechanisms.

Authors:  Piotr J Mak; Ilia G Denisov
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-06-28       Impact factor: 3.036

2.  NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450.

Authors:  Thomas C Pochapsky; Nathan Wong; Yihao Zhuang; Jeffrey Futcher; Maria-Eirini Pandelia; Drew R Teitz; Allison M Colthart
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-05-01       Impact factor: 3.036

3.  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

4.  A Comparative Analysis of the Effector Role of Redox Partner Binding in Bacterial P450s.

Authors:  Dipanwita Batabyal; Ariel Lewis-Ballester; Syun-Ru Yeh; Thomas L Poulos
Journal:  Biochemistry       Date:  2016-11-15       Impact factor: 3.162

5.  Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration.

Authors:  Margherita Maiuri; Ines Delfino; Giulio Cerullo; Cristian Manzoni; Vladimir Pelmenschikov; Yisong Guo; Hongxin Wang; Leland B Gee; Christie H Dapper; William E Newton; Stephen P Cramer
Journal:  J Inorg Biochem       Date:  2015-07-14       Impact factor: 4.155

6.  Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance.

Authors:  Allison M Colthart; Drew R Tietz; Yuhua Ni; Jessica L Friedman; Marina Dang; Thomas C Pochapsky
Journal:  Sci Rep       Date:  2016-02-25       Impact factor: 4.379

7.  Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site.

Authors:  Katrin Adamczyk; Niall Simpson; Gregory M Greetham; Andrea Gumiero; Martin A Walsh; Michael Towrie; Anthony W Parker; Neil T Hunt
Journal:  Chem Sci       Date:  2014-10-22       Impact factor: 9.825

8.  Investigations of the low frequency modes of ferric cytochrome c using vibrational coherence spectroscopy.

Authors:  Venugopal Karunakaran; Yuhan Sun; Abdelkrim Benabbas; Paul M Champion
Journal:  J Phys Chem B       Date:  2014-05-30       Impact factor: 2.991

  8 in total

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