Effect of a Protein Electric Field on the CO Stretch Frequency. Finite Difference Poisson−Boltzmann Calculations on Carbonmonoxycytochromes<i>c</i>

Laberge, Monique; Vanderkooi, and Jane M.; Sharp, Kim A.

doi:10.1021/jp960055g

Cited by 36 publications

(68 citation statements)

References 75 publications

(131 reference statements)

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“…15 spectra were averaged for each sample. To maintain sample integrity, no K 3 Fe(CN) 6 was added to the oxidized samples. UV-visible spectra were ~ recorded before and after the Raman measurements.…”

Section: Methodsmentioning

confidence: 99%

“…The MPCO structure was built and optimized using parameters developed for carbonmonoxycytochrome c (6). The energy of the resulting structure was minimized using the CVFF force field modified for the heme group and carbonyl hemes (6). Missing hydrogens were added using Discover_3, subject to van der Waals constraints.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

“…There are very few small model heme compounds that are soluble in water and do not severely aggregate. We have recently started investigating the effect of the electric field imposed by the protein on the vibrational properties of heme proteins (5)(6)(7) and, in this context, microperoxidase-11 (MP11) could represent a good model to study the properties of the heme in aqueous solution and in the presence of only a few amino acid residues which sets the heme in an environment distinctly different than the hydrophobic pockets of c-type heme proteins.…”

Section: Introductionmentioning

confidence: 99%

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Microperoxidase-11: Molecular Dynamics and Q-Band Excited Resonance Raman of the Oxidized, Reduced and Carbonyl Forms

Laberge

Vreugdenhil

Vanderkooi

et al. 1998

Journal of Biomolecular Structure and Dynamics

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Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undecapeptides are consistent with a six-coordinate, low spin iron in both oxidation states. Porphyrin core size correlations yield a porphyrin-centre to pyrrole-nitrogen distance of 2.00 A for MP11, suggestive of a six-coordinate species in a distorted heme environment. Molecular dynamics results show that the non-planarity of the heme of the parent cytochrome is conserved in the microperoxidase and its carbonmonoxy analog.

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Section: Methodsmentioning

confidence: 99%

Section: Molecular Dynamicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Microperoxidase-11: Molecular Dynamics and Q-Band Excited Resonance Raman of the Oxidized, Reduced and Carbonyl Forms

Laberge

Vreugdenhil

Vanderkooi

et al. 1998

Journal of Biomolecular Structure and Dynamics

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“…27 These authors used a Stark tuning rate of 0.49 cm -1 /(MV/cm) based on the result of a Stark experiment for CO adsorbed at a known orientation on a nickel surface. 20 According to our results, the Stark tuning rate for CO bound to cytochrome c is substantially larger, (2.6/f) cm -1 / (MV/cm).…”

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confidence: 99%

Vibrational Stark Spectroscopy in Proteins: A Probe and Calibration for Electrostatic Fields

et al. 1999

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We report the first measurement of the vibrational Stark effect in a protein, providing quantitative information on the sensitivity of a vibrational transition to an applied electric field. This can be used to interpret changes in the vibrational frequency that are often observed when amino acids are changed or when a protein undergoes a structural change in terms of the change in the internal or matrix electric field associated with the perturbation. The vibrational Stark effect has been measured for the vibration of CO bound to the heme iron in myoglobin. The vibrational Stark effect is surprisingly large, giving a Stark tuning rate of (2.4/f) cm -1 /(MV/cm), where f is the local field correction; this is nearly 4 times larger than for free CO. It is also found that the change in dipole moment is parallel to the transition moment; that is, the change in dipole moment is in the direction perpendicular to the heme plane. Vibrational Stark effect data are also reported as a function of pH, for various mutants, for a modified picket fence porphyrin, and for cytochrome c. The Stark tuning rate is found to be very similar in all cases, indicating that the CO stretch frequency for CO bound to the heme iron is a sensitive and anisotropic local detector of changes in the electrostatic field. This information is used to evaluate electrostatics calculations for heme proteins.Electrostatic interactions are central to understanding the properties of molecules in the condensed phase and are especially important in complex organized systems such as proteins. A large body of theoretical work is directed at understanding the role played by electrostatics in folding, assembly, and catalysis. 1-8 Electrostatic interactions can be probed by measuring pK a shifts for titratable residues, 9-11 shifts in redox potential, 12,13 NMR chemical shifts, 14 and electrochromic band shifts (sometimes called internal Stark shifts). 15,16 Electrochromic band shifts in a protein result from the interaction between a probe chromophore and the electric field due to the surrounding organized environment of the protein matrix and associated prosthetic groups and solvent. This field is collectively called the matrix electric field F matrix , and the observed electrochromic band shift is ∆E ) hc∆ν j ) -∆µ‚F matrix , where ∆µ is the change in dipole moment associated with a spectroscopic transition.To interpret or calculate the electrochromic band shift in terms of the matrix electric field due to the protein or any other ordered environment, it is necessary to know ∆µ as this gives the intrinsic sensitivity of the transition to an electric field. 17 The magnitude and direction of ∆µ can be obtained by Stark spectroscopy which quantifies the effect of an externally applied electric field, F ext , on the transition. Stark spectroscopy of electronic transitions in proteins is now a standard method; 18,19 however, this technique is rarely applied to molecular vibrations. 20,21 In the present communication we report the first measurement of the Stark...

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“…For accurate modeling of CiP, the Heme-CVFF (Consistent Valence Force Field) force fields as implemented in Insight II were used to assign potential and charge to the Fe atom and porphyrin atoms, which produced reliable results of heme protein modeling. [28][29][30] To predict interactions between E328D and water molecules, all crystallographic water molecules were kept in their original position as from 1ARP. For the correct orientation of hydrogen atoms of water molecules, all atoms of CiP and the oxygen atoms of the water molecules were fixed and only the hydrogen atoms were minimized with default parameters using the Discover 3 module.…”

Section: Modeling Of E328d and Molecular Dynamics Simulationmentioning

confidence: 99%

The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design

Kim

Lee

Joo

et al. 2010

Biotechnology Progress

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Protein thermostability is a crucial issue in the practical application of enzymes, such as inorganic synthesis and enzymatic polymerization of phenol derivatives. Much attention has been focused on the enhancement and numerous successes have been achieved through protein engineering methods. Despite fruitful results based on random mutagenesis, it was still necessary to develop a novel strategy that can reduce the time and effort involved in this process. In this study, a rapid and effective strategy is described for increasing the thermal stability of a protein. Instead of random mutagenesis, a rational strategy was adopted to theoretically stabilize the thermo labile residues of a protein using computational methods. Protein residues with high flexibility can be thermo labile due to their large range of movement. Here, residue B factor values were used to identify putatively thermo labile residues and the RosettaDesign program was applied to search for stable sequences. Coprinus cinereus (CiP) heme peroxidase was selected as a model protein for its importance in commercial applications, such as the polymerization of phenolic compounds. Eleven CiP residues with the highest B factor values were chosen as target mutation sites for thermostabilization, and then redesigned using RosettaDesign to identify sequences. Eight mutants based on the redesigns, were produced as functional enzymes and two of these (S323Y and E328D) showed increased thermal stability over the wild-type in addition to conserved catalytic activity. Thus, this strategy can be used as a rapid and effective in silico design tool for obtaining thermostable proteins.

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Effect of a Protein Electric Field on the CO Stretch Frequency. Finite Difference Poisson−Boltzmann Calculations on Carbonmonoxycytochromesc

Cited by 36 publications

References 75 publications

Microperoxidase-11: Molecular Dynamics and Q-Band Excited Resonance Raman of the Oxidized, Reduced and Carbonyl Forms

Microperoxidase-11: Molecular Dynamics and Q-Band Excited Resonance Raman of the Oxidized, Reduced and Carbonyl Forms

Vibrational Stark Spectroscopy in Proteins: A Probe and Calibration for Electrostatic Fields

The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design

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