Corrigendum to: `Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory' [Chem. Phys. Lett. 341 (2001) 645–651]

Sato, Fumitoshi; Yoshihiro, Tamotsu; Era, Makoto; Kashiwagi, Hiroshi

doi:10.1016/j.cplett.2004.05.083

Cited by 30 publications

(56 citation statements)

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“…In particular, in the FMOn/PCM [1] case only the sum of monomer potentials V I is retained, while FMOn/PCM [2] also includes the dimer corrections [the second sum in eq. (6)].…”

Section: Theorymentioning

confidence: 99%

“…(2); such calculations are repeated until self-consistency is achieved. In FMOn/PCM [1] the ASCs are determined by the monomer densities alone; thus, the monomer calculations have to be repeated to self-consistency. In the gas phase FMO method monomer calculations are also performed self-consistently.…”

Section: Theorymentioning

confidence: 99%

“…Using the state-of-the art implementations of the traditional approaches, calculations on systems containing as many as 1738 atoms have been reported. 1 A variety of low-scaling methods specifically designed to efficiently take into account electron correlation has been proposed; [2][3][4] however, their practical applications so far have been mostly limited to fairly small systems.…”

Section: Introductionmentioning

confidence: 99%

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The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

Fedorov¹,

Kitaura²,

Li³

et al. 2006

J Comput Chem

177

169

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The polarizable continuum model (PCM) for the description of solvent effects is combined with the fragment molecular orbital (FMO) method at several levels of theory, using a many-body expansion of the electron density and the corresponding electrostatic potential, thereby determining solute (FMO)-solvent (PCM) interactions. The resulting method, denoted FMO/PCM, is applied to a set of model systems, including alpha-helices and beta-strands of alanine consisting of 10, 20, and 40 residues and their mutants to charged arginine and glutamate residues. The FMO/PCM error in reproducing the PCM solvation energy for a full system is found to be below 1 kcal/mol in all cases if a two-body expansion of the electron density is used in the PCM potential calculation and two residues are assigned to each fragment. The scaling of the FMO/PCM method is demonstrated to be nearly linear at all levels for polyalanine systems. A study of the relative stabilities of alpha-helices and beta-strands is performed, and the magnitude of the contributing factors is determined. The method is applied to three proteins consisting of 20, 129, and 245 residues, and the solvation energy and computational efficiency are discussed.

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“…In particular, in the FMOn/PCM [1] case only the sum of monomer potentials V I is retained, while FMOn/PCM [2] also includes the dimer corrections [the second sum in eq. (6)].…”

Section: Theorymentioning

confidence: 99%

Section: Theorymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

Fedorov¹,

Kitaura²,

Li³

et al. 2006

J Comput Chem

177

169

View full text Add to dashboard Cite

show abstract

“…31) In particular, the low-and high-spin crossover is essentially determined by the hybridization and the crystal-field energy. The study indicates that the valence and magnetic properties of myoglobins are associated with a delocalization of heme-Fe 3d electronic states, suggestive of interaction between the Fe 3d electronic states and the porphyrin, 32) and possibly the proximal histidine that connects to extended states of the polypeptide chain, 33) which will further enable a fine tuning of the valence and spin states of heme-Fe in myoglobins.…”

Section: )mentioning

confidence: 99%

Ligand Energy Controls the Heme-Fe Valence in Aqueous Myoglobins

et al. 2009

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We use resonant X-ray emission spectroscopy and model calculations to quantify the ligand: heme-Fe energy structure of aqueous myoglobins. For reduced (Fe 2þ ) and oxidized (Fe 3þ ) states, the removal or addition of an electron primarily involves charge changes on the ligand-site, and not the Fe-site. The results indicate a finite positive/negative charge-transfer energy Á between the heme-Fe 3d and ligand valence electronic states for Fe 2þ /Fe 3þ . Thus, the energy difference between the ligand and Fe 3d states (þÁ or ÀÁ) determines the charge properties of myoglobins. The study provides a reliable method for characterizing ligand-metal binding of biological systems in solution.

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“…Additionally, differential coupling of the extended Fe(II) heme donor orbital to the acceptor site on CcP also may mitigate structural effects. Molecular orbital calculations on hCc indicate that the heme iron-centered HOMO, which accepts and donates electrons, delocalizes over protein regions relatively distant to the cofactor (48). Thus, coupling of ZnCcP electronic states with this HOMO may compensate changes in the orientation and separation of Cc.…”

Section: Structures and Redox Properties Of Znccp In Complex With Yccmentioning

confidence: 99%

Effects of interface mutations on association modes and electron-transfer rates between proteins

Kang

Crane

2005

Proc. Natl. Acad. Sci. U.S.A.

109

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Although bonding networks determine electron-transfer (ET) rates within proteins, the mechanism by which structure and dynamics influence ET across protein interfaces is not well understood. Measurements of photochemically induced ET and subsequent charge recombination between Zn-porphyrin-substituted cytochrome c peroxidase and cytochrome c in single crystals correlate reactivity with defined structures for different association modes of the redox partners. Structures and ET rates in crystals are consistent with tryptophan oxidation mediating charge recombination reactions. Conservative mutations at the interface can drastically affect how the proteins orient and dispose redox centers. Whereas some configurations are ET inactive, the wild-type complex exhibits the fastest recombination rate. Other association modes generate ET rates that do not correlate with predictions based on cofactor separations or simple bonding pathways. Inhibition of photoinduced ET at <273 K indicates gating by smallamplitude dynamics, even within the crystal. Thus, different associations achieve states of similar reactivity, and within those states conformational fluctuations enable interprotein ET.cytochrome ͉ protein dynamics ͉ protein-protein interaction ͉ electron tunneling M any long-range electron-transfer (ET) reactions in biology occur across transient protein-protein interfaces. Reaction rates depend on factors that control both electron tunneling and conformational dynamics coupled to protein association processes (1-3). As such, interprotein ET is sensitive to structure and dynamics at the interface (1, 4-11). Residue substitution (achieved either by use of protein homologs, site-directed mutants, or computations) has been a popular and powerful approach for probing how interface composition influences interprotein ET (7,(10)(11)(12)(13)(14). Nevertheless, effects of residue variation on interface structure are not often known.The natural redox partners yeast cytochrome c peroxidase (CcP) and yeast cytochrome c (yCc), whose structure as a complex was first determined in 1992 (15) and later as a covalent complex (16), have served as a paradigm for studying interprotein ET reactions (8,17). Hoffman and colleagues (8) have exploited ZnCcP substitution to photoactivate ET reactions and examine the effects of many structural and chemical perturbations on interprotein ET. In this system, the ZnCcP triplet state ( 3 ZnCcP) reduces Fe(III)Cc, and then back ET recombines the charge separation (Fig. 1). Recently, it has been demonstrated that a Trp-191 3 Phe CcP variant has much slower ET back-rates (k eb ) than wild-type (WT) CcP in the 1:1 complex with yCc (18). Thus, electron hopping through Trp-191 may accelerate the recombination reaction (Fig. 1), in analogy to the natural reaction between CcP compound I and Fe(II)Cc (19). Nevertheless, much slower ET back-rates in the complex between CcP and hCc compared with yCc, both in solution (20) and in crystals (21), indicate that ET across the protein-protein interface limits the overa...

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Corrigendum to: `Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory' [Chem. Phys. Lett. 341 (2001) 645–651]

Cited by 30 publications

References 0 publications

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

Ligand Energy Controls the Heme-Fe Valence in Aqueous Myoglobins

Effects of interface mutations on association modes and electron-transfer rates between proteins

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