Theoretical studies on effects of hydrogen bonds attaching to cysteine ligands on 4Fe‐4S clusters

Kitagawa, Yasutaka; Saitô, Tôru; Nakanishi, Yoshito; Koizumi, Kenichi; Kawakami, Takashi; Okumura, Mitsutaka; Yamaguchi, Kizashi

doi:10.1002/qua.21843

Cited by 27 publications

(24 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Heme propionyl groups usually make hydrogen bonds with the side chains of positively charged amino acids like Arg and Lys and the main chain amide groups of protein, working as electrostatic anchors in protein. Our data suggest that strength of hydrogen bonds can regulate the redox potential remarkably consistent with the experimental and theoretical studies of the redox potential of ferredoxins [35,36].…”

Section: Protonation Of Propionyl Groupssupporting

confidence: 85%

Density functional study of roles of porphyrin ring in electronic structures of heme

Takano

Nakamura

2009

Int J of Quantum Chemistry

View full text Add to dashboard Cite

Heme is a prosthetic group that consists of an iron ion contained in the center of a porphyrin, and a widely distributed cofactor in biology. It serves electron transfer and enzyme catalysis. There are many types of heme, which have several heme side chains such as propionyl, vinyl, and hydroxyfarnesylethyl groups. The differences in heme side chains yield many important functions. In this study, we have investigated the roles of porphyrin ring: heme porphyrin ring distortion, heme peripheral substitution, and protonation of propionyl group of heme, by using density functional theory with the polarizable continuum model. The effects of porphyrin ring of heme were discussed from the viewpoint of the charge density difference in the redox reaction and the redox potential.

show abstract

Section: Protonation Of Propionyl Groupssupporting

confidence: 85%

Density functional study of roles of porphyrin ring in electronic structures of heme

Takano

Nakamura

2009

Int J of Quantum Chemistry

View full text Add to dashboard Cite

show abstract

“…A standard electronic embedding scheme [74] was chosen; the fixed MM atomic charges were included into the oneelectron Hamiltonian of the QM calculations, and the QM/MM electrostatic interactions were evaluated from the QM electrostatic potential and the MM atomic charges. Recently, Kitagawa et al [75]. investigated the effect of hydrogen bonds attaching to sulfur atoms of cysteine ligands on 4Fe-4S clusters using the B3LYP method.…”

Section: Qm/mm Calculationsmentioning

confidence: 99%

Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase

Kamachi

Kouno

Doitomi

et al. 2011

Journal of Inorganic Biochemistry

View full text Add to dashboard Cite

“…DFT has been accepted by the ab initio quantum chemistry community as a cost-effective approach for the computation of molecular structures, vibrational frequencies, and energies of chemical reactions. Recently, DFT has been used widely to study H-bond interactions [13][14][15][16]. Generally, the formation of H-bond can be estimated by the structural parameters (e.g.…”

Section: Introductionmentioning

confidence: 99%

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

Huang

Dai

2010

Struct Chem

View full text Add to dashboard Cite

The (CH 3 OH) n (n = 2-8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OHÁÁÁO H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH 3 OH) n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH 3 OH) n (n = 4-8) clusters are remarkably stronger than those in (CH 3 OH) n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH 3 OH) n (n = 6-8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (q b ) and the HÁÁÁO bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.Keywords The quantum theory of atoms in molecule (QTAIM) Á Natural bond orbital (NBO) Á Density functional theory (DFT) Á Hydrogen bond Á Methanol clusters

show abstract

Theoretical studies on effects of hydrogen bonds attaching to cysteine ligands on 4Fe‐4S clusters

Cited by 27 publications

References 26 publications

Density functional study of roles of porphyrin ring in electronic structures of heme

Density functional study of roles of porphyrin ring in electronic structures of heme

Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

Contact Info

Product

Resources

About