Flavin–Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond

Hamdane, Djemel; Bou‐Nader, Charles; Cornu, David; Hui-Bon-Hoa, Gaston; Fontecave, Marc

doi:10.1021/acs.biochem.5b00501

Cited by 20 publications

(31 citation statements)

References 58 publications

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“…In proteins, hydrogen bonds between strongly electronegative nitrogen amine and carbonyl oxygen define the α-helical and β-sheet secondary structure elements [6,9,10] essential to forming compact folded structures [11]. Similarly, oxygen [12,13] and nitrogen [14] atoms present in the amino acid side chains also tend to be involved in canonical hydrogen bonding interactions with water molecules [15] and other electronegative atoms present in ligands [16,17], as well as in the protein itself, involving both the backbone [9] and sidechains [10] (including sulfur atoms in cysteine and methionine [18]). Sulfur is a large, soft atom, unlike the smaller, harder oxygen and nitrogen atoms, and these chemical differences mean that hydrogen bonds formed by sulfur atoms typically have greater contributions from the higher-order electrostatic terms, dispersive interactions, and charge transfer terms and are less well defined by traditional definitions of hydrogen bonding [18].…”

Section: Introductionmentioning

confidence: 99%

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

et al. 2020

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We present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design efforts.

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Section: Introductionmentioning

confidence: 99%

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

et al. 2020

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“…Flavin-mediated oxidation, which involves dioxygen as the electron acceptor, is thermodynamically favorable (Hamdane et al, 2015). Previous studies of the response of flavoproteins to lignin have focused on the role of extracellular flavoprotein during lignocellulose degradation (Hernández-Ortega et al, 2012); however, there have been few reports on the role of intracellular flavoproteins in lignocellulose degradation.…”

Section: Introductionmentioning

confidence: 99%

Differential Proteomic Profiles of Pleurotus ostreatus in Response to Lignocellulosic Components Provide Insights into Divergent Adaptive Mechanisms

Xiao

et al. 2017

Front. Microbiol.

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Pleurotus ostreatus is a white rot fungus that grows on lignocellulosic biomass by metabolizing the main constituents. Extracellular enzymes play a key role in this process. During the hydrolysis of lignocellulose, potentially toxic molecules are released from lignin, and the molecules are derived from hemicellulose or cellulose that trigger various responses in fungus, thereby influencing mycelial growth. In order to characterize the mechanism underlying the response of P. ostreatus to lignin, we conducted a comparative proteomic analysis of P. ostreatus grown on different lignocellulose substrates. In this work, the mycelium proteome of P. ostreatus grown in liquid minimal medium with lignin, xylan, and carboxymethyl cellulose (CMC) was analyzed using the complementary two-dimensional gel electrophoresis (2-DE) approach; 115 proteins were identified, most of which were classified into five types according to their function. Proteins with an antioxidant function that play a role in the stress response were upregulated in response to lignin. Most proteins involving in carbohydrate and energy metabolism were less abundant in lignin. Xylan and CMC may enhanced the process of carbohydrate metabolism by regulating the level of expression of various carbohydrate metabolism-related proteins. The change of protein expression level was related to the adaptability of P. ostreatus to lignocellulose. These findings provide novel insights into the mechanisms underlying the response of white-rot fungus to lignocellulose.

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“…Compared to TrmFO Tt , the identities and spatial locations of all of the residues required to bind FAD and THF are fully conserved in TrmFO-like proteins. Notably, the peculiar Y343 residue that stacks against the isoalloxazine ring in TrmFO Tt and plays an essential role in maintaining active redox state of FAD [64][65][66], is also preserved in TrmFO-like proteins and could feasibly have a similar function. The structural model shows that the two tyrosine residues, Y51 and Y223, occupy positions identical to the two cysteines that they replace in TrmFO Tt .…”

Section: Binding Sites Of Folate and Flavin Are Conserved In Trmfo-limentioning

confidence: 99%

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

et al. 2020

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The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup use the ancestral tetrahydrofolate-dependent TrmFO enzyme to catalyze the formation of m5U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m5U1939 formation in 23S rRNA. RlmFO has replaced the S-adenosyl-L-methionine (SAM)-enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m5U-modifying enzymes that is highly dynamic and has undergone horizontal transfer.

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Flavin–Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond

Cited by 20 publications

References 58 publications

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

Differential Proteomic Profiles of Pleurotus ostreatus in Response to Lignocellulosic Components Provide Insights into Divergent Adaptive Mechanisms

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

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