Roles of active-site residues in catalysis, substrate binding, cooperativity, and the reaction mechanism of the quinoprotein glycine oxidase

Mamounis, Kyle J.; Yukl, Erik T.; Davidson, Victor L.

doi:10.1074/jbc.ra120.013198

Cited by 3 publications

(2 citation statements)

References 28 publications

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“…This homotetrameric enzyme exhibits strong cooperativity toward glycine binding. When the F316A or Y766F mutation at the inter-subunit active-site weakens the glycine binding cooperativity, both the enzyme catalysis potency and the glycine binding potency are also decreased [ 1 ].…”

Section: Introductionmentioning

confidence: 99%

Lipid-dependent sequential allosteric activation of heat-sensing TRPV1 channels by anchor-stereoselective “hot” vanilloid compounds and analogs

Wang

2021

Biochemistry and Biophysics Reports

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Both a silent resident phosphatidylinositol lipid and a “hot” vanilloid agonist capsaicin or resiniferatoxin have been shown to share the same inter-subunit binding pocket between a voltage sensor like domain and a pore domain in TRPV1. However, how the vanilloid competes off the resident lipid for allosteric TRPV1 activation is unknown. Here, the in sillico research suggested that anchor-stereoselective sequential cooperativity between an initial recessive transient silent weak ligand binding site and a subsequent dominant steady-state strong ligand binding site in the vanilloid pocket may facilitate the lipid release for allosteric activation of TRPV1 by vanilloids or analogs upon non-covalent interactions. Thus, the resident lipid may play a critical role in allosteric activation of TRPV1 by vanilloid compounds and analogs.

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Section: Introductionmentioning

confidence: 99%

Lipid-dependent sequential allosteric activation of heat-sensing TRPV1 channels by anchor-stereoselective “hot” vanilloid compounds and analogs

Wang

2021

Biochemistry and Biophysics Reports

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“…The scaffold also may induce specific ligand geometries and configurations of the reactants not otherwise observed. , In essence, it creates an environment around the active site that can control the atomic distribution of charge and functionality. Variances in redox potentials, the orientation and delivery of reactants, and the energetics of the transition state are all influenced by the local environment surrounding the active site and are typical examples of outer-sphere impacts. ,,− …”

Section: Discussionmentioning

confidence: 99%

Bioinspired Catalyst Design Principles: Progress in Emulating Properties of Enzymes in Synthetic Catalysts

Ginovska,

Gutiérrez,

Karkamkar

et al. 2023

ACS Catal.

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Catalysis enables many aspects of modern life, including fuels, products, plastics, and medicines. Recent advances in catalysis have enabled us to realize higher efficiencies and new processes. Ideally, we seek to achieve high rates of selective conversions using catalysts derived from abundantly available elements and operating under mild conditions, specifically lower reaction temperatures and pressures. Such catalysts could enable decentralized, on-demand synthesis of chemicals and energy carriers. Nature has demonstrated the feasibility of this approach with enzymes, which showcase catalytic processes at low temperatures and pressures with nonprecious metals. Current thinking holds that in addition to the active site, the complexity of the enzyme structure, specifically the protein scaffold, is also critical to achieving this performance. Recreating this environment has been a long-standing scientific goal. However, we still understand the functions of enzymes better than we understand the de novo design of catalysts that mimic enzymes features, while also retaining their activity and selectivity under more demanding conditions. In this Perspective, we will critically examine four key areas of catalyst design that incorporate the chemical and structural properties of enzymes into synthetic catalysts: (i) the use of confinement to enhance catalytic activity, (ii) tailoring the environment around the active site, (iii) proton transport, and (iv) bifunctionality and cooperativity.

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Therapeutic Application and Structural Features of Adeno-Associated Virus Vector

Matsuzaka,

Yashiro

2024

CIMB

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Adeno-associated virus (AAV) is characterized by non-pathogenicity, long-term infection, and broad tropism and is actively developed as a vector virus for gene therapy products. AAV is classified into more than 100 serotypes based on differences in the amino acid sequence of the capsid protein. Endocytosis involves the uptake of viral particles by AAV and accessory receptors during AAV infection. After entry into the cell, they are transported to the nucleus through the nuclear pore complex. AAVs mainly use proteoglycans as receptors to enter cells, but the types of sugar chains in proteoglycans that have binding ability are different. Therefore, it is necessary to properly evaluate the primary structure of receptor proteins, such as amino acid sequences and post-translational modifications, including glycosylation, and the higher-order structure of proteins, such as the folding of the entire capsid structure and the three-dimensional (3D) structure of functional domains, to ensure the efficacy and safety of biopharmaceuticals. To further enhance safety, it is necessary to further improve the efficiency of gene transfer into target cells, reduce the amount of vector administered, and prevent infection of non-target cells.

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Roles of active-site residues in catalysis, substrate binding, cooperativity, and the reaction mechanism of the quinoprotein glycine oxidase

Cited by 3 publications

References 28 publications

Lipid-dependent sequential allosteric activation of heat-sensing TRPV1 channels by anchor-stereoselective “hot” vanilloid compounds and analogs

Lipid-dependent sequential allosteric activation of heat-sensing TRPV1 channels by anchor-stereoselective “hot” vanilloid compounds and analogs

Bioinspired Catalyst Design Principles: Progress in Emulating Properties of Enzymes in Synthetic Catalysts

Therapeutic Application and Structural Features of Adeno-Associated Virus Vector

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