Structural characterization of the catalytic γ and regulatory β subunits of phosphorylase kinase in the context of the hexadecameric enzyme complex

Rimmer, Mary Ashley; Nadeau, Owen W.; Artigues, Antonio; Carlson, Gerald M.

doi:10.1002/pro.3340

Cited by 7 publications

(4 citation statements)

References 63 publications

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“…Docking results generated with different numbers of cross-links further demonstrate that, with HDX kinetics adjudication, a high-confidence model can be delivered by using only two intermolecular cross-links. Although HDX-MS has been employed for complementary information in some biological studies − along with XL-MS, the two methods are usually treated individually. Other studies , that incorporated XL-based docking have shown that HDX kinetics can be utilized to examine the constructed 3D model; however, none has assessed the process in a systematic way.…”

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confidence: 99%

An Integrated Approach for Determining a Protein–Protein Binding Interface in Solution and an Evaluation of Hydrogen–Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models

et al. 2019

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We describe an integrated approach of using hydrogen–deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (XL-MS), and molecular docking to characterize the binding interface and to predict the three-dimensional quaternary structure of a protein–protein complex in solution. Interleukin 7 (IL-7) and its α-receptor, IL-7Rα, serving as essential mediators in the immune system, are the model system. HDX kinetics reports widespread protection on IL-7Rα but shows no differential evidence of binding-induced protection or remote conformational change. Cross-linking with reagents that differ in spacer lengths and targeting residues increases the spatial resolution. Using five cross-links as distance restraints for protein–protein docking, we generated a high-confidence model of the IL-7/IL-7Rα complex. Both the predicted binding interface and regions with direct contacts agree well with those in the solid-state structure, as confirmed by previous X-ray crystallography. An additional binding region was revealed to be the C-terminus of helix B of IL-7, highlighting the value of solution-based characterization. To generalize the integrated approach, protein–protein docking was executed with a different number of cross-links. Combining cluster analysis and HDX kinetics adjudication, we found that two intermolecular cross-link-derived restraints are sufficient to generate a high-confidence model with root-mean-square distance (rmsd) value of all alpha carbons below 2.0 Å relative to the crystal structure. The remarkable results of binding-interface determination and quaternary structure prediction highlight the effectiveness and capability of the integrated approach, which will allow more efficient and comprehensive analysis of interprotein interactions with broad applications in the multiple stages of design, implementation, and evaluation for protein therapeutics.

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confidence: 99%

An Integrated Approach for Determining a Protein–Protein Binding Interface in Solution and an Evaluation of Hydrogen–Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models

et al. 2019

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“…Each technique is accompanied by a list of example studies in which the technique has been successfully applied. ( Boczek et al, 2019 ; Doran et al, 2004 ; Garcia et al, 2006 ; Hajdusits et al, 2021 ; Li et al, 2008 ; Lučić et al, 2018 ; Nadeau et al, 2012 ; Pathak et al, 2023 ; Pinkse et al, 2009 ; Rimmer et al, 2018 ; Shaw et al, 2023 ; Sok et al, 2020 ; Torres-Ocampo et al, 2020 ).…”

Section: Interpreting Crystallographic Evidence For Dimerization and ...mentioning

confidence: 99%

A critical evaluation of protein kinase regulation by activation loop autophosphorylation

Reinhardt

Leonard

2023

eLife

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Phosphorylation of proteins is a ubiquitous mechanism of regulating their function, localization, or activity. Protein kinases, enzymes that use ATP to phosphorylate protein substrates are, therefore, powerful signal transducers in eukaryotic cells. The mechanism of phosphoryl-transfer is universally conserved among protein kinases, which necessitates the tight regulation of kinase activity for the orchestration of cellular processes with high spatial and temporal fidelity. In response to a stimulus, many kinases enhance their own activity by autophosphorylating a conserved amino acid in their activation loop, but precisely how this reaction is performed is controversial. Classically, kinases that autophosphorylate their activation loop are thought to perform the reaction in trans, mediated by transient dimerization of their kinase domains. However, motivated by the recently discovered regulation mechanism of activation loop cis-autophosphorylation by a kinase that is autoinhibited in trans, we here review the various mechanisms of autoregulation that have been proposed. We provide a framework for critically evaluating biochemical, kinetic, and structural evidence for protein kinase dimerization and autophosphorylation, and share some thoughts on the implications of these mechanisms within physiological signaling networks.

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“…There are several other examples of such activator proteins, for example, β-N-acetylhexosaminidase (EC 3.2.1.52) requires the presence of a specific activator protein for hydrolysis of the ganglioside GM2 [19], and a number of multisubunit enzymes requires noncatalytically active proteins for their assembly and activity regulation (e.g. [20][21][22][23]), necessitating some caution in the interpretation of the results of simple knock-out experiments.…”

Section: What It Containsmentioning

confidence: 99%

Enzyme nomenclature and classification: the state of the art

McDonald

Tipton

2022

The FEBS Journal

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The IUBMB enzyme classification system, available at the IUBMB ExplorEnz website, uses a four‐component number (the EC number) that identifies an enzyme in terms of reaction catalysed. There were originally six recognized groups of enzymes: Oxidoreductases (EC 1), Transferases (EC 2), Hydrolases (EC 3), Lyases (EC 4), Isomerases (EC 5) and Ligases (EC 6). Of these, the lyases, which are defined as ‘enzymes that cleave C‐C, C‐O, C‐N and other bonds by means other than by hydrolysis or oxidation’, present particular recognition and classification problems. Recently, a new class, the Translocases (EC 7), has been added, which incorporates enzymes that catalyse the movement of ions or molecules across membranes or their separation within membranes. A new subclass of the isomerases has also been included for those enzymes that alter the conformations of proteins and nucleic acids. Newly reported enzymes are being regularly added to the list after validation and where new information affects the classification of an existing entry, a new EC number is created, but the old one is not reused.

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Structural characterization of the catalytic γ and regulatory β subunits of phosphorylase kinase in the context of the hexadecameric enzyme complex

Cited by 7 publications

References 63 publications

An Integrated Approach for Determining a Protein–Protein Binding Interface in Solution and an Evaluation of Hydrogen–Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models

An Integrated Approach for Determining a Protein–Protein Binding Interface in Solution and an Evaluation of Hydrogen–Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models

A critical evaluation of protein kinase regulation by activation loop autophosphorylation

Enzyme nomenclature and classification: the state of the art

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