Aromatic thiol-mediated cleavage of N–O bonds enables chemical ubiquitylation of folded proteins

AbstractThe presence or absence of autoantibodies against citrullinated proteins (ACPAs) distinguishes two main groups of rheumatoid arthritis (RA) patients with different etiologies, prognoses, disease severities, and, presumably, disease pathogenesis. The heterogeneous responses of RA patients to various biologics, even among ACPA-positive patients, emphasize the need for further stratification of the patients. We used high-density protein array technology for fingerprinting of ACPA reactivity. Identification of the proteome recognized by ACPAs may be a step to stratify RA patients according to immune reactivity. Pooled plasma samples from 10 anti-CCP-negative and 15 anti-CCP-positive RA patients were assessed for ACPA content using a modified protein microarray containing 1631 different natively folded proteins citrullinated in situ by protein arginine deiminases (PADs) 2 and PAD4. IgG antibodies from anti-CCP-positive RA plasma showed high-intensity binding to 87 proteins citrullinated by PAD2 and 99 proteins citrullinated by PAD4 without binding significantly to the corresponding native proteins. Curiously, the binding of IgG antibodies in anti-CCP-negative plasma was also enhanced by PAD2- and PAD4-mediated citrullination of 29 and 26 proteins, respectively. For only four proteins, significantly more ACPA binding occurred after citrullination with PAD2 compared to citrullination with PAD4, while the opposite was true for one protein. We demonstrate that PAD2 and PAD4 are equally efficient in generating citrullinated autoantigens recognized by ACPAs. Patterns of proteins recognized by ACPAs may serve as a future diagnostic tool for further subtyping of RA patients.

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Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings

International Journal of Molecular Sciences ◽

10.3390/ijms19113315 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3315 ◽

Cited By ~ 10

Author(s):

Rita Pancsa ◽

Fruzsina Zsolyomi ◽

Peter Tompa

Keyword(s):

Large Scale ◽

Intrinsically Disordered Proteins ◽

Protein Structures ◽

Disordered Proteins ◽

Cellular Interaction ◽

Structural Constraints ◽

Protein Residues ◽

Intrinsically Disordered ◽

Evolutionary Changes ◽

Folded Proteins

Although improved strategies for the detection and analysis of evolutionary couplings (ECs) between protein residues already enable the prediction of protein structures and interactions, they are mostly restricted to conserved and well-folded proteins. Whereas intrinsically disordered proteins (IDPs) are central to cellular interaction networks, due to the lack of strict structural constraints, they undergo faster evolutionary changes than folded domains. This makes the reliable identification and alignment of IDP homologs difficult, which led to IDPs being omitted in most large-scale residue co-variation analyses. By preforming a dedicated analysis of phylogenetically widespread bacterial IDP–partner interactions, here we demonstrate that partner binding imposes constraints on IDP sequences that manifest in detectable interprotein ECs. These ECs were not detected for interactions mediated by short motifs, rather for those with larger IDP–partner interfaces. Most identified coupled residue pairs reside close (<10 Å) to each other on the interface, with a third of them forming multiple direct atomic contacts. EC-carrying interfaces of IDPs are enriched in negatively charged residues, and the EC residues of both IDPs and partners preferentially reside in helices. Our analysis brings hope that IDP–partner interactions difficult to study could soon be successfully dissected through residue co-variation analysis.

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Dynamics of Small, Folded Proteins

Protein Modelling ◽

10.1007/978-3-319-09976-7_10 ◽

2014 ◽

pp. 223-248

Author(s):

Petra Rovó ◽

Dóra K. Menyhárd ◽

Gábor Náray-Szabó ◽

András Perczel

Keyword(s):

Folded Proteins

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Model of a folded polypeptide chain

Proceedings of the Royal Society of London Series B Biological Sciences ◽

10.1098/rspb.1950.0023 ◽

1950 ◽

Vol 137 (886) ◽

pp. 79-79

Keyword(s):

Amino Acid ◽

Polypeptide Chain ◽

Molecular Model ◽

Polymer Chains ◽

Side Chains ◽

Amino Acid Residues ◽

Infra Red ◽

New Type ◽

Folded Proteins ◽

Red Radiation

The models on view in the ante-room show a way of folding a polypeptide chain which is consistent with some observations we have recently made with polarized infra-red radiation (Ambrose & Hanby 1949; Ambrose, Elliott & Temple 1949). The α -folded proteins, keratin, myosin and tropomyosin, have been found when oriented to show greater absorption of the N-H frequency when the electric vector of the absorbed radiation is in the direction of the fibre axis, hence the N-H bond must be preferentially oriented in this direction. A study of models has suggested that the only likely folding of the polypeptide chain consistent with this fact involves a seven-membered ring containing two amino-acid residues; the ring is completed by hydrogen bonds: A new type of atomic model which has been developed in our laboratories has been used. The scale is 0·8 in. to the Angstrom unit. The valency links, while allowing free rotation about single co-valent bonds, also allow some distortion of the bond angles when strains occur but are strong enough to allow long polymer chains to be built. The molecular model exhibited shows twenty-four amino-acid residues, with side chains on one side of the back-bone, representative of those occurring in myosin; the side chains on the other side have been removed for clearness and their positions indicated by single carbon atoms.

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