scholarly journals Crystal structure ofPorphyromonas gingivalispeptidylarginine deiminase: implications for autoimmunity in rheumatoid arthritis

2015 ◽  
Vol 75 (6) ◽  
pp. 1255-1261 ◽  
Author(s):  
Anna B Montgomery ◽  
Jolanta Kopec ◽  
Leela Shrestha ◽  
Marie-Laetitia Thezenas ◽  
Nicola A Burgess-Brown ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Crystal Structure ◽  
Active Form ◽  
3D Structure ◽  
Periodontal Pathogen ◽  
3D Structures ◽  
Highly Active ◽  
Lack Of Information ◽  
Arginine Residues ◽  
Citrullinated Proteins

BackgroundPeriodontitis (PD) is a known risk factor for rheumatoid arthritis (RA) and there is increasing evidence that the link between the two diseases is due to citrullination by the unique bacterial peptidylarginine deiminase (PAD) enzyme expressed by periodontal pathogenPophyromonas gingivalis(PPAD). However, the precise mechanism by which PPAD could generate potentially immunogenic peptides has remained controversial due to lack of information about the structural and catalytic mechanisms of the enzyme.ObjectivesBy solving the 3D structure of PPAD we aim to characterise activity and elucidate potential mechanisms involved in breach of tolerance to citrullinated proteins in RA.MethodsPPAD and a catalytically inactive mutant PPADC351Awere crystallised and their 3D structures solved. Key residues identified from 3D structures were examined by mutations. Fibrinogen and α-enolase were incubated with PPAD andP. gingivalisarginine gingipain (RgpB) and citrullinated peptides formed were sequenced and quantified by mass spectrometry.ResultsHere, we solve the crystal structure of a truncated, highly active form of PPAD. We confirm catalysis is mediated by the following residues: Asp130, His236, Asp238, Asn297 and Cys351 and show Arg152 and Arg154 may determine the substrate specificity of PPAD for C-terminal arginines. We demonstrate the formation of 37 C-terminally citrullinated peptides from fibrinogen and 11 from α-enolase following incubation with tPPAD and RgpB.ConclusionsPPAD displays an unequivocal specificity for C-terminal arginine residues and readily citrullinates peptides from key RA autoantigens. The formation of these novel citrullinated peptides may be involved in breach of tolerance to citrullinated proteins in RA.

scholarly journals Latent and activeabPPO4 mushroom tyrosinase cocrystallized with hexatungstotellurate(VI) in a single crystal

2014 ◽  
Vol 70 (9) ◽  
pp. 2301-2315 ◽  
Author(s):  
Stephan Gerhard Mauracher ◽  
Christian Molitor ◽  
Rami Al-Oweini ◽  
Ulrich Kortz ◽  
Annette Rompel
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Agaricus Bisporus ◽  
Crystal Packing ◽  
Active Form ◽  
Activation Mechanism ◽  
Mushroom Tyrosinase ◽  
Polyphenol Oxidases ◽  
Highly Active ◽  
Eukaryotic Organisms

Tyrosinases, bifunctional metalloenzymes, catalyze the oxidation of monophenols ando-diphenols too-quinones, the precursor compounds of the brown-coloured pigment melanin. In eukaryotic organisms, tyrosinases are expressed as latent zymogens that have to be proteolytically cleaved in order to form highly active enzymes. This activation mechanism, known as the tyrosinase maturation process, has scientific and industrial significance with respect to biochemical and technical applications of the enzyme. Here, not only the first crystal structure of the mushroom tyrosinaseabPPO4 is presented in its active form (Ser2–Ser383) and in its 21 kDa heavier latent form (Ser2–Thr545), but furthermore the simultaneous presence of both forms within one single-crystal structure is shown. This allows for a simple approach to investigate the transition between these two forms. IsoformabPPO4 was isolated and extensively purified from the natural source (Agaricus bisporus), which contains a total of six polyphenol oxidases (PPOs). The enzyme formed crystals (diffracting to a resolution of 2.76 Å) owing to the employment of the 6-tungstotellurate(VI) salt (Na6[TeW6O24]·22H2O) as a cocrystallization agent. Two of these disc-shaped Anderson-type polyoxoanions [TeW6O24]6−separate two asymmetric units comprising one crystallographic heterodimer ofabPPO4, thus resulting in very interesting crystal packing.

scholarly journals OP0034 DOES THE RISK OF VENOUS THROMBOEMBOLISM VARY WITH DISEASE ACTIVITY IN RHEUMATOID ARTHRITIS?

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 23.2-24
Author(s):  
V. Molander ◽  
H. Bower ◽  
J. Askling
Keyword(s):  
Rheumatoid Arthritis ◽  
Logistic Regression ◽  
Venous Thromboembolism ◽  
Disease Activity ◽  
Das28 Score ◽  
Logistic Regression Models ◽  
Highly Active ◽  
Increased Risk ◽  
Das28 Remission ◽  
One Year

Background:Patients with rheumatoid arthritis (RA) are at increased risk for venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE) (1). Several established risk factors of VTE, such as age, immobilization and comorbid conditions, occur more often patients with RA (2). In addition, inflammation may in itself also increase VTE risk by upregulating procoagolatory factors and causing endothelial damage (3). Recent reports indicate an increased risk of VTE in RA patients treated with JAK-inhibitors (4), pointing to the need to better understand how inflammation measured as clinical RA disease activity influences VTE risk.Objectives:To investigate the relationship between clinical RA disease activity and incidence of VTE.Methods:Patients with RA were identified from the Swedish Rheumatology Quality Register (SRQ) between July 1st2006 and December 31st2017. Clinical rheumatology data for these patients were obtained from the visits recorded in SRQ, and linked to national registers capturing data on VTE events and comorbid conditions. For each such rheumatologist visit, we defined a one-year period after the visit and determined whether a VTE event had occurred within this period or not. A visit followed by a VTE event was categorized as a case, all other visits were used as controls. Each patient could contribute to several visits. The DAS28 score registered at the visit was stratified into remission (0-2.5) vs. low (2.6-3.1), moderate (3.2-5.1) and high (>5.1) disease activity. Logistic regression with robust cluster standard errors was used to estimate the association between the DAS28 score and VTE.Results:We identified 46,311 patients with RA who contributed data from 320,094 visits. Among these, 2,257 visits (0.7% of all visits) in 1345 unique individuals were followed by a VTE within the one-year window. Of these, 1391 were DVT events and 866 were PE events. Figure 1 displays the absolute probabilities of a VTE in this one-year window, and odds ratios for VTE by each DAS28 category, using DAS28 remission as reference. The one-year risk of a VTE increased from 0.5% in patients in DAS28 remission, to 1.1% in patients with DAS28 high disease activity (DAS28 above 5.1). The age- and sex-adjusted odds ratio for a VTE event in highly active RA compared to RA in remission was 2.12 (95% CI 1.80-2.47). A different analysis, in which each patient could only contribute to one visit, yielded similar results.Figure 1.Odds ratios (OR) comparing the odds of VTE for DAS28 activity categories versus remission. Grey estimates are from unadjusted logistic regression models, black estimates are from logistic regression models adjusted for age and sex. Absolute one-year risk of VTE are estimated from unadjusted models.Conclusion:This study demonstrates a strong association between clinical RA inflammatory activity as measured through DAS28 and risk of VTE. Among patients with high disease activity one in a hundred will develop a VTE within the coming year. These findings highlight the need for proper VTE risk assessment in patients with active RA, and confirm that patients with highly active RA, such as those recruited to trials for treatment with new drugs, are already at particularly elevated risk of VTE.References:[1]Holmqvist et al. Risk of venous thromboembolism in patients with rheumatoid arthritis and association with disease duration and hospitalization. JAMA. 2012;308(13):1350-6.[2]Cushman M. Epidemiology and risk factors for venous thrombosis. Semin Hematol. 2007;44(2):62-9.[3]Xu J et al. Inflammation, innate immunity and blood coagulation. Hamostaseologie. 2010;30(1):5-6, 8-9.[4]FDA. Safety trial finds risk of blood clots in the lungs and death with higher dose of tofacitinib (Xeljanz, Xeljanz XR) in rheumatoid arthritis patients; FDA to investigate. 2019.Acknowledgments:Many thanks to all patients and rheumatologists persistently filling out the SRQ.Disclosure of Interests:Viktor Molander: None declared, Hannah Bower: None declared, Johan Askling Grant/research support from: JA acts or has acted as PI for agreements between Karolinska Institutet and the following entities, mainly in the context of the ARTIS national safety monitoring programme of immunomodulators in rheumatology: Abbvie, BMS, Eli Lilly, Merck, MSD, Pfizer, Roche, Samsung Bioepis, Sanofi, and UCB Pharma

scholarly journals Identification of potential autoantigens in anti-CCP-positive and anti-CCP-negative rheumatoid arthritis using citrulline-specific protein arrays

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Thomas B. G. Poulsen ◽  
Dres Damgaard ◽  
Malene M. Jørgensen ◽  
Ladislav Senolt ◽  
Jonathan M. Blackburn ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Protein Microarray ◽  
Specific Protein ◽  
Immune Reactivity ◽  
Igg Antibodies ◽  
Native Proteins ◽  
Array Technology ◽  
Citrullinated Proteins ◽  
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.

Crystal structure of meso ‐substituted pyrazolyl porphyrin complexes and their highly active catalyst for oxidation of alkylbenzenes

2017 ◽  
Vol 32 (3) ◽  
pp. e4184 ◽  
Author(s):  
Yahong Yao ◽  
Yanxia Du ◽  
Jun Li ◽  
Chen Wang ◽  
Zengqi Zhang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Catalyst ◽  
Highly Active

Preparation of a highly active form of nisin from Streptococcus lactis

1971 ◽  
Vol 17 (1) ◽  
pp. 61-67 ◽  
Author(s):  
F. J. Bailey ◽  
A. Hurst
Keyword(s):  
Active Form ◽  
Gradient Elution ◽  
Antibiotic Activity ◽  
Complex Medium ◽  
Main Peak ◽  
Acetone Precipitation ◽  
Highly Active ◽  
Streptococcus Lactis ◽  
Constant Ph ◽  
Ph Gradient Elution

Cells of Streptococcus lactis (354/07) synthesized and retained nisin when grown in a complex medium with 2.5% glucose at a constant pH of 6.7. Nisin was extracted from cells by a previously used method with hot 0.05 N HCl but milder methods of extraction from whole and broken cells using a variety of solvents were also tested. In the preferred method broken cells were extracted with 0.05 N HCl at 2 °C. The Cl− ions of the extract were exchanged for acetate on columns of the resin Amberlite CG 4B and the eluate was concentrated by acetone precipitation at −19 °C. The nisin was finally purified by pH gradient elution from CM cellulose columns. Three peaks with antibiotic activity were found, two of the peaks were minor and represented less than 5% of the nisin. The main peak gave a single band on electrophoresis. Electrophoresis of the material from the CM cellulose peaks revealed about 44 bands of basic proteins. Nisin made by the hot or cold HCl extraction behaved similarly in electrophoresis and CM cellulose chromatography but the antibiotic activity of the material isolated from the cold extract was nine times greater than that of the material isolated from the hot extract.

scholarly journals Crystal structure of an active form of RAS protein, a complex of a GTP analog and the HRAS p21 catalytic domain.

1990 ◽  
Vol 87 (12) ◽  
pp. 4849-4853 ◽  
Author(s):  
A. T. Brunger ◽  
M. V. Milburn ◽  
L. Tong ◽  
A. M. deVos ◽  
J. Jancarik ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Domain ◽  
Active Form ◽  
Protein A ◽  
Ras Protein

Sequence analysis, structure prediction of receptor proteins and In silico study of potential inhibitors for management of life threatening COVID-19

2021 ◽  
Vol 18 ◽  
Author(s):  
Hriday K. Basak ◽  
Soumen Saha ◽  
Joydeep Ghosh ◽  
Uttam Paswan ◽  
Sujoy Karmakar ◽  
...  
Keyword(s):  
Binding Site ◽  
Ursolic Acid ◽  
Density Functional ◽  
Actinomycin D ◽  
3D Structure ◽  
Natural Compounds ◽  
Surface Glycoprotein ◽  
Basis Set ◽  
3D Structures ◽  
Potential Inhibitors

Background: Treatment of the Covid-19 pandemic caused by the highly contagious and pathogenic SARS-CoV-2 is a global menace. Day by day this pandemic is getting worse. Doctors, Scientists and Researchers across the world are urgently scrambling for a cure for novel corona virus and continuously working at break neck speed to develop vaccine or drugs. But to date, there are no specific drugs or vaccine available in the market to cope up the virus. Objective: The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also to identify best natural compounds as potential inhibitors against COVID-19. Methods: The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool. Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study a small library of natural compounds (fifty compounds) was docked to the ACE2 binding site of the modelled surface glycoprotein of SARS-CoV-2 using Auto Dock Vina to repurpose these inhibitors for SARS-CoV-2. Conceptual density functional theory calculations of best eight compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and drug likeliness of the compounds were analyzed in the swissADME website. Results: In this study we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein and envelope protein obtained from different parts of the globe. We have modelled all the different sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular target which is essential for the development of therapeutics. Different electronic properties of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARS-CoV-2 showed that all the eight inhibitors (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here many folds better compared to hydroxychloroquine which has been found to be effective to treat patients suffering fromCOVID-19 pandemic. All the inhibitors meet most of criteria of drug likeness assessment. Conclusion: We will expect that eight compounds (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors against SARS-CoV-2.

scholarly journals Crystal structure of human mARC1 reveals its exceptional position among eukaryotic molybdenum enzymes

2018 ◽  
Vol 115 (47) ◽  
pp. 11958-11963 ◽  
Author(s):  
Christian Kubitza ◽  
Florian Bittner ◽  
Carsten Ginsel ◽  
Antje Havemeyer ◽  
Bernd Clement ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Full Range ◽  
3D Structure ◽  
Cytochrome P450 Enzymes ◽  
Oxygenated Compounds ◽  
Online Databases ◽  
Starting Point ◽  
Wide Range ◽  
Nitrogen Containing Compounds

Biotransformation enzymes ensure a viable homeostasis by regulating reversible cycles of oxidative and reductive reactions. The metabolism of nitrogen-containing compounds is of high pharmaceutical and toxicological relevance because N-oxygenated metabolites derived from reactions mediated by cytochrome P450 enzymes or flavin-dependent monooxygenases are in some cases highly toxic or mutagenic. The molybdenum-dependent mitochondrial amidoxime-reducing component (mARC) was found to be an extremely efficient counterpart, which is able to reduce the full range of N-oxygenated compounds and thereby mediates detoxification reactions. However, the 3D structure of this enzyme was unknown. Here we present the high-resolution crystal structure of human mARC. We give detailed insight into the coordination of its molybdenum cofactor (Moco), the catalytic mechanism, and its ability to reduce a wide range of N-oxygenated compounds. The identification of two key residues will allow future discrimination between mARC paralogs and ensure correct annotation. Since our structural findings contradict in silico predictions that are currently made by online databases, we propose domain definitions for members of the superfamily of Moco sulfurase C-terminal (MOSC) domain-containing proteins. Furthermore, we present evidence for an evolutionary role of mARC for the emergence of the xanthine oxidase protein superfamily. We anticipate the hereby presented crystal structure to be a starting point for future descriptions of MOSC proteins, which are currently poorly structurally characterized.

scholarly journals Cell Bioprinting: The 3D-Bioplotter™ Case

Materials ◽  
2019 ◽  
Vol 12 (23) ◽  
pp. 4005 ◽  
Author(s):  
Angelats Lobo ◽  
Ginestra
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Petri Dish ◽  
Two Dimensions ◽  
Point Of View ◽  
Lack Of Information ◽  
Synthetic Materials ◽  
Different Types ◽  
Available Information ◽  
User Friendly

The classic cell culture involves the use of support in two dimensions, such as a well plate or a Petri dish, that allows the culture of different types of cells. However, this technique does not mimic the natural microenvironment where the cells are exposed to. To solve that, three-dimensional bioprinting techniques were implemented, which involves the use of biopolymers and/or synthetic materials and cells. Because of a lack of information between data sources, the objective of this review paper is, to sum up, all the available information on the topic of bioprinting and to help researchers with the problematics with 3D bioprinters, such as the 3D-Bioplotter™. The 3D-Bioplotter™ has been used in the pre-clinical field since 2000 and could allow the printing of more than one material at the same time, and therefore to increase the complexity of the 3D structure manufactured. It is also very precise with maximum flexibility and a user-friendly and stable software that allows the optimization of the bioprinting process on the technological point of view. Different applications have resulted from the research on this field, mainly focused on regenerative medicine, but the lack of information and/or the possible misunderstandings between papers makes the reproducibility of the tests difficult. Nowadays, the 3D Bioprinting is evolving into another technology called 4D Bioprinting, which promises to be the next step in the bioprinting field and might promote great applications in the future.

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