scholarly journals A summary of the measured pKvalues of the ionizable groups in folded proteins

2008 ◽  
pp. NA-NA ◽  
Author(s):  
Gerald R. Grimsley ◽  
J. Martin Scholtz ◽  
C. Nick Pace
Keyword(s):  
Folded Proteins ◽  
Ionizable Groups

BODIPY Fluorophores for Membrane Potential Imaging

2019 ◽  
Author(s):  
Jenna Franke ◽  
Benjamin Raliski ◽  
Steven Boggess ◽  
Divya Natesan ◽  
Evan Koretsky ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Water Solubility ◽  
Water Soluble ◽  
Voltage Sensitivity ◽  
Chemical Transformations ◽  
Direct Modification ◽  
Biological Compatibility ◽  
Meso Position ◽  
Ionizable Groups ◽  
Boron Center

Fluorophores based on the BODIPY scaffold are prized for their tunable excitation and emission profiles, mild syntheses, and biological compatibility. Improving the water-solubility of BODIPY dyes remains an outstanding challenge. The development of water-soluble BODIPY dyes usually involves direct modification of the BODIPY fluorophore core with ionizable groups or substitution at the boron center. While these strategies are effective for the generation of water-soluble fluorophores, they are challenging to implement when developing BODIPY-based indicators: direct modification of BODIPY core can disrupt the electronics of the dye, complicating the design of functional indicators; and substitution at the boron center often renders the resultant BODIPY incompatible with the chemical transformations required to generate fluorescent sensors. In this study, we show that BODIPYs bearing a sulfonated aromatic group at the meso position provide a general solution for water-soluble BODIPYs. We outline the route to a suite of 5 new sulfonated BODIPYs with 2,6-disubstitution patterns spanning a range of electron-donating and -withdrawing propensities. To highlight the utility of these new, sulfonated BODIPYs, we further functionalize them to access 13 new, BODIPY-based voltage-sensitive fluorophores. The most sensitive of these BODIPY VF dyes displays a 48% ΔF/F per 100 mV in mammalian cells. Two additional BODIPY VFs show good voltage sensitivity (≥24% ΔF/F) and excellent brightness in cells. These compounds can report on action potential dynamics in both mammalian neurons and human stem cell-derived cardiomyocytes. Accessing a range of substituents in the context of a water soluble BODIPY fluorophore provides opportunities to tune the electronic properties of water-soluble BODIPY dyes for functional indicators.

scholarly journals Emulsion Formation and Stabilizing Properties of Olive Oil Cake Crude Extracts

Processes ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 633
Author(s):  
Firdaous Fainassi ◽  
Noamane Taarji ◽  
Fatiha Benkhalti ◽  
Abdellatif Hafidi ◽  
Marcos A. Neves ◽  
...  
Keyword(s):  
Olive Oil ◽  
Ethanol Extract ◽  
Active Components ◽  
Oil In Water ◽  
Surface Active ◽  
Ph Conditions ◽  
Oil Water ◽  
Surface Active Compounds ◽  
Ionizable Groups ◽  
Emulsifying Ability

The surface-active and emulsifying properties of crude aqueous ethanolic extracts from untreated olive oil cake (OOC) were investigated. OOC extracts contained important concentrations of surface-active components including proteins, saponins and polyphenols (1.2–2.8%, 7.8–9.5% and 0.7–4.5% (w/w), respectively) and reduced the interfacial tension by up to 46% (14.0 ± 0.2 mN m−1) at the oil–water interface. The emulsifying ability of OOC extracts was not correlated, however, with their interfacial activity or surface-active composition. Eighty percent aqueous ethanol extract produced the most stable oil-in-water (O/W) emulsions by high-pressure homogenization. The emulsions had average volume mean droplet diameters of approximately 0.4 µm and negative ζ-potentials of about -45 mV, and were stable for up to 1 month of storage at 5, 25 and 50 °C. They were sensitive, however, to acidic pH conditions (<5) and NaCl addition (≥25 mM), indicating that the main stabilization mechanism is electrostatic due to the presence of surface-active compounds with ionizable groups, such as saponins.

scholarly journals The effect of heme-linked ionizable groups on cyanide binding to methemoglobin.

1986 ◽  
Vol 261 (23) ◽  
pp. 10576-10581
Author(s):  
F J Vega-Catalan ◽  
O J Odeyemi ◽  
K O Okonjo
Keyword(s):  
Cyanide Binding ◽  
Ionizable Groups

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.

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

2018 ◽  
Vol 19 (11) ◽  
pp. 3315 ◽  
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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