affinity

Synthesis and evaluation of photoaffinity labeling reagents for identifying binding sites of sulfated neurosteroids on NMDA and GABAA receptors

RSC Adv., 2024, 14,36352-36369
DOI: 10.1039/D4RA07074G, Paper
Open Access
  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.
Mingxing Qian, Yuanjian Xu, Hong-Jin Shu, Zi-Wei Chen, Lei Wang, Charles F. Zorumski, Alex S. Evers, Steven Mennerick, Douglas F. Covey
Photoaffinity labels (PALs) for sulfated steroid binding sites on GABAA and NMDA receptors. The PALs have varying profiles of positive and negative modulatory (PAM and NAM) actions.
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affinity

Affinity

Affinity of London Silver Jewellery




affinity

Affinity Acquires Opinary: Expanding Global Presence in Europe

Affinity Global Inc, a globally-diversified ad tech firm that provides privacy-friendly advertising solutions and SaaS platforms, has announced its acquisition of Opinary, a Berlin-based consumer engagement focused media tech company.




affinity

Affinity Nightlife's Post Television Awards After Party Celebrated with the Industry's Biggest Stars

Adam Glove's 'Dream in Gold' Gala was One of the Hottest Events in Hollywood with a Packed House




affinity

Can I Import Photoshop Brushes into Affinity Photo?

This post: Can I Import Photoshop Brushes into Affinity Photo? was first published on Beyond Photo Tips by Susheel Chandradhas

Digital brushes are a powerful tool for digital artists, designers, and photographers. The brushes allow them to create a wide range of textures, patterns, and effects in image editing apps. Can Affinity Photo use existing Photoshop Brushes? Over the years, many professionals and hobbyists have curated extensive collections of Photoshop brushes over time, tailored to […]

This post: Can I Import Photoshop Brushes into Affinity Photo? was first published on Beyond Photo Tips




affinity

Affinity Spring Sale: Up to 50% Off

This post: Affinity Spring Sale: Up to 50% Off was first published on Beyond Photo Tips by Susheel Chandradhas

You might have seen some of my articles about Affinity Photo and how it is a wonderfully cost-effective solution for both advanced amateurs and professional photographers when it comes to retouching images. Well, if you have been holding out for a discount on purchase of Affinity apps, then now might be the right time to […]

This post: Affinity Spring Sale: Up to 50% Off was first published on Beyond Photo Tips




affinity

Affinity Acquired by Canva.com

This post: Affinity Acquired by Canva.com was first published on Beyond Photo Tips by Susheel Chandradhas

Today, Affinity and Canva, together announced the acquisition of Serif, the makers of the Affinity apps, by Canva. This is a significant development in the progress of the Affinity suite, and we are both excited, and hesitant at this development. What Is Affinity? Affinity is a suite of apps that allows designers, photographers, and publishers […]

This post: Affinity Acquired by Canva.com was first published on Beyond Photo Tips




affinity

Littler Appoints New Leadership to Its Affinity Groups and Diversity & Inclusion Council

(March 22, 2021) – Littler, the world’s largest employment and labor law practice representing management, is pleased to announce new leadership for its ‘Ohana and Reunión affinity groups. Additionally, the firm’s Diversity & Inclusion (D&I) Council added six new members.




affinity

The Promise and Perils of Affinity Groups; Or, How Not to Bargain with your Employee Resource Group

A properly structured and implemented Affinity Group (AKA Employee Resource Group) is a powerful tool in an employer’s Diversity Equity & Inclusion tool belt. But, unwary employers may risk violating the National Labor Relations Act if they bargain with an Affinity Group. In this month’s podcast, Alyesha Asghar Dotson discusses the do’s and don’ts of interacting with an active Affinity Group within your organization.
  




affinity

Littler Names Jeremy Hawpe as Pride Affinity Group Co-Chair

(June 3, 2021) – Littler, the world’s largest employment and labor law practice representing management, has selected Shareholder Jeremy Hawpe (Dallas) as co-chair of its Pride affinity group, joining Shareholder Lauren Schwartzreich (Denver), and succeeding Shareholder Darren Gibson (Austin) who is stepping down to focus on his growing and active practice.




affinity

Littler Selects New Leaders for Bollo Affinity Group

(March 26, 2024) – Littler, the world’s largest employment and labor law practice representing management, has appointed new leadership for its Bollo affinity group. Shareholders Kimberly N. Dobson (Long Island) and Kimberly J. Duplechain (Washington, D.C.) will serve as co-chairs, succeeding Shareholders Eric Mack (Providence) and LaToi Mayo (Lexington). Bollo provides support, development and networking opportunities for attorneys who identify as Black, African American, African, and Caribbean, and their allies.




affinity

Littler Appoints New Leadership to Its 'Ohana Affinity Group and SOAR Program

(August 7, 2024) – Littler, the world’s largest employment and labor law practice representing management, has selected Devjani H. Mishra (Shareholder, New York) and Nicole S. LeFave (Shareholder, Austin) to lead its 'Ohana affinity group and SOAR Program, respectively.




affinity

High affinity binding of SARS-CoV-2 spike protein enhances ACE2 carboxypeptidase activity [Molecular Bases of Disease]

The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged to a pandemic and caused global public health crisis. Human angiotensin-converting enzyme 2(ACE2) was identified as the entry receptor for SARS-CoV-2. As a carboxypeptidase, ACE2 cleaves many biological substrates besides angiotensin II to control vasodilatation and vascular permeability. Given the nanomolar high affinity between ACE2 and SARS-CoV-2 spike protein, we investigated how this interaction would affect the enzymatic activity of ACE2. Surprisingly, SARS-CoV-2 trimeric spike protein increased ACE2 proteolytic activity ∼3-10 fold against model peptide substrates, such as caspase-1 substrate and Bradykinin-analog. The enhancement in ACE2 enzymatic function was mediated by the binding of SARS-CoV-2 spike RBD domain. These results highlighted the potential for SARS-CoV-2 infection to enhance ACE2 activity, which may be relevant to the cardiovascular symptoms associated with COVID-19.




affinity

A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions: Application in Ubiquitin Profiling and Protein Complex Identification Combined with in vivoCross-Linking

Christian Tagwerker
Apr 1, 2006; 5:737-748
Research




affinity

Microtubule affinity-regulating kinase 4 with an Alzheimer's disease-related mutation promotes tau accumulation and exacerbates neurodegeneration [Neurobiology]

Accumulation of the microtubule-associated protein tau is associated with Alzheimer's disease (AD). In AD brain, tau is abnormally phosphorylated at many sites, and phosphorylation at Ser-262 and Ser-356 plays critical roles in tau accumulation and toxicity. Microtubule affinity–regulating kinase 4 (MARK4) phosphorylates tau at those sites, and a double de novo mutation in the linker region of MARK4, ΔG316E317D, is associated with an elevated risk of AD. However, it remains unclear how this mutation affects phosphorylation, aggregation, and accumulation of tau and tau-induced neurodegeneration. Here, we report that MARK4ΔG316E317D increases the abundance of highly phosphorylated, insoluble tau species and exacerbates neurodegeneration via Ser-262/356–dependent and –independent mechanisms. Using transgenic Drosophila expressing human MARK4 (MARK4wt) or a mutant version of MARK4 (MARK4ΔG316E317D), we found that coexpression of MARK4wt and MARK4ΔG316E317D increased total tau levels and enhanced tau-induced neurodegeneration and that MARK4ΔG316E317D had more potent effects than MARK4wt. Interestingly, the in vitro kinase activities of MARK4wt and MARK4ΔG316E317D were similar. When tau phosphorylation at Ser-262 and Ser-356 was blocked by alanine substitutions, MARK4wt did not promote tau accumulation or exacerbate neurodegeneration, whereas coexpression of MARK4ΔG316E317D did. Both MARK4wt and MARK4ΔG316E317D increased the levels of oligomeric forms of tau; however, only MARK4ΔG316E317D further increased the detergent insolubility of tau in vivo. Together, these findings suggest that MARK4ΔG316E317D increases tau levels and exacerbates tau toxicity via a novel gain-of-function mechanism and that modification in this region of MARK4 may affect disease pathogenesis.




affinity

Design, Synthesis, and Preclinical Evaluation of a High-Affinity 18F-Labeled Radioligand for Myocardial Growth Hormone Secretagogue Receptor Before and After Myocardial Infarction

The peptide hormone ghrelin is produced in cardiomyocytes and acts through the myocardial growth hormone secretagogue receptor (GHSR) to promote cardiomyocyte survival. Administration of ghrelin may have therapeutic effects on post–myocardial infarction (MI) outcomes. Therefore, there is a need to develop molecular imaging probes that can track the dynamics of GHSR in health and disease to better predict the effectiveness of ghrelin-based therapeutics. We designed a high-affinity GHSR ligand labeled with 18F for imaging by PET and characterized its in vivo properties in a canine model of MI. Methods: We rationally designed and radiolabeled with 18F a quinazolinone derivative ([18F]LCE470) with subnanomolar binding affinity to GHSR. We determined the sensitivity and in vivo and ex vivo specificity of [18F]LCE470 in a canine model of surgically induced MI using PET/MRI, which allowed for anatomic localization of tracer uptake and simultaneous determination of global cardiac function. Uptake of [18F]LCE470 was determined by time–activity curve and SUV analysis in 3 regions of the left ventricle—area of infarct, territory served by the left circumflex coronary artery, and remote myocardium—over a period of 1.5 y. Changes in cardiac perfusion were tracked by [13N]NH3 PET. Results: The receptor binding affinity of LCE470 was measured at 0.33 nM, the highest known receptor binding affinity for a radiolabeled GHSR ligand. In vivo blocking studies in healthy hounds and ex vivo blocking studies in myocardial tissue showed the specificity of [18F]LCE470, and sensitivity was demonstrated by a positive correlation between tracer uptake and GHSR abundance. Post-MI changes in [18F]LCE470 uptake occurred independently of perfusion tracer distributions and changes in global cardiac function. We found that the regional distribution of [18F]LCE470 within the left ventricle diverged significantly within 1 d after MI and remained that way throughout the 1.5-y duration of the study. Conclusion: [18F]LCE470 is a high-affinity PET tracer that can detect changes in the regional distribution of myocardial GHSR after MI. In vivo PET molecular imaging of the global dynamics of GHSR may lead to improved GHSR-based therapeutics in the treatment of post-MI remodeling.




affinity

Tuning the affinity of probes with transmembrane proteins by constructing peptide-conjugated cis/trans isomers based on molecular scaffolds

J. Mater. Chem. B, 2024, Advance Article
DOI: 10.1039/D4TB01801J, Paper
Jing-Jing Hu, Juliang Yang, Yiheng Liu, Guangwen Lu, Zujin Zhao, Fan Xia, Xiaoding Lou
Peptide-conjugated cis/trans isomers were designed. cis-RTP interacts more stably with cell membranes than trans-RTP, and it has shown more excellent properties in inhibiting cell migration and killing cells.
To cite this article before page numbers are assigned, use the DOI form of citation above.
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affinity

Enhanced glucose-responsivity of PBA–diol hydrogel networks by reducing crosslink affinity

Mol. Syst. Des. Eng., 2024, Advance Article
DOI: 10.1039/D4ME00106K, Paper
Open Access
Sijie Xian, Yuanhui Xiang, Svenja Deichmann, Matthew J. Webber
New diol chemistries are explored for insulin delivery from glucose-responsive hydrogels comprised of dynamic-covalent crosslinking interactions between phenylboronic acids and diols.
To cite this article before page numbers are assigned, use the DOI form of citation above.
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

Study on the affinity sites of cadmium's binding to ligands by thermodynamics and nuclear magnetic resonance spectroscopy

Anal. Methods, 2024, Advance Article
DOI: 10.1039/D3AY02253F, Paper
Jinsong Yu, Xu Huang, Xiuxiu Wu, Hui Cao, Min Yuan, Tai Ye, Fei Xu
According to the experimental parameters for the interaction of Cd(II) with ligands, the binding sites of Cys and GSH were –SH, –NH2 and –COOH, and the thermodynamic behaviour of Cd(II) with Cys/GSH in boric acid and HEPES buffers was different, exothermic in HEPES but endothermic in boric acid.
To cite this article before page numbers are assigned, use the DOI form of citation above.
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

The preparation of a boronate affinity-based controlled oriented imprinting coating on a silica nanoparticle surface for the separation and purification of shikimic acid in herbal medicine

Anal. Methods, 2024, Advance Article
DOI: 10.1039/D4AY00219A, Paper
Yumin Yang, Daojin Li, Bingqian Liu
Shikimic acid (SA) is one of the most effective drugs against the A (H1N1) virus and has high medicinal value.
To cite this article before page numbers are assigned, use the DOI form of citation above.
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

3-Thio-3,4,5-Trisubstituted-1,2,4-Triazoles: High Affinity Somatostatin Receptor-4 Agonist Synthesis and Structure-Activity Relationships

RSC Med. Chem., 2024, Accepted Manuscript
DOI: 10.1039/D4MD00597J, Research Article
Albert Michael Crider, Audrey Hospital, Karin Sandoval, William Neumann, Stephen Kukielski, Lejla Garic, Kristen Ingold, Matthew Dunahoo, Khush Srabony, Rafael Frare, Olivia Slater, Nathan Peel, Maria Kontoyianni, Ken Witt
Somatostatin receptor-4 (SST4) is a therapeutic target for several conditions, including Alzheimer’s disease, seizures, neuropsychiatric disorders, and pain. Our previous work on 1,2,4-triazole derivatives led to enhanced SST4 binding affinity,...
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

SIGMAP: an explainable artificial intelligence tool for SIGMA-1 receptor affinity Prediction

RSC Med. Chem., 2024, Accepted Manuscript
DOI: 10.1039/D4MD00722K, Research Article
Open Access
  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.
Maria Cristina Lomuscio, Nicola Corriero, Vittoria Nanna, Antonio Piccinno, Michele Saviano, Rosa Lanzilotti, Carmen Abate, Domenico Alberga, Giuseppe Felice Mangiatordi
Developing sigma-1 receptor (S1R) modulators is considered a valuable therapeutic strategy to counteract neurodegeneration, cancer progression, and viral infections, including COVID-19. In this context, in-silico tools capable of accurately predicting...
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

Structure affinity of the Langmuir monolayer and the corresponding Langmuir–Blodgett film revealed by X-ray techniques

Soft Matter, 2024, 20,8601-8609
DOI: 10.1039/D4SM01050G, Paper
Alvina V. Alexandrova, Maxim A. Shcherbina, Yuriy L. Repchenko, Yuriy M. Selivantiev, Alexander V. Shokurov, Vladimir V. Arslanov, Sofiya L. Selektor
Using X-ray techniques, crown-substituted chromoionophore Langmuir–Blodgett films were proved to preserve the fine structure and functional features of pre-organized monolayers.
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

Investigation of the hypoglycemic bioactive components of Phyllanthi Fructus through biological assessment combined with ultrafiltration affinity mass spectrometry

Food Funct., 2024, Accepted Manuscript
DOI: 10.1039/D4FO04198D, Paper
Yifan Zhang, Qiang Yu, Peng Tan, Shimin Tian, Jun-zhi Lin, Mengqi Li, Li Han, Haozhou Huang, Ding-kun Zhang
Phyllanthi Fructus (PF) is a tropical fruit with the potential to effectively reduce postprandial blood glucose, making it highly promising for the development of functional foods. However, the lack of...
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

Lipid sulfoxide polymers as potential inhalable drug delivery platforms with differential albumin binding affinity

Biomater. Sci., 2024, Accepted Manuscript
DOI: 10.1039/D3BM02020G, Paper
Gayathri Ediriweera, Neville Butcher, Ashok Kothapalli, Jiacheng Zhao, Joanne Therese Blanchfield, Christopher N. Subasic, James Lynden Grace, Changkui Fu, Xiao Tan, John F. Quinn, David Ascher, Michael R Whittaker, Andrew Whittaker, Lisa Kaminskas
Inhalable nanomedicines are increasingly being developed to optimise the pharmaceutical treatment of respiratory diseases. Large lipid-based nanosystems at the forefront of the inhalable nanomedicines development pipeline, though, have a number...
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinity

Nanoscale, 2020, Advance Article
DOI: 10.1039/C9NR10638C, Paper
Kaifang Huang, Song Luo, Yalong Cong, Susu Zhong, John Z. H. Zhang, Lili Duan
Modifying the energy term and considering the entropic contribution by IE method significantly improve the accuracy of predicted binding free energy in MM/PBSA method.
To cite this article before page numbers are assigned, use the DOI form of citation above.
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications [Immunology]

Antibodies are widely used as cancer therapeutics, but their current use is limited by the low number of antigens restricted to cancer cells. A receptor tyrosine kinase, receptor tyrosine kinase-like orphan receptor 2 (ROR2), is normally expressed only during embryogenesis and is tightly down-regulated in postnatal healthy tissues. However, it is up-regulated in a diverse set of hematologic and solid malignancies, thus ROR2 represents a candidate antigen for antibody-based cancer therapy. Here we describe the affinity maturation and humanization of a rabbit mAb that binds human and mouse ROR2 but not human ROR1 or other human cell-surface antigens. Co-crystallization of the parental rabbit mAb in complex with the human ROR2 kringle domain (hROR2-Kr) guided affinity maturation by heavy-chain complementarity-determining region 3 (HCDR3)-focused mutagenesis and selection. The affinity-matured rabbit mAb was then humanized by complementarity-determining region (CDR) grafting and framework fine tuning and again co-crystallized with hROR2-Kr. We show that the affinity-matured and humanized mAb retains strong affinity and specificity to ROR2 and, following conversion to a T cell–engaging bispecific antibody, has potent cytotoxicity toward ROR2-expressing cells. We anticipate that this humanized affinity-matured mAb will find application for antibody-based cancer therapy of ROR2-expressing neoplasms.




affinity

Precipitation-free high-affinity multivalent binding by inline lectin ligands

Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC01744B, Edge Article
Open Access
Philipp Rohse, Sabrina Weickert, Malte Drescher, Valentin Wittmann
Integration of sugar epitopes into a backbone structure generates multivalent lectin ligands with a defined binding mode and high affinity without precipitating the protein.
To cite this article before page numbers are assigned, use the DOI form of citation above.
The content of this RSS Feed (c) The Royal Society of Chemistry




affinity

The dimeric organization that enhances the microtubule end-binding affinity of EB1 is susceptible to phosphorylation [RESEARCH ARTICLE]

Yinlong Song, Yikan Zhang, Ying Pan, Jianfeng He, Yan Wang, Wei Chen, Jing Guo, Haiteng Deng, Yi Xue, Xianyang Fang, and Xin Liang

Microtubules dynamics is regulated by the plus end-tracking proteins (+TIPs) in cells. End binding protein 1 (EB1) acts as a master regulator in +TIPs networks by targeting microtubule growing ends and recruiting other factors. However, the molecular mechanism of how EB1 binds to microtubule ends with a high affinity remains to be an open question. Using single-molecule imaging, we show that the end-binding kinetics of EB1 changes along with the polymerizing and hydrolysis rate of tubulin dimers, confirming the binding of EB1 to GTP/GDP-Pi tubulin at microtubule growing ends. The affinity of wild-type EB1 to these sites is higher than monomeric EB1 mutants, suggesting that two CH domains in the dimer contribute to the end-binding. Introducing phosphomimicking mutations into the linker domain of EB1 weakens the end-binding affinity and confers a more curved conformation to EB1 dimer without compromising dimerization, suggesting that the overall architecture of EB1 is important for the end-binding affinity. Taken together, our results provide insights into understanding how the high-affinity end-binding of EB1 can be achieved and how this activity may be regulated in cells.




affinity

Affinity Airbrush Shading Brushes for Premium Members

Access All Areas members have been requesting more Affinity Designer resources, so this week members can download this great set of Airbrush Shading Brushes made specifically for Affinity, courtesy of The Artifex Forge. Add organic texture shading to designs and illustrations with ease! This versatile shading brush pack contains a wide variety of textures – […]

The post Affinity Airbrush Shading Brushes for Premium Members appeared first on Spoon Graphics.




affinity

Dynamically improving memory affinity of logical partitions

In a computer system that includes multiple nodes and multiple logical partitions, a dynamic partition manager computes current memory affinity and potential memory affinity to help determine whether a reallocation of resources between nodes may improve memory affinity for a logical partition or for the computer system. If so, the reallocation of resources is performed so memory affinity for the logical partition or computer system is improved. Memory affinity is computed relative to the physical layout of the resources according to a hardware domain hierarchy that includes a plurality of primary domains and a plurality of secondary domains.




affinity

Muteins of hNGAL and related proteins with affinity for a given target

The present invention relates to novel muteins derived from human lipocalin 2 (hNGAL) and related proteins that bind a given non-natural ligand with detectable affinity. The invention also related to corresponding nucleic acid molecules encoding such a mutein and to a method for their generation. The invention further relates to a method for producing such a mutein. Furthermore, the invention is directed to a pharmaceutical composition comprising such a lipocalin mutein as well as to various uses of the mutein.




affinity

Support for affinity chromatography and method for isolating immunoglobulin

Provided are a support for affinity chromatography which has excellent alkali resistance, and a method for isolating immunoglobulin. A support for affinity chromatography, containing an immobilized protein ligand represented by the following formula (1): R—R2 (1) wherein R represents a polypeptide consisting of 4 to 30 amino acid residues that contains an amino acid sequence represented by ATK or ASK; and R2 represents a polypeptide consisting of 50 to 500 amino acid residues containing an immunoglobulin-binding domain consisting of an amino acid sequence represented by SEQ ID NO: 1 or SEQ ID NO: 2, the partial sequence thereof, or an amino acid sequence having 70% or more identity to these sequences; with the proviso that a terminus at which R2 binds to R is C-terminus or N-terminus of the immunoglobulin-binding domain.




affinity

A neuroglobin-based high-affinity ligand trap reverses carbon monoxide-induced mitochondrial poisoning [Molecular Biophysics]

Carbon monoxide (CO) remains the most common cause of human poisoning. The consequences of CO poisoning include cardiac dysfunction, brain injury, and death. CO causes toxicity by binding to hemoglobin and by inhibiting mitochondrial cytochrome c oxidase (CcO), thereby decreasing oxygen delivery and inhibiting oxidative phosphorylation. We have recently developed a CO antidote based on human neuroglobin (Ngb-H64Q-CCC). This molecule enhances clearance of CO from red blood cells in vitro and in vivo. Herein, we tested whether Ngb-H64Q-CCC can also scavenge CO from CcO and attenuate CO-induced inhibition of mitochondrial respiration. Heart tissue from mice exposed to 3% CO exhibited a 42 ± 19% reduction in tissue respiration rate and a 33 ± 38% reduction in CcO activity compared with unexposed mice. Intravenous infusion of Ngb-H64Q-CCC restored respiration rates to that of control mice correlating with higher electron transport chain CcO activity in Ngb-H64Q-CCC–treated compared with PBS-treated, CO-poisoned mice. Further, using a Clark-type oxygen electrode, we measured isolated rat liver mitochondrial respiration in the presence and absence of saturating solutions of CO (160 μm) and nitric oxide (100 μm). Both CO and NO inhibited respiration, and treatment with Ngb-H64Q-CCC (100 and 50 μm, respectively) significantly reversed this inhibition. These results suggest that Ngb-H64Q-CCC mitigates CO toxicity by scavenging CO from carboxyhemoglobin, improving systemic oxygen delivery and reversing the inhibitory effects of CO on mitochondria. We conclude that Ngb-H64Q-CCC or other CO scavengers demonstrate potential as antidotes that reverse the clinical and molecular effects of CO poisoning.




affinity

A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions: Application in Ubiquitin Profiling and Protein Complex Identification Combined with in vivoCross-Linking

Christian Tagwerker
Apr 1, 2006; 5:737-748
Research




affinity

Specificity and affinity of the N-terminal residues in staphylocoagulase in binding to prothrombin [Computational Biology]

In Staphylococcus aureus–caused endocarditis, the pathogen secretes staphylocoagulase (SC), thereby activating human prothrombin (ProT) and evading immune clearance. A previous structural comparison of the SC(1–325) fragment bound to thrombin and its inactive precursor prethrombin 2 has indicated that SC activates ProT by inserting its N-terminal dipeptide Ile1-Val2 into the ProT Ile16 pocket, forming a salt bridge with ProT's Asp194, thereby stabilizing the active conformation. We hypothesized that these N-terminal SC residues modulate ProT binding and activation. Here, we generated labeled SC(1–246) as a probe for competitively defining the affinities of N-terminal SC(1–246) variants preselected by modeling. Using ProT(R155Q,R271Q,R284Q) (ProTQQQ), a variant refractory to prothrombinase- or thrombin-mediated cleavage, we observed variant affinities between ∼1 and 650 nm and activation potencies ranging from 1.8-fold that of WT SC(1–246) to complete loss of function. Substrate binding to ProTQQQ caused allosteric tightening of the affinity of most SC(1–246) variants, consistent with zymogen activation through occupation of the specificity pocket. Conservative changes at positions 1 and 2 were well-tolerated, with Val1-Val2, Ile1-Ala2, and Leu1-Val2 variants exhibiting ProTQQQ affinity and activation potency comparable with WT SC(1–246). Weaker binding variants typically had reduced activation rates, although at near-saturating ProTQQQ levels, several variants exhibited limiting rates similar to or higher than that of WT SC(1–246). The Ile16 pocket in ProTQQQ appears to favor nonpolar, nonaromatic residues at SC positions 1 and 2. Our results suggest that SC variants other than WT Ile1-Val2-Thr3 might emerge with similar ProT-activating efficiency.




affinity

A neuroglobin-based high-affinity ligand trap reverses carbon monoxide-induced mitochondrial poisoning [Molecular Biophysics]

Carbon monoxide (CO) remains the most common cause of human poisoning. The consequences of CO poisoning include cardiac dysfunction, brain injury, and death. CO causes toxicity by binding to hemoglobin and by inhibiting mitochondrial cytochrome c oxidase (CcO), thereby decreasing oxygen delivery and inhibiting oxidative phosphorylation. We have recently developed a CO antidote based on human neuroglobin (Ngb-H64Q-CCC). This molecule enhances clearance of CO from red blood cells in vitro and in vivo. Herein, we tested whether Ngb-H64Q-CCC can also scavenge CO from CcO and attenuate CO-induced inhibition of mitochondrial respiration. Heart tissue from mice exposed to 3% CO exhibited a 42 ± 19% reduction in tissue respiration rate and a 33 ± 38% reduction in CcO activity compared with unexposed mice. Intravenous infusion of Ngb-H64Q-CCC restored respiration rates to that of control mice correlating with higher electron transport chain CcO activity in Ngb-H64Q-CCC–treated compared with PBS-treated, CO-poisoned mice. Further, using a Clark-type oxygen electrode, we measured isolated rat liver mitochondrial respiration in the presence and absence of saturating solutions of CO (160 μm) and nitric oxide (100 μm). Both CO and NO inhibited respiration, and treatment with Ngb-H64Q-CCC (100 and 50 μm, respectively) significantly reversed this inhibition. These results suggest that Ngb-H64Q-CCC mitigates CO toxicity by scavenging CO from carboxyhemoglobin, improving systemic oxygen delivery and reversing the inhibitory effects of CO on mitochondria. We conclude that Ngb-H64Q-CCC or other CO scavengers demonstrate potential as antidotes that reverse the clinical and molecular effects of CO poisoning.




affinity

Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications [Immunology]

Antibodies are widely used as cancer therapeutics, but their current use is limited by the low number of antigens restricted to cancer cells. A receptor tyrosine kinase, receptor tyrosine kinase-like orphan receptor 2 (ROR2), is normally expressed only during embryogenesis and is tightly down-regulated in postnatal healthy tissues. However, it is up-regulated in a diverse set of hematologic and solid malignancies, thus ROR2 represents a candidate antigen for antibody-based cancer therapy. Here we describe the affinity maturation and humanization of a rabbit mAb that binds human and mouse ROR2 but not human ROR1 or other human cell-surface antigens. Co-crystallization of the parental rabbit mAb in complex with the human ROR2 kringle domain (hROR2-Kr) guided affinity maturation by heavy-chain complementarity-determining region 3 (HCDR3)-focused mutagenesis and selection. The affinity-matured rabbit mAb was then humanized by complementarity-determining region (CDR) grafting and framework fine tuning and again co-crystallized with hROR2-Kr. We show that the affinity-matured and humanized mAb retains strong affinity and specificity to ROR2 and, following conversion to a T cell–engaging bispecific antibody, has potent cytotoxicity toward ROR2-expressing cells. We anticipate that this humanized affinity-matured mAb will find application for antibody-based cancer therapy of ROR2-expressing neoplasms.




affinity

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker

Karl A. T. Makepeace
Apr 1, 2020; 19:624-639
Research




affinity

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker [Research]

An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonstrated improvements in the application of the CLMS technique, in terms of the detection, acquisition, and identification of crosslinker-modified peptides. This approach was evaluated on intact yeast mitochondria, and the results showed that hundreds of unique protein-protein interactions could be identified on an organelle proteome-wide scale. Both known and previously unknown protein-protein interactions were identified. These interactions were assessed based on their known sub-compartmental localizations. Additionally, the identified crosslinking distance constraints are in good agreement with existing structural models of protein complexes involved in the mitochondrial electron transport chain.




affinity

Separation of postprandial lipoproteins: improved purification of chylomicrons using an ApoB100 immunoaffinity method [Methods]

Elevated levels of triglyceride-rich lipoproteins (TRLs), both fasting and postprandial, are associated with increased risk for atherosclerosis. However, guidelines for treatment are defined solely by fasting lipid levels, even though postprandial lipids may be more informative. In the postprandial state, circulating lipids consist of dietary fat transported from the intestine in chylomicrons (CMs; containing ApoB48) and fat transported from the liver in VLDL (containing ApoB100). Research into the roles of endogenous versus dietary fat has been hindered because of the difficulty in separating these particles by ultracentrifugation. CM fractions have considerable contamination from VLDL (purity, 10%). To separate CMs from VLDL, we produced polyclonal antibodies against ApoB100 and generated immunoaffinity columns. TRLs isolated by ultracentrifugation of plasma were applied to these columns, and highly purified CMs were collected (purity, 90–94%). Overall eight healthy unmedicated adult volunteers (BMI, 27.2 ± 1.4 kg/m2; fasting triacylglycerol, 102.6 ± 19.5 mg/dl) participated in a feeding study, which contained an oral stable-isotope tracer (1-13C acetate). We then used this technique on plasma samples freshly collected during an 8 h human feeding study from a subset of four subjects. We analyzed fractionated lipoproteins by Western blot, isolated and derivatized triacylglycerols, and calculated fractional de novo lipogenesis. The results demonstrated effective separation of postprandial lipoproteins and substantially improved purity compared with ultracentrifugation protocols, using the immunoaffinity method. This method can be used to better delineate the role of dietary sugar and fat on postprandial lipids in cardiovascular risk and explore the potential role of CM remnants in atherosclerosis.




affinity

Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications [Immunology]

Antibodies are widely used as cancer therapeutics, but their current use is limited by the low number of antigens restricted to cancer cells. A receptor tyrosine kinase, receptor tyrosine kinase-like orphan receptor 2 (ROR2), is normally expressed only during embryogenesis and is tightly down-regulated in postnatal healthy tissues. However, it is up-regulated in a diverse set of hematologic and solid malignancies, thus ROR2 represents a candidate antigen for antibody-based cancer therapy. Here we describe the affinity maturation and humanization of a rabbit mAb that binds human and mouse ROR2 but not human ROR1 or other human cell-surface antigens. Co-crystallization of the parental rabbit mAb in complex with the human ROR2 kringle domain (hROR2-Kr) guided affinity maturation by heavy-chain complementarity-determining region 3 (HCDR3)-focused mutagenesis and selection. The affinity-matured rabbit mAb was then humanized by complementarity-determining region (CDR) grafting and framework fine tuning and again co-crystallized with hROR2-Kr. We show that the affinity-matured and humanized mAb retains strong affinity and specificity to ROR2 and, following conversion to a T cell–engaging bispecific antibody, has potent cytotoxicity toward ROR2-expressing cells. We anticipate that this humanized affinity-matured mAb will find application for antibody-based cancer therapy of ROR2-expressing neoplasms.




affinity

A Critical Insulin TCR Contact Residue Selects High-Affinity and Pathogenic Insulin-Specific T Cells

Type 1 diabetes is an autoimmune-mediated disease that culminates in the targeted destruction of insulin-producing β-cells. CD4 responses in NOD mice are dominated by insulin epitope B:9-23 (InsB9-23) specificity, and mutation of the key T-cell receptor (TCR) contact residue within the epitope prevents diabetes development. However, it is not clear how insulin self-antigen controls the selection of autoimmune and regulatory T cells (Tregs). Here we demonstrate that mutation of insulin epitope results in escape of highly pathogenic T cells. We observe an increase in antigen reactivity, clonality, and pathogenicity of insulin-specific T cells that develop in the absence of cognate antigen. Using a single TCR system, we demonstrate that Treg development is greatly diminished in mice with the Y16A mutant epitope. Collectively, these results suggest that the tyrosine residue at position 16 is necessary to constrain TCR reactivity for InsB9-23 by both limiting the development of pathogenic T cells and supporting the selection of Tregs.




affinity

A Hybrid Insulin Epitope Maintains High 2D Affinity for Diabetogenic T Cells in the Periphery

β-Cell antigen recognition by autoreactive T cells is essential in type 1 diabetes (T1D) pathogenesis. Recently, insulin hybrid peptides (HIPs) were identified as strong agonists for CD4 diabetogenic T cells. Here, using BDC2.5 transgenic and NOD mice, we investigated T-cell recognition of the HIP2.5 epitope, which is a fusion of insulin C-peptide and chromogranin A (ChgA) fragments, and compared it with the WE14 and ChgA29–42 epitopes. We measured in situ two-dimensional affinity on individual live T cells from thymus, spleen, pancreatic lymph nodes, and islets before and after diabetes. Although preselection BDC2.5 thymocytes possess higher affinity than splenic BDC2.5 T cells for all three epitopes, peripheral splenic T cells maintained high affinity only to the HIP2.5 epitope. In polyclonal NOD mice, a high frequency (~40%) of HIP2.5-specific islet T cells were identified at both prediabetic and diabetic stages comprising two distinct high- and low-affinity populations that differed in affinity by 100-fold. This high frequency of high- and low-affinity HIP2.5 T cells in the islets potentially represents a major risk factor in diabetes pathogenesis.




affinity

Specificity and affinity of the N-terminal residues in staphylocoagulase in binding to prothrombin [Computational Biology]

In Staphylococcus aureus–caused endocarditis, the pathogen secretes staphylocoagulase (SC), thereby activating human prothrombin (ProT) and evading immune clearance. A previous structural comparison of the SC(1–325) fragment bound to thrombin and its inactive precursor prethrombin 2 has indicated that SC activates ProT by inserting its N-terminal dipeptide Ile1-Val2 into the ProT Ile16 pocket, forming a salt bridge with ProT's Asp194, thereby stabilizing the active conformation. We hypothesized that these N-terminal SC residues modulate ProT binding and activation. Here, we generated labeled SC(1–246) as a probe for competitively defining the affinities of N-terminal SC(1–246) variants preselected by modeling. Using ProT(R155Q,R271Q,R284Q) (ProTQQQ), a variant refractory to prothrombinase- or thrombin-mediated cleavage, we observed variant affinities between ∼1 and 650 nm and activation potencies ranging from 1.8-fold that of WT SC(1–246) to complete loss of function. Substrate binding to ProTQQQ caused allosteric tightening of the affinity of most SC(1–246) variants, consistent with zymogen activation through occupation of the specificity pocket. Conservative changes at positions 1 and 2 were well-tolerated, with Val1-Val2, Ile1-Ala2, and Leu1-Val2 variants exhibiting ProTQQQ affinity and activation potency comparable with WT SC(1–246). Weaker binding variants typically had reduced activation rates, although at near-saturating ProTQQQ levels, several variants exhibited limiting rates similar to or higher than that of WT SC(1–246). The Ile16 pocket in ProTQQQ appears to favor nonpolar, nonaromatic residues at SC positions 1 and 2. Our results suggest that SC variants other than WT Ile1-Val2-Thr3 might emerge with similar ProT-activating efficiency.




affinity

A neuroglobin-based high-affinity ligand trap reverses carbon monoxide-induced mitochondrial poisoning [Molecular Biophysics]

Carbon monoxide (CO) remains the most common cause of human poisoning. The consequences of CO poisoning include cardiac dysfunction, brain injury, and death. CO causes toxicity by binding to hemoglobin and by inhibiting mitochondrial cytochrome c oxidase (CcO), thereby decreasing oxygen delivery and inhibiting oxidative phosphorylation. We have recently developed a CO antidote based on human neuroglobin (Ngb-H64Q-CCC). This molecule enhances clearance of CO from red blood cells in vitro and in vivo. Herein, we tested whether Ngb-H64Q-CCC can also scavenge CO from CcO and attenuate CO-induced inhibition of mitochondrial respiration. Heart tissue from mice exposed to 3% CO exhibited a 42 ± 19% reduction in tissue respiration rate and a 33 ± 38% reduction in CcO activity compared with unexposed mice. Intravenous infusion of Ngb-H64Q-CCC restored respiration rates to that of control mice correlating with higher electron transport chain CcO activity in Ngb-H64Q-CCC–treated compared with PBS-treated, CO-poisoned mice. Further, using a Clark-type oxygen electrode, we measured isolated rat liver mitochondrial respiration in the presence and absence of saturating solutions of CO (160 μm) and nitric oxide (100 μm). Both CO and NO inhibited respiration, and treatment with Ngb-H64Q-CCC (100 and 50 μm, respectively) significantly reversed this inhibition. These results suggest that Ngb-H64Q-CCC mitigates CO toxicity by scavenging CO from carboxyhemoglobin, improving systemic oxygen delivery and reversing the inhibitory effects of CO on mitochondria. We conclude that Ngb-H64Q-CCC or other CO scavengers demonstrate potential as antidotes that reverse the clinical and molecular effects of CO poisoning.




affinity

Purification of Recombinant Adeno-Associated Virus 2 (rAAV2) by Heparin Column Affinity Chromatography

This protocol describes a simple single-step column purification (SSCP) of rAAV2 by gravity flow based on its affinity to heparin, without ultracentrifugation.




affinity

BCR selection and affinity maturation in Peyer’s patch germinal centres




affinity

[ASAP] Remodeling of the Oligosaccharide Conformational Space in the Prebound State To Improve Lectin-Binding Affinity

Biochemistry
DOI: 10.1021/acs.biochem.9b00594




affinity

[ASAP] Affinity-Driven Design of Cargo-Switching Nanoparticles to Leverage a Cholesterol-Rich Microenvironment for Atherosclerosis Therapy

ACS Nano
DOI: 10.1021/acsnano.9b08216