1,391 results match your criteria affinity expanded


Microfluidic Integrated Organic Electrochemical Transistor with a Nanoporous Membrane for Amyloid-β Detection.

ACS Nano 2021 Mar 30. Epub 2021 Mar 30.

Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

Alzheimer's disease (AD) is a neurodegenerative disorder associated with a severe loss in thinking, learning, and memory functions of the brain. To date, no specific treatment has been proven to cure AD, with the early diagnosis being vital for mitigating symptoms. A common pathological change found in AD-affected brains is the accumulation of a protein named amyloid-β (Aβ) into plaques. Read More

View Article and Full-Text PDF

Chemical Phosphoproteomics Sheds New Light on the Targets and Modes of Action of AKT Inhibitors.

ACS Chem Biol 2021 Apr 23;16(4):631-641. Epub 2021 Mar 23.

Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany.

Due to its important roles in oncogenic signaling, AKT has been subjected to extensive drug discovery efforts leading to small molecule inhibitors investigated in advanced clinical trials. To better understand how these drugs exert their therapeutic effects at the molecular level, we combined chemoproteomic target affinity profiling using kinobeads and phosphoproteomics to analyze the five clinical AKT inhibitors AZD5363 (Capivasertib), GSK2110183 (Afuresertib), GSK690693, Ipatasertib, and MK-2206 in BT-474 breast cancer cells. Kinobead profiling identified between four and 29 nM targets for these compounds and showed that AKT1 and AKT2 were the only common targets. Read More

View Article and Full-Text PDF

Protective low-avidity anti-tumour CD8+ T cells are selectively attenuated by regulatory T cells.

Immunother Adv 2021 Jan 25;1(1):ltaa001. Epub 2020 Nov 25.

Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, UK.

Objectives: Regulatory T cells (Treg) play a major role in the suppression of protective anti-tumour T cell responses. In the CT26 BALB/c murine model of colorectal carcinoma, Tregs differentially suppress responses to two characterised CD8+ T epitopes, AH1 and GSW11, which results in an absence of detectable IFN-γ-producing GSW11-specific T cells in the spleen and lymph nodes of tumour challenged mice. Activation of GSW11-specific T cells correlates with protection against tumour progression. Read More

View Article and Full-Text PDF
January 2021

Global Profiling of the Lysine Crotonylome in Different Pluripotent States.

Genomics Proteomics Bioinformatics 2021 Mar 18. Epub 2021 Mar 18.

Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China. Electronic address:

Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for developmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifications of proteins. Read More

View Article and Full-Text PDF

Transnasal endoscopic skull base surgery in the COVID-19 era: Recommendations for increasing the safety of the method.

Adv Med Sci 2021 Mar 4;66(1):221-230. Epub 2021 Mar 4.

Lynne Shepard Jones Chair in Head & Neck Oncology, The Ohio State University Wexner Medical Center, USA.

Transnasal endoscopic skull base surgery (eSBS) has been adopted in recent years, in great part to replace the extended procedures required by external approaches. Though sometimes perceived as "minimally invasive", eSBS still necessitates extensive manipulations within the nose/paranasal sinuses. Furthermore, exposure of susceptible cerebral structures to light and heat emanated by the telescope should be considered to comprehensively evaluate the safety of the method. Read More

View Article and Full-Text PDF

Insights into the interaction dynamics between volatile anesthetics and tubulin through computational molecular modelling.

J Biomol Struct Dyn 2021 Mar 10:1-15. Epub 2021 Mar 10.

Department of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Turin, Italy.

General anesthetics, able to reversibly suppress all conscious brain activity, have baffled medical science for decades, and little is known about their exact molecular mechanism of action. Given the recent scientific interest in the exploration of microtubules as putative functional targets of anesthetics, and the involvement thereof in neurodegenerative disorders, the present work focuses on the investigation of the interaction between human tubulin and four volatile anesthetics: ethylene, desflurane, halothane and methoxyflurane. Interaction sites on different tubulin isotypes are predicted through docking, along with an estimate of the binding affinity ranking. Read More

View Article and Full-Text PDF

Coordinated control of the type IV pili and c-di-GMP-dependent antifungal antibiotic production in Lysobacter by the response regulator PilR.

Mol Plant Pathol 2021 May 11;22(5):602-617. Epub 2021 Mar 11.

College of Plant Protection (Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P.R. China.

In the soil gammaproteobacterium Lysobacter enzymogenes, a natural fungal predator, the response regulator PilR controls type IV pili (T4P)-mediated twitching motility as well as synthesis of the heat-stable antifungal factor (HSAF). Earlier we showed that PilR acts via the second messenger, c-di-GMP; however, the mechanism remained unknown. Here, we describe how PilR, c-di-GMP signalling, and HSAF synthesis are connected. Read More

View Article and Full-Text PDF

Machine learning optimization of peptides for presentation by class II MHCs.

Bioinformatics 2021 Mar 10. Epub 2021 Mar 10.

Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.

T cells play a critical role in cellular immune responses to pathogens and cancer and can be activated and expanded by MHC-presented antigens contained in peptide vaccines. We present a machine learning method to optimize the presentation of peptides by class II MHCs by modifying their anchor residues. Our method first learns a model of peptide affinity for a class II MHC using an ensemble of deep residual networks, and then uses the model to propose anchor residue changes to improve peptide affinity. Read More

View Article and Full-Text PDF

RNA-Centric Approaches to Profile the RNA-Protein Interaction Landscape on Selected RNAs.

Authors:
André P Gerber

Noncoding RNA 2021 Feb 15;7(1). Epub 2021 Feb 15.

Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.

RNA-protein interactions frame post-transcriptional regulatory networks and modulate transcription and epigenetics. While the technological advances in RNA sequencing have significantly expanded the repertoire of RNAs, recently developed biochemical approaches combined with sensitive mass-spectrometry have revealed hundreds of previously unrecognized and potentially novel RNA-binding proteins. Nevertheless, a major challenge remains to understand how the thousands of RNA molecules and their interacting proteins assemble and control the fate of each individual RNA in a cell. Read More

View Article and Full-Text PDF
February 2021

New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure.

J Virol 2021 Mar 3. Epub 2021 Mar 3.

Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA

Previously, we showed that substitution of HIV-1 Env residue 375-Ser by bulky aromatic residues enhances binding to rhesus CD4 and enables primary HIV-1 Envs to support efficient replication as simian-human immunodeficiency virus (SHIV) chimeras in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing SHIVs containing ten primary Envs corresponding to HIV-1 subtypes A, B, C, AE and AG. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4 T cells, but only one replicated efficiently in primary rhesus cells. Read More

View Article and Full-Text PDF

Lysine crotonylation is widespread on proteins of diverse functions and localizations in Toxoplasma gondii.

Parasitol Res 2021 Mar 3. Epub 2021 Mar 3.

College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, People's Republic of China.

Lysine crotonylation (Kcr) is an evolutionally conserved post-translational modification (PTM) on histone proteins. However, information about Kcr and its involvement in the biology and metabolism of Toxoplasma gondii is limited. In the present study, a global Kcr proteome analysis using LC-MS/MS in combination with immune-affinity method was performed. Read More

View Article and Full-Text PDF

Structural analysis of EhPSP in complex with 3-phosphoglyceric acid from Entamoeba histolytica reveals a basis for its lack of phosphoglycerate mutase activity.

Int J Biol Macromol 2021 Feb 23;178:1-10. Epub 2021 Feb 23.

School of Life Sciences, Jawaharlal Nehru University, New Delhi, India. Electronic address:

Entamoeba histolytica phosphoserine phosphatase (EhPSP), a regulatory enzyme in the serine biosynthetic pathway, is also a structural homolog of cofactor-dependent phosphoglycerate mutase (dPGM). However, despite sharing many of its catalytic residues with dPGM, EhPSP displays no significant mutase activity. In the current work, we determined a crystal structure of EhPSP in complex with 3-PGA to 2. Read More

View Article and Full-Text PDF
February 2021

T Cells Induced by Vaccination and Following SIV Challenge Support Env-Specific Humoral Immunity in the Rectal-Genital Tract and Circulation of Female Rhesus Macaques.

Front Immunol 2020 28;11:608003. Epub 2021 Jan 28.

Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.

T follicular helper (T) cells are pivotal in lymph node (LN) germinal center (GC) B cell affinity maturation. Circulating CXCR5 CD4 T (cT) cells have supported memory B cell activation and broadly neutralizing antibodies in HIV controllers. We investigated the contribution of LN SIV-specific T and cT cells to Env-specific humoral immunity in female rhesus macaques following a mucosal Ad5hr-SIV recombinant priming and SIV gp120 intramuscular boosting vaccine regimen and following SIV vaginal challenge. Read More

View Article and Full-Text PDF
January 2021

Restriction of an intron size en route to endothermy.

Nucleic Acids Res 2021 03;49(5):2460-2487

University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK.

Ca2+-insensitive and -sensitive E1 subunits of the 2-oxoglutarate dehydrogenase complex (OGDHC) regulate tissue-specific NADH and ATP supply by mutually exclusive OGDH exons 4a and 4b. Here we show that their splicing is enforced by distant lariat branch points (dBPs) located near the 5' splice site of the intervening intron. dBPs restrict the intron length and prevent transposon insertions, which can introduce or eliminate dBP competitors. Read More

View Article and Full-Text PDF

Ligand-directed two-step labeling to quantify neuronal glutamate receptor trafficking.

Nat Commun 2021 02 5;12(1):831. Epub 2021 Feb 5.

Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.

The regulation of glutamate receptor localization is critical for development and synaptic plasticity in the central nervous system. Conventional biochemical and molecular biological approaches have been widely used to analyze glutamate receptor trafficking, especially for α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate-type glutamate receptors (AMPARs). However, conflicting findings have been reported because of a lack of useful tools for analyzing endogenous AMPARs. Read More

View Article and Full-Text PDF
February 2021

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.

Structure 2021 Jan 29. Epub 2021 Jan 29.

University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA. Electronic address:

Accurate predictive modeling of antibody-antigen complex structures and structure-based antibody design remain major challenges in computational biology, with implications for biotherapeutics, immunity, and vaccines. Through a systematic search for high-resolution structures of antibody-antigen complexes and unbound antibody and antigen structures, in conjunction with identification of experimentally determined binding affinities, we have assembled a non-redundant set of test cases for antibody-antigen docking and affinity prediction. This benchmark more than doubles the number of antibody-antigen complexes and corresponding affinities available in our previous benchmarks, providing an unprecedented view of the determinants of antibody recognition and insights into molecular flexibility. Read More

View Article and Full-Text PDF
January 2021

Role of amino terminal substitutions in the pharmacological, rewarding and psychostimulant profiles of novel synthetic cathinones.

Neuropharmacology 2021 03 30;186:108475. Epub 2021 Jan 30.

Department of Pharmacology, Toxicology and Therapeutic Chemistry, Pharmacology Section and Institute of Biomedicine (IBUB), Faculty of Pharmacy, University of Barcelona, Barcelona, Spain.

The emergence of new synthetic cathinones continues to be a matter of public health concern. In fact, they are quickly replaced by new structurally related alternatives. The main goal of the present study was to characterize the pharmacological profile, the psychostimulant and rewarding properties of novel cathinones (pentedrone, N-ethyl-pentedrone, α-PVP, N,N-diethyl-pentedrone and α-PpVP) which only differs in their amino terminal substitution. Read More

View Article and Full-Text PDF

Fully Integrated and Multiplexed Sample Preparation Technology for Sensitive Interactome Profiling.

Anal Chem 2021 02 31;93(5):3026-3034. Epub 2021 Jan 31.

Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.

Affinity purification coupled to mass spectrometry (AP-MS) is a popular approach for deciphering the architecture of protein interaction networks. Protein lysates (100 μg) are typically required for multistep sample processing in large volumes, which often causes sample loss and reduces the MS analysis sensitivity. Herein, we reported a fully integrated spintip-based AP-MS technology, termed FISAP, for multiplexed and sensitive interactome profiling. Read More

View Article and Full-Text PDF
February 2021

A Labeling Strategy for Living Specimens in Long-Term/Super-Resolution Fluorescence Imaging.

Front Chem 2020 15;8:601436. Epub 2021 Jan 15.

State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.

Despite the urgent need to image living specimens for cutting-edge biological research, most existing fluorescent labeling methods suffer from either poor optical properties or complicated operations required to realize cell-permeability and specificity. In this study, we introduce a method to overcome these limits-taking advantage of the intrinsic affinity of bright and photostable fluorophores, no matter if they are supposed to be live-cell incompatible or not. Incubated with living cells and tissues in particular conditions (concentration and temperature), some Atto and BODIPY dyes show live-cell labeling capability for specific organelles without physical cell-penetration or chemical modifications. Read More

View Article and Full-Text PDF
January 2021

Mutations during the adaptation of H7N9 avian influenza virus to mice lungs enhance human-like sialic acid binding activity and virulence in mice.

Vet Microbiol 2021 Mar 20;254:109000. Epub 2021 Jan 20.

Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China(26116120), Yangzhou University, Yangzhou, China. Electronic address:

The first avian H7N9 influenza outbreak in spring of 2013 emerged in an unprecedented transmission from infected poultry to humans in the Yangtze delta area, eastern China, posing a dual challenge to public health and poultry industry. However, the mechanism for how avian H7N9 influenza virus adapts to mammalian hosts has not been clearly understood. Here, to identify adaptive changes that confer enhanced virulence of H7N9 virus in mammals, we generated a mouse-adapted H7N9 variant virus (S8) by serial lung-to-lung passages of the wild-type SDL124 virus in mice and compared their phenotype in vivo and in vitro. Read More

View Article and Full-Text PDF

Preclinical Evaluation of Invariant Natural Killer T Cells Modified with CD38 or BCMA Chimeric Antigen Receptors for Multiple Myeloma.

Int J Mol Sci 2021 Jan 22;22(3). Epub 2021 Jan 22.

Cancer Center Amsterdam, Department of Haematology, Amsterdam UMC, VU Amsterdam, 1081 HV Amsterdam, The Netherlands.

Due to the CD1d restricted recognition of altered glycolipids, Vα24-invariant natural killer T (iNKT) cells are excellent tools for cancer immunotherapy with a significantly reduced risk for graft-versus-host disease when applied as off-the shelf-therapeutics across Human Leukocyte Antigen (HLA) barriers. To maximally harness their therapeutic potential for multiple myeloma (MM) treatment, we here armed iNKT cells with chimeric antigen receptors (CAR) directed against the MM-associated antigen CD38 and the plasma cell specific B cell maturation antigen (BCMA). We demonstrate that both CD38- and BCMA-CAR iNKT cells effectively eliminated MM cells in a CAR-dependent manner, without losing their T cell receptor (TCR)-mediated cytotoxic activity. Read More

View Article and Full-Text PDF
January 2021

Chemical Diversification of Simple Synthetic Antibodies.

ACS Chem Biol 2021 02 22;16(2):344-359. Epub 2021 Jan 22.

Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States.

Antibodies possess properties that make them valuable as therapeutics, diagnostics, and basic research tools. However, antibody chemical reactivity and covalent antigen binding are constrained, or even prevented, by the narrow range of chemistries encoded in canonical amino acids. In this work, we investigate strategies for leveraging an expanded range of chemical functionality using yeast displayed antibodies containing noncanonical amino acids (ncAAs) in or near antibody complementarity determining regions (CDRs). Read More

View Article and Full-Text PDF
February 2021

How a Fragment Draws Attention to Selectivity Discriminating Features between the Related Proteases Trypsin and Thrombin.

J Med Chem 2021 02 20;64(3):1611-1625. Epub 2021 Jan 20.

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

In the S pocket, the serine proteases thrombin and trypsin commonly feature Asp189 and a Ala190Ser and Glu192Gln exchange. Nevertheless, thrombin cleaves peptide chains solely after Arg, and trypsin after Lys and Arg. Thrombin exhibits a Na+-binding site next to Asp189, which is missing in trypsin. Read More

View Article and Full-Text PDF
February 2021

A short ORF-encoded transcriptional regulator.

Proc Natl Acad Sci U S A 2021 Jan;118(4)

Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;

Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. Read More

View Article and Full-Text PDF
January 2021

A multifunctional α-amylase BSGH13 from Bacillus subtilis BS-5 possessing endoglucanase and xylanase activities.

Int J Biol Macromol 2021 Feb 6;171:166-176. Epub 2021 Jan 6.

College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China. Electronic address:

Exploring new multifunctional enzymes and understanding the mechanisms of catalytic promiscuity will be of enormous industrial and academic values. In the present study, we reported the discovery and characterization of a multifunctional enzyme BSGH13 from Bacillus subtilis BS-5. Remarkably, BSGH13 possessed α-amylase, endoglucanase, and xylanase activities. Read More

View Article and Full-Text PDF
February 2021

Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries.

SLAS Discov 2021 Feb 8;26(2):263-280. Epub 2021 Jan 8.

Discovery Sciences, Pfizer Inc., Groton, CT, USA.

Over the past 20 years, the toolbox for discovering small-molecule therapeutic starting points has expanded considerably. Pharmaceutical researchers can now choose from technologies that, in addition to traditional high-throughput knowledge-based and diversity screening, now include the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). Each of these techniques has its own unique combination of advantages and limitations that makes them more, or less, suitable for different target classes or discovery objectives, such as desired mechanism of action. Read More

View Article and Full-Text PDF
February 2021

Copper-binding properties of microplastic-derived dissolved organic matter revealed by fluorescence spectroscopy and two-dimensional correlation spectroscopy.

Water Res 2021 Feb 23;190:116775. Epub 2020 Dec 23.

Department of Environment and Energy, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea. Electronic address:

Despite numerous studies on microplastics (MPs), little attention has been paid to the dissolved organic substances leached from MPs and their environmental fate. In this study, we explored the copper-binding characteristics of MP-derived dissolved organic matter (MP-DOM) leached from several MP types, including commercial polypropylene, polyvinylchloride, and expanded polystyrene, under dark and UV irradiation conditions. The copper-binding affinity of MP-DOM was examined using fluorescence quenching method based on different fluorophores identified via the excitation emission matrix-parallel factor analysis (EEM-PARAFAC). Read More

View Article and Full-Text PDF
February 2021

Direct Kinetic Fingerprinting for High-Accuracy Single-Molecule Counting of Diverse Disease Biomarkers.

Acc Chem Res 2021 01 31;54(2):388-402. Epub 2020 Dec 31.

Methods for detecting and quantifying disease biomarkers in biofluids with high specificity and sensitivity play a pivotal role in enabling clinical diagnostics, including point-of-care tests. The most widely used molecular biomarkers include proteins, nucleic acids, hormones, metabolites, and other small molecules. While numerous methods have been developed for analyzing biomarkers, most techniques are challenging to implement for clinical use due to insufficient analytical performance, high cost, and/or other practical shortcomings. Read More

View Article and Full-Text PDF
January 2021

CD38 knockout natural killer cells expressing an affinity optimized CD38 chimeric antigen receptor successfully target acute myeloid leukemia with reduced effector cell fratricide.

Haematologica 2020 Dec 30;Online ahead of print. Epub 2020 Dec 30.

National University of Ireland Galway, Galway.

There is a strong biological rationale for the augmentation of allogeneic natural killer (NK) cell therapies with a chimeric antigen receptor (CAR) to enhance acute myeloid leukemia (AML) targeting. CD38 is an established immunotherapeutic target in multiple myeloma and under investigation as a target antigen in AML. CD38 expression on NK cells and its further induction during ex vivo NK cell expansion represents a barrier to the development of a CD38 CAR-NK cell therapy. Read More

View Article and Full-Text PDF
December 2020

FRCaMP, a Red Fluorescent Genetically Encoded Calcium Indicator Based on Calmodulin from Schizosaccharomyces Pombe Fungus.

Int J Mol Sci 2020 Dec 24;22(1). Epub 2020 Dec 24.

Complex of NBICS Technologies, National Research Center "Kurchatov Institute", 123182 Moscow, Russia.

Red fluorescent genetically encoded calcium indicators (GECIs) have expanded the available pallet of colors used for the visualization of neuronal calcium activity in vivo. However, their calcium-binding domain is restricted by calmodulin from metazoans. In this study, we developed red GECI, called FRCaMP, using calmodulin (CaM) from fungus as a calcium binding domain. Read More

View Article and Full-Text PDF
December 2020