Статті в журналах: "Affinity-Based protein profiling"

1

Wirsing, Lisette, Kai Naumann, and Thomas Vogt. "Arabidopsis methyltransferase fingerprints by affinity-based protein profiling." Analytical Biochemistry 408, no. 2 (January 2011): 220–25. http://dx.doi.org/10.1016/j.ab.2010.09.029.

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2

Lafreniere, Matthew A., Geneviève F. Desrochers, Kedous Mekbib, and John Paul Pezacki. "An affinity-based probe for methyltransferase enzymes based on sinefungin." Canadian Journal of Chemistry 95, no. 10 (October 2017): 1059–63. http://dx.doi.org/10.1139/cjc-2017-0168.

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Epigenetics control numerous cellular processes such as gene transcription, signal transduction, and protein stabilization. An understanding of epigenetic mechanisms can lead to the development of therapeutic agents for various diseases. Herein, we report the design and synthesis of a sinefungin affinity-probe (BpyneSF) that targets methyltranferase enzymes and proteins involved in recognition of methylation. This probe contains a bioorthogonal alkyne residue for conjugation using the copper-catalyzed azide–alkyne cycloaddition and a photoactivatable crosslinker group for covalent attachment of the probe to its proteomic targets. We investigate the efficiency and selectivity of the probe to inhibit and label methyltransferase enzymes, and we demonstrate, through in-gel fluorescence, on-bead digestion, and tandem mass spectrometry, that BpyneSF can label methyltransferase SETD2 and reader proteins in vitro. These results establish the utility of BpyneSF as a tool for affinity-based protein profiling in complex biological environments.

3

Buneeva, Olga, Arthur Kopylov, Oksana Gnedenko, Marina Medvedeva, Alexander Veselovsky, Alexis Ivanov, Victor Zgoda, and Alexei Medvedev. "Proteomic Profiling of Mouse Brain Pyruvate Kinase Binding Proteins: A Hint for Moonlighting Functions of PKM1?" International Journal of Molecular Sciences 24, no. 8 (April 21, 2023): 7634. http://dx.doi.org/10.3390/ijms24087634.

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Affinity-based proteomic profiling is widely used for the identification of proteins involved in the formation of various interactomes. Since protein–protein interactions (PPIs) reflect the role of particular proteins in the cell, identification of interaction partners for a protein of interest can reveal its function. The latter is especially important for the characterization of multifunctional proteins, which can play different roles in the cell. Pyruvate kinase (PK), a classical glycolytic enzyme catalyzing the last step of glycolysis, exists in four isoforms: PKM1, PKM2, PKL, and PKR. The enzyme isoform expressed in actively dividing cells, PKM2, exhibits many moonlighting (noncanonical) functions. In contrast to PKM2, PKM1, predominantly expressed in adult differentiated tissues, lacks well-documented moonlighting functions. However, certain evidence exists that it can also perform some functions unrelated to glycolysis. In order to evaluate protein partners, bound to PKM1, in this study we have combined affinity-based separation of mouse brain proteins with mass spectrometry identification. The highly purified PKM1 and a 32-mer synthetic peptide (PK peptide), sharing high sequence homology with the interface contact region of all PK isoforms, were used as the affinity ligands. This proteomic profiling resulted in the identification of specific and common proteins bound to both affinity ligands. Quantitative affinity binding to the affinity ligands of selected identified proteins was validated using a surface plasmon resonance (SPR) biosensor. Bioinformatic analysis has shown that the identified proteins, bound to both full-length PKM1 and the PK peptide, form a protein network (interactome). Some of these interactions are relevant for the moonlighting functions of PKM1. The proteomic dataset is available via ProteomeXchange with the identifier PXD041321.

4

Jung, Se-Hui, Kangseung Lee, Deok-Hoon Kong, Woo Jin Kim, Young-Myeong Kim, and Kwon-Soo Ha. "Integrative Proteomic Profiling of Protein Activity and Interactions Using Protein Arrays." Molecular & Cellular Proteomics 11, no. 11 (July 26, 2012): 1167–76. http://dx.doi.org/10.1074/mcp.m112.016964.

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Proteomic studies based on abundance, activity, or interactions have been used to investigate protein functions in normal and pathological processes, but their combinatory approach has not been attempted. We present an integrative proteomic profiling method to measure protein activity and interaction using fluorescence-based protein arrays. We used an on-chip assay to simultaneously monitor the transamidating activity and binding affinity of transglutaminase 2 (TG2) for 16 TG2-related proteins. The results of this assay were compared with confidential scores provided by the STRING database to analyze the functional interactions of TG2 with these proteins. We further created a quantitative activity-interaction map of TG2 with these 16 proteins, categorizing them into seven groups based upon TG2 activity and interaction. This integrative proteomic profiling method can be applied to quantitative validation of previously known protein interactions, and in understanding the functions and regulation of target proteins in biological processes of interest.

5

Ma, Nan, Zhi-Min Zhang, Jun-Seok Lee, Ke Cheng, Ligen Lin, Dong-Mei Zhang, Piliang Hao, Ke Ding, Wen-Cai Ye, and Zhengqiu Li. "Affinity-Based Protein Profiling Reveals Cellular Targets of Photoreactive Anticancer Inhibitors." ACS Chemical Biology 14, no. 12 (November 19, 2019): 2546–52. http://dx.doi.org/10.1021/acschembio.9b00784.

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6

Chen, Xiong, Menglin Li, Manru Li, Dongmei Wang, and Jinlan Zhang. "Harnessing affinity-based protein profiling to reveal a novel target of nintedanib." Chemical Communications 57, no. 25 (2021): 3139–42. http://dx.doi.org/10.1039/d1cc00354b.

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We identified tripeptidyl-peptidase 1 (TPP1) as one of the direct targets of nintedanib (NDNB) employing clickable photoaffinity probes, which provides insights into the functional meaning of the well-known IPF therapeutic drug.

7

Chou, Po-Hung, Shu-Hua Chen, Hsin-Kai Liao, Po-Chiao Lin, Gour-Rong Her, Alan Chuan-Ying Lai, Jenn-Han Chen, Chun-Cheng Lin, and Yu-Ju Chen. "Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma." Analytical Chemistry 77, no. 18 (September 2005): 5990–97. http://dx.doi.org/10.1021/ac050655o.

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8

Lyu, Peng, Shengrong Li, Ying Han, Shengnan Shen, Zheling Feng, Piliang Hao, Zhengqiu Li, and Ligen Lin. "Affinity-based protein profiling-driven discovery of myricanol as a Nampt activator." Bioorganic Chemistry 133 (April 2023): 106435. http://dx.doi.org/10.1016/j.bioorg.2023.106435.

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9

Cheng, Xiamin, Lin Li, Mahesh Uttamchandani, and Shao Q. Yao. "A tuned affinity-based staurosporine probe for in situ profiling of protein kinases." Chemical Communications 50, no. 22 (2014): 2851. http://dx.doi.org/10.1039/c4cc00184b.

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10

Mezentsev, Yuri, Pavel Ershov, Evgeniy Yablokov, Leonid Kaluzhskiy, Konstantin Kupriyanov, Oksana Gnedenko, and Alexis Ivanov. "Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate." International Journal of Molecular Sciences 23, no. 24 (December 10, 2022): 15697. http://dx.doi.org/10.3390/ijms232415697.

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Most proteins function as part of various complexes, forming via stable and dynamic protein–protein interactions (PPIs). The profiling of PPIs expands the fundamental knowledge about the structures, functions, and regulation patterns of protein complexes and intracellular molecular machineries. Protein interactomics aims at solving three main tasks: (1) identification of protein partners and parts of complex intracellular structures; (2) analysis of PPIs parameters (affinity, molecular-recognition specificity, kinetic rate constants, and thermodynamic-parameters determination); (3) the study of the functional role of novel PPIs. The purpose of this work is to update the current state and prospects of multi-omics approaches to profiling of proteins involved in the formation of stable complexes. Methodological paradigm includes a development of protein-extraction and -separation techniques from tissues or cellular lysates and subsequent identification of proteins using mass-spectrometry analysis. In addition, some aspects of authors’ experimental platforms, based on high-performance size-exclusion chromatography, procedures of molecular fishing, and protein identification, as well as the possibilities of interactomic taxonomy of each protein, are discussed.

11

Battenberg, Oliver A., Matthew B. Nodwell та Stephan A. Sieber. "Evaluation of α-Pyrones and Pyrimidones as Photoaffinity Probes for Affinity-Based Protein Profiling". Journal of Organic Chemistry 76, № 15 (5 серпня 2011): 6075–87. http://dx.doi.org/10.1021/jo201281c.

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12

Palermo, Giulia, Wietse M. Schouten, Luis Lago Alonso, Chris Ulens, Jeroen Kool, and Julien Slagboom. "Acetylcholine-Binding Protein Affinity Profiling of Neurotoxins in Snake Venoms with Parallel Toxin Identification." International Journal of Molecular Sciences 24, no. 23 (November 26, 2023): 16769. http://dx.doi.org/10.3390/ijms242316769.

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Snakebite is considered a concerning issue and a neglected tropical disease. Three-finger toxins (3FTxs) in snake venoms primarily cause neurotoxic effects since they have high affinity for nicotinic acetylcholine receptors (nAChRs). Their small molecular size makes 3FTxs weakly immunogenic and therefore not appropriately targeted by current antivenoms. This study aims at presenting and applying an analytical method for investigating the therapeutic potential of the acetylcholine-binding protein (AChBP), an efficient nAChR mimic that can capture 3FTxs, for alternative treatment of elapid snakebites. In this analytical methodology, snake venom toxins were separated and characterised using high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) and high-throughput venomics. By subsequent nanofractionation analytics, binding profiling of toxins to the AChBP was achieved with a post-column plate reader-based fluorescence-enhancement ligand displacement bioassay. The integrated method was established and applied to profiling venoms of six elapid snakes (Naja mossambica, Ophiophagus hannah, Dendroaspis polylepis, Naja kaouthia, Naja haje and Bungarus multicinctus). The methodology demonstrated that the AChBP is able to effectively bind long-chain 3FTxs with relatively high affinity, but has low or no binding affinity towards short-chain 3FTxs, and as such provides an efficient analytical platform to investigate binding affinity of 3FTxs to the AChBP and mutants thereof and to rapidly identify bound toxins.

13

Qiu, Wen-Wei, Jie Xu, Jing-Ya Li, Jia Li, and Fa-Jun Nan. "Activity-Based Protein Profiling for Type I Methionine Aminopeptidase by Using Photo-Affinity Trimodular Probes." ChemBioChem 8, no. 12 (August 13, 2007): 1351–58. http://dx.doi.org/10.1002/cbic.200700148.

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14

Jones, Hannah B. L., Raphael Heilig, Simon Davis, Roman Fischer, Benedikt M. Kessler, and Adán Pinto-Fernández. "ABPP-HT*—Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced DIA Mass Spectrometry Methods." International Journal of Molecular Sciences 23, no. 6 (March 17, 2022): 3263. http://dx.doi.org/10.3390/ijms23063263.

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Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and cells, challenging the ABP-enzyme complex formation with a small molecule can simultaneously inform on potency, selectivity, reversibility/binding affinity, permeability, and stability. ABPP can also be applied to pharmacodynamic studies to inform on cellular target engagement within specific organs when applied to in vivo models. Recently, we established separate high depth and high throughput ABPP (ABPP-HT) protocols for the profiling of deubiquitylating enzymes (DUBs). However, the combination of the two, deep and fast, in one method has been elusive. To further increase the sensitivity of the current ABPP-HT workflow, we implemented state-of-the-art data-independent acquisition (DIA) and data-dependent acquisition (DDA) MS analysis tools. Hereby, we describe an improved methodology, ABPP-HT* (enhanced high-throughput-compatible activity-based protein profiling) that in combination with DIA MS methods, allowed for the consistent profiling of 35–40 DUBs and provided a reduced number of missing values, whilst maintaining a throughput of 100 samples per day.

15

Ryu, Soyoung, Byron Gallis, Young Ah Goo, Scott A. Shaffer, Dragan Radulovic, and David R. Goodlett. "Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method." Cancer Informatics 6 (January 2008): CIN.S385. http://dx.doi.org/10.4137/cin.s385.

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Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA) and compared it to two other methods, a simpler label free method known as spectral counting and the isotope coded affinity tag (ICAT) method. Data analysis by these methods of a standard mixture containing proteins of known, but varying, concentrations showed that they performed similarly with a mean squared error of 0.09. Additionally, complex bacterial protein mixtures spiked with known concentrations of standard proteins were analyzed using the PICA label-free method. These results indicated that the PICA method detected all levels of standard spiked proteins at the 90% confidence level in this complex biological sample. This finding confirms that label-free methods, based on direct measurement of the area under a single ion current trace, performed as well as the standard ICAT method. Given the fact that the label-free methods provide ease in experimental design well beyond pair-wise comparison, label-free methods such as our PICA method are well suited for proteomic expression profiling of large numbers of samples as is needed in clinical analysis.

16

Won, Sang Joon, Joseph D. Eschweiler, Jaimeen D. Majmudar, Fei San Chong, Sin Ye Hwang, Brandon T. Ruotolo, and Brent R. Martin. "Affinity-Based Selectivity Profiling of an In-Class Selective Competitive Inhibitor of Acyl Protein Thioesterase 2." ACS Medicinal Chemistry Letters 8, no. 2 (December 20, 2016): 215–20. http://dx.doi.org/10.1021/acsmedchemlett.6b00441.

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17

Huang, Shuai, Fu-Jia Wang, Hao Lin, Tian Liu, Cheng-Xiao Zhao, and Lian-Guo Chen. "Affinity-based protein profiling to reveal targets of puerarin involved in its protective effect on cardiomyocytes." Biomedicine & Pharmacotherapy 134 (February 2021): 111160. http://dx.doi.org/10.1016/j.biopha.2020.111160.

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Cheng, Bo, Qi Tang, Che Zhang, and Xing Chen. "Glycan Labeling and Analysis in Cells and In Vivo." Annual Review of Analytical Chemistry 14, no. 1 (June 5, 2021): 363–87. http://dx.doi.org/10.1146/annurev-anchem-091620-091314.

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As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied to label glycans with fluorophores, which enables the visualization and tracking of glycans in cells, tissues, and living organisms. Alternatively, labeling glycans with affinity tags has enabled the enrichment of glycoproteins for glycoproteomic profiling. Built on the glycan labeling methods, strategies enabling cell-selective and tissue-specific glycan labeling and protein-specific glycan imaging have been developed. With these methods and strategies, researchers are now better poised than ever to dissect the biological function of glycans in physiological or pathological contexts.

19

Lopez, Mary F., Alvydas Mikulskis, Scott Kuzdzal, Eva Golenko, Emanuel F. Petricoin, Lance A. Liotta, Wayne F. Patton, et al. "A Novel, High-Throughput Workflow for Discovery and Identification of Serum Carrier Protein-Bound Peptide Biomarker Candidates in Ovarian Cancer Samples." Clinical Chemistry 53, no. 6 (June 1, 2007): 1067–74. http://dx.doi.org/10.1373/clinchem.2006.080721.

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Abstract Background: Most cases of ovarian cancer are detected at later stages when the 5-year survival is ∼15%, but 5-year survival approaches 90% when the cancer is detected early (stage I). To use mass spectrometry (MS) of serum proteins for early detection, a seamless workflow is needed that provides an opportunity for rapid profiling along with direct identification of the underpinning ions. Methods: We used carrier protein–bound affinity enrichment of serum samples directly coupled with MALDI orthagonal TOF MS profiling to rapidly search for potential ion signatures that contained discriminatory power. These ions were subsequently directly subjected to tandem MS for sequence identification. Results: We discovered several biomarker panels that enabled differentiation of stage I ovarian cancer from unaffected (age-matched) patients with no evidence of ovarian cancer, with positive results in >93% of samples from patients with disease-negative results and in 97% of disease-free controls. The carrier protein–based approach identified additional protein fragments, many from low-abundance proteins or proteins not previously seen in serum. Conclusions: This workflow system using a highly reproducible, high-resolution MALDI-TOF platform enables rapid enrichment and profiling of large numbers of clinical samples for discovery of ion signatures and integration of direct sequencing and identification of the ions without need for additional offline, time-consuming purification strategies.

20

Ivanov, A. S., and A. E. Medvedev. "Optical surface plasmon resonance biosensors in molecular fishing." Biomeditsinskaya Khimiya 61, no. 2 (2015): 231–38. http://dx.doi.org/10.18097/pbmc20156102231.

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An optical biosensor employing surface plasmon resonance is a highly efficient instrument applicable for direct real time registration of molecular interactions without additional use of any labels or coupled processes. As an independent approach it is especially effective in analysis of various ligand receptor interactions. SPR-biosensors are used for validation of studies on intermolecular interactions in complex biological systems (affinity profiling of various groups of proteins, etc.). Recently, potential application of the SPR-biosensor for molecular fishing (direct affinity binding of target molecules from complex biological mixtures on the optical biosensor surface followed by their elution for identification by LC-MS/MS) has been demonstrated. Using SPR-biosensors in such studies it is possible to solve the following tasks: (a) SPR-based selection of immobilization conditions required for the most effective affinity separation of a particular biological sample; (b) SPR-based molecular fishing for subsequent protein identification by mass spectrometry; (c) SPR-based validation of the interaction of identified proteins with immobilized ligand. This review considers practical application of the SPR technology in the context of recent studies performed in the Institute of Biomedical Chemistry on molecular fishing of real biological objects.

21

Bennett, Kristen, Natalie C. Sadler, Aaron T. Wright, Chris Yeager, and Michael R. Hyman. "Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea." Applied and Environmental Microbiology 82, no. 8 (January 29, 2016): 2270–79. http://dx.doi.org/10.1128/aem.03556-15.

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ABSTRACTNitrosomonas europaeais an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2−) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2uptake byN. europaeaby 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization–tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA.

22

Timmer, John C., Mari Enoksson, Eric Wildfang, Wenhong Zhu, Yoshinobu Igarashi, Jean-Benard Denault, Yuliang Ma, et al. "Profiling constitutive proteolytic events in vivo." Biochemical Journal 407, no. 1 (September 12, 2007): 41–48. http://dx.doi.org/10.1042/bj20070775.

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Most known organisms encode proteases that are crucial for constitutive proteolytic events. In the present paper, we describe a method to define these events in proteomes from Escherichia coli to humans. The method takes advantage of specific N-terminal biotinylation of protein samples, followed by affinity enrichment and conventional LC (liquid chromatography)–MS/MS (tandem mass spectrometry) analysis. The method is simple, uses conventional and easily obtainable reagents, and is applicable to most proteomics facilities. As proof of principle, we demonstrate profiles of proteolytic events that reveal exquisite in vivo specificity of methionine aminopeptidase in E. coli and unexpected processing of mitochondrial transit peptides in yeast, mouse and human samples. Taken together, our results demonstrate how to rapidly distinguish real proteolysis that occurs in vivo from the predictions based on in vitro experiments.

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Azkargorta, Mikel, Ibon Iloro, Iraide Escobes, Diana Cabrera, Juan M. Falcon-Perez, Felix Elortza, and Felix Royo. "Human Serum Extracellular Vesicle Proteomic Profile Depends on the Enrichment Method Employed." International Journal of Molecular Sciences 22, no. 20 (October 15, 2021): 11144. http://dx.doi.org/10.3390/ijms222011144.

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The proteomic profiling of serum samples supposes a challenge due to the large abundance of a few blood proteins in comparison with other circulating proteins coming from different tissues and cells. Although the sensitivity of protein detection has increased enormously in the last years, specific strategies are still required to enrich less abundant proteins and get rid of abundant proteins such as albumin, lipoproteins, and immunoglobulins. One of the alternatives that has become more promising is to characterize circulating extracellular vesicles from serum samples that have great interest in biomedicine. In the present work, we enriched the extracellular vesicles fraction from human serum by applying different techniques, including ultracentrifugation, size-exclusion chromatography, and two commercial precipitation methods based on different mechanisms of action. To improve the performance and efficacy of the techniques to promote purity of the preparations, we have employed a small volume of serum samples (<100 mL). The comparative proteomic profiling of the enriched preparations shows that ultracentrifugation procedure yielded a larger and completely different set of proteins than other techniques, including mitochondrial and ribosome related proteins. The results showed that size exclusion chromatography carries over lipoprotein associated proteins, while a polymer-based precipitation kit has more affinity for proteins associated with granules of platelets. The precipitation kit that targets glycosylation molecules enriches differentially protein harboring glycosylation sites, including immunoglobulins and proteins of the membrane attack complex.

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Cheng, Ann-Joy, Li-Chiu Chen, Kun-Yi Chien, Yin-Ju Chen, Joseph Tung-Chieh Chang, Hung-Ming Wang, Chun-Ta Liao, and I.-How Chen. "Oral Cancer Plasma Tumor Marker Identified with Bead-Based Affinity-Fractionated Proteomic Technology." Clinical Chemistry 51, no. 12 (December 1, 2005): 2236–44. http://dx.doi.org/10.1373/clinchem.2005.052324.

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Abstract Background: There is no plasma marker for detecting oral cancer, one of the most frequent cancers worldwide. We developed a bead-based affinity-fractionated proteomic method to discover a novel plasma marker for oral cancer. Methods: Affinity purification of heparinized plasma with magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were used to screen potential oral cancer markers. We compiled MS protein profiles for 57 patients with oral cancer and compared them with profiles from 29 healthy controls. The spectra were analyzed statistically using flexAnalysis™ and ClinProt™ bioinformatic software. In each MS analysis, the peak intensities of interest were normalized with an internal standard (adrenocorticotropic hormone 18–39). For identification, affinity bead–purified plasma protein was subjected to MALDI TOF/TOF analysis followed by Mascot identification of the peptide sequences and a search of the National Center for Biotechnology Information protein database. Results: To optimize MALDI-TOF analysis based on the best discriminator of the cancer and control spectra, copper-chelated beads were used for plasma protein profiling. The within- and between-run CVs for assays were <4% and 7%, respectively. Six markers that differentiated between cancer and control spectra were found, with mean (SD) molecular masses of 2664 (1), 2850 (1), 3250 (1), 7735 (2), 7927 (2), and 9240 (2) Da. The 2664-Da marker, identified as a fragment of the fibrinogen α-chain, had the highest sensitivity (100%) and specificity (97%) for cancer. Conclusion: The high specificity and sensitivity of the fibrinogen α-chain fragment suggest that it may be a clinical useful tumor marker.

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Minamitani, Takeharu, Teruhito Yasui, Yijie Ma, Hufeng Zhou, Daisuke Okuzaki, Chiau-Yuang Tsai, Shuhei Sakakibara, Benjamin E. Gewurz, Elliott Kieff, and Hitoshi Kikutani. "Evasion of affinity-based selection in germinal centers by Epstein–Barr virus LMP2A." Proceedings of the National Academy of Sciences 112, no. 37 (August 24, 2015): 11612–17. http://dx.doi.org/10.1073/pnas.1514484112.

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Epstein–Barr virus (EBV) infects germinal center (GC) B cells and establishes persistent infection in memory B cells. EBV-infected B cells can cause B-cell malignancies in humans with T- or natural killer-cell deficiency. We now find that EBV-encoded latent membrane protein 2A (LMP2A) mimics B-cell antigen receptor (BCR) signaling in murine GC B cells, causing altered humoral immune responses and autoimmune diseases. Investigation of the impact of LMP2A on B-cell differentiation in mice that conditionally express LMP2A in GC B cells or all B-lineage cells found LMP2A expression enhanced not only BCR signals but also plasma cell differentiation in vitro and in vivo. Conditional LMP2A expression in GC B cells resulted in preferential selection of low-affinity antibody-producing B cells despite apparently normal GC formation. GC B-cell–specific LMP2A expression led to systemic lupus erythematosus-like autoimmune phenotypes in an age-dependent manner. Epigenetic profiling of LMP2A B cells found increased H3K27ac and H3K4me1 signals at the zinc finger and bric-a-brac, tramtrack domain-containing protein 20 locus. We conclude that LMP2A reduces the stringency of GC B-cell selection and may contribute to persistent EBV infection and pathogenesis by providing GC B cells with excessive prosurvival effects.

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Kang, Yoon‐Tae, Emma Purcell, Colin Palacios‐Rolston, Ting‐Wen Lo, Nithya Ramnath, Shruti Jolly, and Sunitha Nagrath. "Isolation and Profiling of Circulating Tumor‐Associated Exosomes Using Extracellular Vesicular Lipid–Protein Binding Affinity Based Microfluidic Device." Small 15, no. 47 (October 7, 2019): 1903600. http://dx.doi.org/10.1002/smll.201903600.

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Le, Lyly, Kim Chi, Scott Tyldesley, Stephane Flibotte, Deborah L. Diamond, Michael A. Kuzyk, and Marianne D. Sadar. "Identification of Serum Amyloid A as a Biomarker to Distinguish Prostate Cancer Patients with Bone Lesions." Clinical Chemistry 51, no. 4 (April 1, 2005): 695–707. http://dx.doi.org/10.1373/clinchem.2004.041087.

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Abstract Background: Prostate cancer has a propensity to metastasize to the bone. Currently, there are no curative treatments for this stage of the disease. Sensitive biomarkers that can be monitored in the blood to indicate the presence or development of bone metastases and/or response to therapies are lacking. Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) is an affinity-based approach that allows sensitive and high-throughput protein profiling and screening of biological samples. Methods: We used SELDI-TOF MS for protein profiling of sera from prostate cancer patients (n = 38) with and without bone metastases in our effort to identify individual or multiple serum markers that may be of added benefit to those in current use. Serum was applied to ProteinChip® surfaces (H4 and IMAC) to quickly screen samples and detect peaks predominating in the samples obtained from patients with bone metastases. Unique proteins in the bone metastasis cohort observed by SELDI-TOF MS were identified by two-dimensional gel electrophoresis, in-gel trypsin digestion, and tandem MS. The identities of the proteins were confirmed by ELISA and immunodepletion assays. Results: The cluster of unique proteins in the sera of patients with bone metastases was identified as isoforms of serum amyloid A. Machine-learning algorithms were also used to identify patients with bone metastases with a sensitivity and specificity of 89.5%. Conclusions: SELDI-TOF MS protein profiling in combination with other proteomic approaches may provide diagnostic tools with potential clinical applications and serve as tools to aid in the discovery of biomarkers associated with various diseases.

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Kim, Evelyn H., and David E. Misek. "Glycoproteomics-Based Identification of Cancer Biomarkers." International Journal of Proteomics 2011 (September 28, 2011): 1–10. http://dx.doi.org/10.1155/2011/601937.

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Protein glycosylation is one of the most common posttranslational modifications in mammalian cells. It is involved in many biological pathways and molecular functions and is well suited for proteomics-based disease investigations. Aberrant protein glycosylation may be associated with disease processes. Specific glycoforms of glycoproteins may serve as potential biomarkers for the early detection of disease or as biomarkers for the evaluation of therapeutic efficacy for treatment of cancer, diabetes, and other diseases. Recent technological developments, including lectin affinity chromatography and mass spectrometry, have provided researchers the ability to obtain detailed information concerning protein glycosylation. These in-depth investigations, including profiling and quantifying glycoprotein expression, as well as comprehensive glycan structural analyses may provide important information leading to the development of disease-related biomarkers. This paper describes methodologies for the detection of cancer-related glycoprotein and glycan structural alterations and briefly summarizes several current cancer-related findings.

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Kempf, Karl, Oxana Kempf, Yoan Capello, Christian Molitor, Claire Lescoat, Rana Melhem, Stéphane Chaignepain, et al. "Synthesis of Flavonol-Bearing Probes for Chemoproteomic and Bioinformatic Analyses of Asteraceae Petals in Search of Novel Flavonoid Enzymes." International Journal of Molecular Sciences 24, no. 11 (June 3, 2023): 9724. http://dx.doi.org/10.3390/ijms24119724.

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This study aimed at searching for the enzymes that are responsible for the higher hydroxylation of flavonols serving as UV-honey guides for pollinating insects on the petals of Asteraceae flowers. To achieve this aim, an affinity-based chemical proteomic approach was developed by relying on the use of quercetin-bearing biotinylated probes, which were thus designed and synthesized to selectively and covalently capture relevant flavonoid enzymes. Proteomic and bioinformatic analyses of proteins captured from petal microsomes of two Asteraceae species (Rudbeckia hirta and Tagetes erecta) revealed the presence of two flavonol 6-hydroxylases and several additional not fully characterized proteins as candidates for the identification of novel flavonol 8-hydroxylases, as well as relevant flavonol methyl- and glycosyltransferases. Generally speaking, this substrate-based proteome profiling methodology constitutes a powerful tool for the search for unknown (flavonoid) enzymes in plant protein extracts.

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Song, Jiabao, and Y. George Zheng. "Bioorthogonal Reporters for Detecting and Profiling Protein Acetylation and Acylation." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 2 (November 11, 2019): 148–62. http://dx.doi.org/10.1177/2472555219887144.

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Protein acylation, exemplified by lysine acetylation, is a type of indispensable and widespread protein posttranslational modification in eukaryotes. Functional annotation of various lysine acetyltransferases (KATs) is critical to understanding their regulatory roles in abundant biological processes. Traditional radiometric and immunosorbent assays have found broad use in KAT study but have intrinsic limitations. Designing acyl–coenzyme A (CoA) reporter molecules bearing chemoselective chemical warhead groups as surrogates of the native cofactor acetyl-CoA for bioorthogonal labeling of KAT substrates has come into a technical innovation in recent years. This chemical biology platform equips molecular biologists with empowering tools in acyltransferase activity detection and substrate profiling. In the bioorthogonal labeling, protein substrates are first enzymatically modified with a functionalized acyl group. Subsequently, the chemical warhead on the acyl chain conjugates with either an imaging chromophore or an affinity handle or any other appropriate probes through an orthogonal chemical ligation. This bioorganic strategy reformats the chemically inert acetylation and acylation marks into a chemically maneuverable functionality and generates measurable signals without recourse to radioisotopes or antibodies. It offers ample opportunities for facile sensitive detection of KAT activity with temporal and spatial resolutions as well as allows for chemoproteomic profiling of protein acetylation pertaining to specific KATs of interest on the global scale. We reviewed here the past and current advances in bioorthogonal protein acylations and highlighted their wide-spectrum applications. We also discussed the design of other related acyl-CoA and CoA-based chemical probes and their deployment in illuminating protein acetylation and acylation biology.

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Hamza, Ghaith M., Vladislav B. Bergo, Sergey Mamaev, Don M. Wojchowski, Paul Toran, Camilla R. Worsfold, M. Paola Castaldi, and Jeffrey C. Silva. "Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics." International Journal of Molecular Sciences 21, no. 6 (March 16, 2020): 2016. http://dx.doi.org/10.3390/ijms21062016.

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The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed “Affinity-Bead Assisted Mass Spectrometry” (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.

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Wen, Jiachen, and M. Kyle Hadden. "Affinity-based protein profiling identifies vitamin D3 as a heat shock protein 70 antagonist that regulates hedgehog transduction in murine basal cell carcinoma." European Journal of Medicinal Chemistry 228 (January 2022): 114005. http://dx.doi.org/10.1016/j.ejmech.2021.114005.

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Du, Hongyan, Dejun Jiang, Junbo Gao, Xujun Zhang, Lingxiao Jiang, Yundian Zeng, Zhenxing Wu, et al. "Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network." Research 2022 (July 22, 2022): 1–15. http://dx.doi.org/10.34133/2022/9873564.

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Covalent ligands have attracted increasing attention due to their unique advantages, such as long residence time, high selectivity, and strong binding affinity. They also show promise for targets where previous efforts to identify noncovalent small molecule inhibitors have failed. However, our limited knowledge of covalent binding sites has hindered the discovery of novel ligands. Therefore, developing in silico methods to identify covalent binding sites is highly desirable. Here, we propose DeepCoSI, the first structure-based deep graph learning model to identify ligandable covalent sites in the protein. By integrating the characterization of the binding pocket and the interactions between each cysteine and the surrounding environment, DeepCoSI achieves state-of-the-art predictive performances. The validation on two external test sets which mimic the real application scenarios shows that DeepCoSI has strong ability to distinguish ligandable sites from the others. Finally, we profiled the entire set of protein structures in the RCSB Protein Data Bank (PDB) with DeepCoSI to evaluate the ligandability of each cysteine for covalent ligand design, and made the predicted data publicly available on website.

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Kanderova, Veronika, Daniela Kuzilkova, Jan Stuchly, Weiwei Wu, Anders Holm, Heidi Slåstad, Karel Fiser, Ondrej Hrusak, Fridtjof Lund-Johansen, and Tomas Kalina. "Novel Flow Cytometry-Based Method Of Affinity Proteomics Revealing Expression, Post-Translational Modification and Proteolysis In Primary Childhood Acute Leukemias." Blood 122, no. 21 (November 15, 2013): 2553. http://dx.doi.org/10.1182/blood.v122.21.2553.2553.

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Abstract Leukemia is a complex disease pathologically manifested at the DNA, mRNA and protein level. Understanding leukemia pathogenesis is prevalently focused on mutations at the DNA (or mRNA) level, however the functional consequences of these changes on cellular machineries are not fully clarified. Since proteome analysis provides link between gene sequence and cellular physiology, proteomics can contribute to elucidate mechanism of disease and response to treatment. Moreover some alterations are manifested only at the protein level including subcellular localisation, post-translational modification (e.g. phosphorylation), protein cleavage or protein-protein interactions. Performing large-scale protein analysis of primary leukemia samples requires the development of more effective proteomic approaches as well as new analytical strategies. Here, we present novel microsphere-based antibody array format with automatical analysis tool that can follow changes in expression and post-translational modification of leukemia associated proteins with regards to intracellular localisation and protein cleavage in primary childhood acute leukemia (AL). Size Exclusion Chromatography-Microsphere-based Affinity Proteomics (SEC-MAP) is a set of 1728 populations of fluorescently-labeled microbeads, each carrying an antibody against respective human protein. Native cellular proteins (and their complexes) are isolated using detergents, labeled with biotin and subjected to size exclusion chromatography to obtain 24 molecular weight fractions. The fractions are incubated with SEC-MAP microbeads and the antibody-protein binding is detected using fluorescently-labeled streptavidin by flow cytometry. Flow cytometer resolves color-code of each microbead population and reads the amount of bound protein. The signals from 24 size fractions are combined and protein binding is detected as protein reactivity peaks similar to bands on western blot. The analysis is performed using automatic software created in R. It allows for automatic processing of fcs files as well as advanced follow-up analysis including quality control, normalisation, protein peaks recognition and clustering of results We have examined the expression of cytoplasmic (n=980) and membrane (n=769) proteins in 69 primary samples of AL obtained at diagnosis according to the Institutional Ethics Committee Giudelines. For the normalisation of protein expression we have used Loess normalisation commonly used in mRNA profiling studies. Due to ability of SEC-MAP to separate proteins according their molecular weight we have identified not only the expression of proteins but also the size that corresponds to its monomeric or multimeric presence and furthermore could serve as a control of proteolysis. We have revealed the sensitivity to proteolysis of 4 standard house-keeping proteins (Akt, Abl, β-actin and β2-microglobulin). Abl and Akt proved to be better controls of proteolysis. Detected with SEC-MAP or western blot, β-actin and β2-microglobulin, unlike Abl and Akt, have not been found in their cleaved forms in the proteolytically digested samples. Thus we have identified proteolysis in 12 samples which have been subsequently excluded from the analysis. So far we have identified 44 proteins (including CD markers distinguishing lineage specificity e.g. CD22, CD3, CD33) which have been differentially expressed in different subtypes of AL (B-cell precursor acute lymphoblastic leukemia, BCP-ALL, n=35), T-cell acute lymphoblastic leukemia (T-ALL, n=9) and acute myeloid leukemia (AML, n=13) (Multiple Testing Procedures - Bioconductor Package multtest, p<0.05). We have verified the expression using flow cytometry or western blot. From non-CD markers, we have found e.g. BLNK, DBN1, PAX5, PTK2 overexpressed in BCP-ALL, EIF5A, LAT, SH2D1A, SSEA4 overexpressed in T-ALL and CEBPA, CTBP2, GLUD1, LCP(pY145) and PTPN6 overexpressed in AML. In summary, SEC-MAP proved to be strong proteomic tool capable of identifying leukemia phenotype as well as providing novel insights into the protein expression and post-translational modification of primary childhood AL. Moreover it can bring complementary information about proteolysis not captured by planar arrays (western blot) which can significantly affect proteomic results. Supported by GAUK 596912, IGA NT13462, IGA NT12397, P302/12/G101, UNCE 204012, 00064203. Disclosures: No relevant conflicts of interest to declare.

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Lu, Kuan-Yi, Sheng-Ce Tao, Tzu-Ching Yang, Yu-Hsuan Ho, Chia-Hsien Lee, Chen-Ching Lin, Hsueh-Fen Juan, et al. "Profiling Lipid–protein Interactions Using Nonquenched Fluorescent Liposomal Nanovesicles and Proteome Microarrays." Molecular & Cellular Proteomics 11, no. 11 (July 26, 2012): 1177–90. http://dx.doi.org/10.1074/mcp.m112.017426.

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Fluorescent liposomal nanovesicles (liposomes) are commonly used for lipid research and/or signal enhancement. However, the problem of self-quenching with conventional fluorescent liposomes limits their applications because these liposomes must be lysed to detect the fluorescent signals. Here, we developed a nonquenched fluorescent (NQF)1 liposome by optimizing the proportion of sulforhodamine B (SRB) encapsulant and lissamine rhodamine B-dipalmitoyl phosphatidylethanol (LRB-DPPE) on a liposomal surface for signal amplification. Our study showed that 0.3% of LRB-DPPE with 200 μm of SRB provided the maximal fluorescent signal without the need to lyse the liposomes. We also observed that the NQF liposomes largely eliminated self-quenching effects and produced greatly enhanced signals than SRB-only liposomes by 5.3-fold. To show their application in proteomics research, we constructed NQF liposomes that contained phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) and profiled its protein interactome using a yeast proteome microarray. Our profiling led to the identification of 162 PI(3,5)P2-specific binding proteins (PI(3,5)P2-BPs). We not only recovered many proteins that possessed known PI(3,5)P2-binding domains, but we also found two unknown Pfam domains (Pfam-B_8509 and Pfam-B_10446) that were enriched in our dataset. The validation of many newly discovered PI(3,5)P2-BPs was performed using a bead-based affinity assay. Further bioinformatics analyses revealed that the functional roles of 22 PI(3,5)P2-BPs were similar to those associated with PI(3,5)P2, including vesicle-mediated transport, GTPase, cytoskeleton, and kinase. Among the 162 PI(3,5)P2-BPs, we found a novel motif, HRDIKP[ES]NJLL that showed statistical significance. A docking simulation showed that PI(3,5)P2 interacted primarily with lysine or arginine side chains of the newly identified PI(3,5)P2-binding kinases. Our study showed that this new tool would greatly benefit profiling lipid–protein interactions in high-throughput studies.

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Rolland, Catherine, Rafael Gozalbes, Eric Nicolaï, Marie-France Paugam, Laurent Coussy, Frédérique Barbosa, Dragos Horvath, and Frédéric Revah. "G-Protein-Coupled Receptor Affinity Prediction Based on the Use of a Profiling Dataset: QSAR Design, Synthesis, and Experimental Validation." Journal of Medicinal Chemistry 48, no. 21 (October 2005): 6563–74. http://dx.doi.org/10.1021/jm0500673.

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Ogbeide, Uyi, Eunice Oriotor, and Henry Okeri. "Molecular docking assessment of the tocolytic potential of phytoconstituents of five medicinal plants used against preterm labour." Journal of Science and Practice of Pharmacy 10, no. 1 (December 31, 2023): 522–32. http://dx.doi.org/10.47227/jsppharm.v10i1.5.

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Introduction: Preterm labour is currently being treated with a number of medications with untoward side effects, but many medicinal plants have also been found useful. This study aims to assess the tocolytic potentials of the phytoconstituents of Barteria fistulosa, Ficus capensis, Ficus exasperate, Newbouldia laevis and Zingiber officinale. Methods: Phytoconstituents present in these plants were obtained from literature sources, their 3D SDF structures were obtained from PubChem; the protein Beta-2 adrenergic receptor (7DHI) was processed using Chimera and molecular docking was done using PyRx software. Post-docking analysis was done using Bio-discovery Studio 2.0 and ADMET profiling was done using the Swiss ADME web server and ProTox-II virtual lab. Results: A binding affinity value of less than -7 kcal/mol was found for nine (9) phytoconstituents in Zingiber officinale, fourteen (14) phytoconstituents in Ficus capensis, three (3) phytoconstituents in Ficus exasperata, one (1) phytoconstituent in Barteria fistulosa and forty-four (44) phytoconstituents in Newbouldia laevis. Following post-docking analysis and ADMET profiling of specific ligands from the plants, Kaempferol, Chrysoeriol and Lapachol - all present in Newbouldia laevis - were identified as putative drug molecules based on their higher binding affinity and hydrogen bond interaction with the target proteins' active site amino acid residues. Conclusion: The tocolytic potential of Zingiber officinale, Ficus capensis, Barteria fistulosa and Newbouldia laevis as a medicinal plant for the treatment of preterm labour is validated. Kaempferol, Chrysoeriol and Lapachol, phytoconstituents in Newbouldia laevis possess the potential as a source of new drugs for the treatment of preterm labour. Keywords: Preterm labour, tocolysis, molecular docking, drug design

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Ramatapa, Thabo, Anathi Msobo, Pfano W. Maphari, Efficient N. Ncube, Noluyolo Nogemane, and Msizi I. Mhlongo. "Identification of Plant-Derived Bioactive Compounds Using Affinity Mass Spectrometry and Molecular Networking." Metabolites 12, no. 9 (September 14, 2022): 863. http://dx.doi.org/10.3390/metabo12090863.

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Affinity selection-mass spectrometry (AS-MS) is a label-free binding assay system that uses UHPLC-MS size-based separation methods to separate target-compound complexes from unbound compounds, identify bound compounds, classify compound binding sites, quantify the dissociation rate constant of compounds, and characterize affinity-extracted ligands. This label-free binding assay, in contrast to conventional biochemical (i.e., high-throughput screening (HTS)) approaches, is applicable to any drug target, and is also concise, accurate, and adaptable. Although AS-MS is an innovative approach for identifying lead compounds, the possibilities of finding bioactive compounds are limited by competitive binding, which occurs during the equilibration of extracts with the target protein(s). Here, we discuss the potential for metabolite profiling complemented with molecular networking to be used alongside AS-MS to improve the identification of bioactive compounds in plant extracts. AS-MS has gained significant prominence in HTS labs and shows potential to emerge as the driving force behind novel drug development in the future.

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Williamson, Yulanda M., Hercules Moura, Jennifer Whitmon, Adrian R. Woolfitt, David M. Schieltz, Jon C. Rees, Stephanie Guo, et al. "A Proteomic Characterization of Bordetella pertussis Clinical Isolates Associated with a California State Pertussis Outbreak." International Journal of Proteomics 2015 (May 24, 2015): 1–12. http://dx.doi.org/10.1155/2015/536537.

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Bordetella pertussis (Bp) is the etiologic agent of pertussis (whooping cough), a highly communicable infection. Although pertussis is vaccine preventable, in recent years there has been increased incidence, despite high vaccine coverage. Possible reasons for the rise in cases include the following: Bp strain adaptation, waning vaccine immunity, increased surveillance, and improved clinical diagnostics. A pertussis outbreak impacted California (USA) in 2010; children and preadolescents were the most affected but the burden of disease fell mainly on infants. To identify protein biomarkers associated with this pertussis outbreak, we report a whole cellular protein characterization of six Bp isolates plus the pertussis acellular vaccine strain Bp Tohama I (T), utilizing gel-free proteomics-based mass spectrometry (MS). MS/MS tryptic peptide detection and protein database searching combined with western blot analysis revealed three Bp isolates in this study had markedly reduced detection of pertactin (Prn), a subunit of pertussis acellular vaccines. Additionally, antibody affinity capture technologies were implemented using anti-Bp T rabbit polyclonal antisera and whole cellular proteins to identify putative immunogens. Proteome profiling could shed light on pathogenesis and potentially lay the foundation for reduced infection transmission strategies and improved clinical diagnostics.

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Verkhivker, Gennady, Steve Agajanian, Ryan Kassab, and Keerthi Krishnan. "Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms." Biomolecules 12, no. 7 (July 10, 2022): 964. http://dx.doi.org/10.3390/biom12070964.

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In this study, we combined all-atom MD simulations, the ensemble-based mutational scanning of protein stability and binding, and perturbation-based network profiling of allosteric interactions in the SARS-CoV-2 spike complexes with a panel of cross-reactive and ultra-potent single antibodies (B1-182.1 and A23-58.1) as well as antibody combinations (A19-61.1/B1-182.1 and A19-46.1/B1-182.1). Using this approach, we quantify the local and global effects of mutations in the complexes, identify protein stability centers, characterize binding energy hotspots, and predict the allosteric control points of long-range interactions and communications. Conformational dynamics and distance fluctuation analysis revealed the antibody-specific signatures of protein stability and flexibility of the spike complexes that can affect the pattern of mutational escape. A network-based perturbation approach for mutational profiling of allosteric residue potentials revealed how antibody binding can modulate allosteric interactions and identified allosteric control points that can form vulnerable sites for mutational escape. The results show that the protein stability and binding energetics of the SARS-CoV-2 spike complexes with the panel of ultrapotent antibodies are tolerant to the effect of Omicron mutations, which may be related to their neutralization efficiency. By employing an integrated analysis of conformational dynamics, binding energetics, and allosteric interactions, we found that the antibodies that neutralize the Omicron spike variant mediate the dominant binding energy hotpots in the conserved stability centers and allosteric control points in which mutations may be restricted by the requirements of the protein folding stability and binding to the host receptor. This study suggested a mechanism in which the patterns of escape mutants for the ultrapotent antibodies may not be solely determined by the binding interaction changes but are associated with the balance and tradeoffs of multiple local and global factors, including protein stability, binding affinity, and long-range interactions.

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Stenke, Leif, Lukas Orre, Sumeer Dhar, Rolf Larsson, Rolf Lewensohn, and Janne Lehtiö. "Detection of Proteins Related to Therapeutic Outcome, Including Drug Resistance, in Acute Myeloid Leukemia Using Mass Spectrometry and Gel Based Proteomic Profiling." Blood 106, no. 11 (November 16, 2005): 2367. http://dx.doi.org/10.1182/blood.v106.11.2367.2367.

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Abstract To further improve and individualize curative treatment approaches for patients with AML, novel proteins and protein functions need to be discovered. In particular, the mechanisms responsible for chemotherapy resistance appear essential to unravel. Clinical proteomics may help to provide such information. We have used a chip-based technique, surface enhanced laser desorption/ionization mass spectrometry (SELDI-MS), to compare protein expression profiles in AML. With this technique proteins in the molecular weight area of 2–40 kDa can be spotted. For selected samples, a two-dimensional electrophoresis (2DE) method was employed, allowing detection of proteins between 15–120kDa. In the first part of the study, mononuclear peripheral blood cells were obtained from 8 AML patients clinically sensitive to and 7 patients clinically resistant to doxorubicin-containing induction chemotherapy. The clinical outcome correlated to results from parallel in vitro drug testing using the FMCA method. In addition, two variants of the human leukemic cell line CEM, one sensitive and one resistant to teniposide (CEM/VMI), were analysed. In the second part of the study, global proteomic profiles from 24 selected AML patients with good vs. poor clinical outcome (remission duration) were investigated. A total of 812 proteins were detected in the mononuclear cells obtained from the 15 doxorubicin-treated patients. Twenty of these proteins were distinguished as different between the sensitive vs. resistant patient groups. Assessing the CEM cell lines by utilizing four different affinity surfaces on ProteinChip™ arrays, approximately 450 peptides and proteins were detected. Between 29 and up to 65 proteins were detected as differentially expressed between the sensitive and the resistant CEM variants. Using the 2DE technology, approximately 1000 spots were matched on the CEM cell lines, with 47 clear expression level differences between the sub cell lines. In clustering analysis using the protein profile data we could demonstrate clear clustering of sensitive and resistant patient and cell line cells according to sensitivity measurements (IC50). Using these methods we have selected a panel of putative resistance related proteins, which are currently being identified and validated. Data from the second phase of the study, derived from 24 selected AML cell populations, are presently being analyzed. In conclusion, significant differences in protein profile expression were observed between cells obtained from AML patients with clinically divergent treatment responses. Further studies aim at identifying key proteins and protein functions to allow for improved therapeutic efficacy.

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Lupitha, Santhik Subhasingh, Pramod Darvin, Aneesh Chandrasekharan, Shankara Narayanan Varadarajan, Soumya Jaya Divakaran, Sreekumar Easwaran, Shijulal Nelson-Sathi, et al. "A rapid bead-based assay for screening of SARS-CoV-2 neutralizing antibodies." Antibody Therapeutics 5, no. 2 (March 17, 2022): 100–110. http://dx.doi.org/10.1093/abt/tbac007.

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Abstract Quantitative determination of neutralizing antibodies against Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) is paramount in immunodiagnostics, vaccine efficacy testing, and immune response profiling among the vaccinated population. Cost-effective, rapid, easy-to-perform assays are essential to support the vaccine development process and immunosurveillance studies. We describe a bead-based screening assay for S1-neutralization using recombinant fluorescent proteins of hACE2 and SARS-CoV2-S1, immobilized on solid beads employing nanobodies/metal-affinity tags. Nanobody-mediated capture of SARS-CoV-2-Spike (S1) on agarose beads served as the trap for soluble recombinant ACE2-GFPSpark, inhibited by neutralizing antibody. The first approach demonstrates single-color fluorescent imaging of ACE2-GFPSpark binding to His-tagged S1-Receptor Binding Domain (RBD-His) immobilized beads. The second approach is dual-color imaging of soluble ACE2-GFPSpark to S1-Orange Fluorescent Protein (S1-OFPSpark) beads. Both methods showed a good correlation with the gold standard pseudovirion assay and can be adapted to any fluorescent platforms for screening.

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Limaye, Akanksha, Jajoriya Sweta, Maddala Madhavi, Urvy Mudgal, Sourav Mukherjee, Shreshtha Sharma, Tajamul Hussain, Anuraj Nayarisseri, and Sanjeev Kumar Singh. "In Silico Insights on GD2 : A Potential Target for Pediatric Neuroblastoma." Current Topics in Medicinal Chemistry 19, no. 30 (January 3, 2020): 2766–81. http://dx.doi.org/10.2174/1568026619666191112115333.

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Background: Originating from the abnormal growth of neuroblasts, pediatric neuroblastoma affects the age group below 15 years. It is an aggressive heterogenous cancer with a high morbidity rate. Biological marker GD2 synthesised by the GD2 gene acts as a powerful predictor of neuroblastoma cells. GD2 gangliosides are sialic acid-containing glycosphingolipids. Differential expression during brain development governs the function of the GD2. The present study explains the interaction of the GD2 with its established inhibitors and discovers the compound having a high binding affinity against the target protein. Technically, during the development of new compounds through docking studies, the best drug among all pre-exist inhibitors was filtered. Hence in reference to the best docked compound, the study proceeded further. Methodology: The In silico approach provides a platform to determine and establish potential inhibitor against GD2 in Pediatric neuroblastoma. The 3D structure of GD2 protein was modelled by homology base fold methods using Smith-Watermans’ Local alignment. A total of 18 established potent compounds were subjected to molecular docking and Etoposide (CID: 36462) manifested the highest affinity. The similarity search presented 336 compounds similar to Etoposide. Results: Through virtual screening, the compound having PubChem ID 10254934 showed a better affinity towards GD2 than the established inhibitor. The comparative profiling of the two compounds based on various interactions such as H-bond interaction, aromatic interactions, electrostatic interactions and ADMET profiling and toxicity studies were performed using various computational tools. Conclusion: The docking separated the virtual screened drug (PubChemID: 10254934) from the established inhibitor with a better re-rank score of -136.33. The toxicity profile of the virtual screened drug was also lesser (less lethal) than the established drug. The virtual screened drug was observed to be bioavailable as it does not cross the blood-brain barrier. Conclusively, the virtual screened compound obtained in the present investigation is better than the established inhibitor and can be further augmented by In vitro analysis, pharmacodynamics and pharmacokinetic studies.

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Özenver, Nadire, Onat Kadioglu, Yujie Fu, and Thomas Efferth. "Kinome-Wide Profiling Identifies Human WNK3 as a Target of Cajanin Stilbene Acid from Cajanus cajan (L.) Millsp." International Journal of Molecular Sciences 23, no. 3 (January 28, 2022): 1506. http://dx.doi.org/10.3390/ijms23031506.

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Pigeon Pea (Cajanus cajan (L.) Millsp.) is a common food crop used in many parts of the world for nutritional purposes. One of its chemical constituents is cajanin stilbene acid (CSA), which exerts anticancer activity in vitro and in vivo. In an effort to identify molecular targets of CSA, we performed a kinome-wide approach based on the measurement of the enzymatic activities of 252 human kinases. The serine-threonine kinase WNK3 (also known as protein kinase lysine-deficient 3) was identified as the most promising target of CSA with the strongest enzymatic activity inhibition in vitro and the highest binding affinity in molecular docking in silico. The lowest binding affinity and the predicted binding constant pKi of CSA (−9.65 kcal/mol and 0.084 µM) were comparable or even better than those of the known WNK3 inhibitor PP-121 (−9.42 kcal/mol and 0.123 µM). The statistically significant association between WNK3 mRNA expression and cellular responsiveness to several clinically established anticancer drugs in a panel of 60 tumor cell lines and the prognostic value of WNK3 mRNA expression in sarcoma biopsies for the survival time of 230 patients can be taken as clues that CSA-based inhibition of WNK3 may improve treatment outcomes of cancer patients and that CSA may serve as a valuable supplement to the currently used combination therapy protocols in oncology.

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Qi, Yue, Xiangmin Zhang, Berhane Seyoum, Zaher Msallaty, Abdullah Mallisho, Michael Caruso, Divyasri Damacharla, et al. "Kinome Profiling Reveals Abnormal Activity of Kinases in Skeletal Muscle From Adults With Obesity and Insulin Resistance." Journal of Clinical Endocrinology & Metabolism 105, no. 3 (December 26, 2019): 644–59. http://dx.doi.org/10.1210/clinem/dgz115.

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Abstract Context Obesity-related insulin resistance (OIR) is one of the main contributors to type 2 diabetes and other metabolic diseases. Protein kinases are implicated in insulin signaling and glucose metabolism. Molecular mechanisms underlying OIR involving global kinase activities remain incompletely understood. Objective To investigate abnormal kinase activity associated with OIR in human skeletal muscle. Design Utilization of stable isotopic labeling-based quantitative proteomics combined with affinity-based active enzyme probes to profile in vivo kinase activity in skeletal muscle from lean control (Lean) and OIR participants. Participants A total of 16 nondiabetic adults, 8 Lean and 8 with OIR, underwent hyperinsulinemic-euglycemic clamp with muscle biopsy. Results We identified the first active kinome, comprising 54 active protein kinases, in human skeletal muscle. The activities of 23 kinases were different in OIR muscle compared with Lean muscle (11 hyper- and 12 hypo-active), while their protein abundance was the same between the 2 groups. The activities of multiple kinases involved in adenosine monophosphate–activated protein kinase (AMPK) and p38 signaling were lower in OIR compared with Lean. On the contrary, multiple kinases in the c-Jun N-terminal kinase (JNK) signaling pathway exhibited higher activity in OIR vs Lean. The kinase-substrate–prediction based on experimental data further confirmed a potential downregulation of insulin signaling (eg, inhibited phosphorylation of insulin receptor substrate-1 and AKT1/2). Conclusions These findings provide a global view of the kinome activity in OIR and Lean muscle, pinpoint novel specific impairment in kinase activities in signaling pathways important for skeletal muscle insulin resistance, and may provide potential drug targets (ie, abnormal kinase activities) to prevent and/or reverse skeletal muscle insulin resistance in humans.

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Li, Jinong, Zhen Zhang, Jason Rosenzweig, Young Y. Wang, and Daniel W. Chan. "Proteomics and Bioinformatics Approaches for Identification of Serum Biomarkers to Detect Breast Cancer." Clinical Chemistry 48, no. 8 (August 1, 2002): 1296–304. http://dx.doi.org/10.1093/clinchem/48.8.1296.

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Abstract Background: Surface-enhanced laser desorption/ionization (SELDI) is an affinity-based mass spectrometric method in which proteins of interest are selectively adsorbed to a chemically modified surface on a biochip, whereas impurities are removed by washing with buffer. This technology allows sensitive and high-throughput protein profiling of complex biological specimens. Methods: We screened for potential tumor biomarkers in 169 serum samples, including samples from a cancer group of 103 breast cancer patients at different clinical stages [stage 0 (n = 4), stage I (n = 38), stage II (n = 37), and stage III (n = 24)], from a control group of 41 healthy women, and from 25 patients with benign breast diseases. Diluted serum samples were applied to immobilized metal affinity capture Ciphergen ProteinChip® Arrays previously activated with Ni2+. Proteins bound to the chelated metal were analyzed on a ProteinChip Reader Model PBS II. Complex protein profiles of different diagnostic groups were compared and analyzed using the ProPeak software package. Results: A panel of three biomarkers was selected based on their collective contribution to the optimal separation between stage 0–I breast cancer patients and noncancer controls. The same separation was observed using independent test data from stage II–III breast cancer patients. Bootstrap cross-validation demonstrated that a sensitivity of 93% for all cancer patients and a specificity of 91% for all controls were achieved by a composite index derived by multivariate logistic regression using the three selected biomarkers. Conclusions: Proteomics approaches such as SELDI mass spectrometry, in conjunction with bioinformatics tools, could greatly facilitate the discovery of new and better biomarkers. The high sensitivity and specificity achieved by the combined use of the selected biomarkers show great potential for the early detection of breast cancer.

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Ogawa, Tomohisa, Rie Sato, Takako Naganuma, Kayeu Liu, Agness Ethel Lakudzala, Koji Muramoto, Makoto Osada, et al. "Glycan Binding Profiling of Jacalin-Related Lectins from the Pteria Penguin Pearl Shell." International Journal of Molecular Sciences 20, no. 18 (September 18, 2019): 4629. http://dx.doi.org/10.3390/ijms20184629.

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We determined the primary structures of jacalin-related lectins termed PPL3s (PPL3A, 3B, and 3C, which are dimers consisting of sequence variants α + α, α + β, β + β, respectively) and PPL4, which is heterodimer consisting of α + β subunits, isolated from mantle secretory fluid of Pteria penguin (Mabe) pearl shell. Their carbohydrate-binding properties were analyzed, in addition to that of PPL2A, which was previously reported as a matrix protein. PPL3s and PPL4 shared only 35–50% homology to PPL2A, respectively; they exhibited significantly different carbohydrate-binding specificities based on the multiple glycan binding profiling data sets from frontal affinity chromatography analysis. The carbohydrate-binding specificity of PPL3s was similar to that of PPL2A, except only for Man3Fuc1Xyl1GlcNAc2 oligosaccharide, while PPL4 showed different carbohydrate-binding specificity compared with PPL2A and PPL3s. PPL2A and PPL3s mainly recognize agalactosylated- and galactosylated-type glycans. On the other hand, PPL4 binds to high-mannose-and hybrid-type N-linked glycans but not agalactosylated- and galactosylated-type glycans.

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Fazilat, Ahmad, Nadia Rashid, Aruna Nigam, Shadab Anjum, Nimisha Gupta, and Saima Wajid. "Differential Expression of MARK4 Protein and Related Perturbations in Females with Ovulatory PCOS." Endocrine, Metabolic & Immune Disorders - Drug Targets 19, no. 7 (October 11, 2019): 1064–74. http://dx.doi.org/10.2174/1871530319666190719145823.

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Background: Ovulatory PCOS (OPCOS) is the mildest form of the polycystic ovarian syndrome among all four determined phenotypes. Though the females with OPCOS are ovulating, hyperandrogenism and polycystic ovarian morphology increase the susceptibility of cardiovascular diseases, insulin resistance, hyperlipidemia and metabolic syndrome in these females. Objectives: The aim of the study was to identify the significance associated with OPCOS phenotype through serum proteomic profiling of OPCOS females and normal age-matched healthy ovulating females. Methods: One and two-dimensional gel-based proteomic approaches were adopted to fractionate the complex serum proteome. Differential protein profiles generated were analyzed with PD-QUEST Software. Protein spots differing in intensity by >2-fold were selected and identified further by MALDI-TOF MS. Validation of identified protein was carried out by Biolayer Interferometry. Results: One and two-dimensional gel profiles revealed a differential expression pattern of proteins. 10 selected spots were identified as GMP synthase [glutamine hydrolyzing], zinc finger protein 518A, pericentriolar material 1 protein, BCLAF1 and THRAP3 family member 3, MAP/microtubule affinityregulating kinase 4, H/ACA ribonucleoprotein complex subunit 1, Melanoma-associated antigen B3 and Zinc finger protein 658B. Expression of MAP/microtubule affinity-regulating kinase 4 (MARK4) was found to be downregulated in OPCOS females as compared to controls on validation. Conclusion: Reduced expression of MARK4 protein in OPCOS increases the associated risk of hyperlipidemia, hyperandrogenism and metabolic syndrome, thus the protein holds strong candidature as a drug target for the syndrome.

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Lopez, Mary F., Alvydas Mikulskis, Scott Kuzdzal, David A. Bennett, Jeremiah Kelly, Eva Golenko, Joseph DiCesare, et al. "High-Resolution Serum Proteomic Profiling of Alzheimer Disease Samples Reveals Disease-Specific, Carrier-Protein–Bound Mass Signatures." Clinical Chemistry 51, no. 10 (October 1, 2005): 1946–54. http://dx.doi.org/10.1373/clinchem.2005.053090.

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Abstract Background: Researchers typically search for disease markers using a “targeted” approach in which a hypothesis about the disease mechanism is tested and experimental results either confirm or disprove the involvement of a particular gene or protein in the disease. Recently, there has been interest in developing disease diagnostics based on unbiased quantification of differences in global patterns of protein and peptide masses, typically in blood from individuals with and without disease. We combined a suite of methods and technologies, including novel sample preparation based on carrier-protein capture and biomarker enrichment, high-resolution mass spectrometry, a unique cohort of well-characterized persons with and without Alzheimer disease (AD), and powerful bioinformatic analysis, that add statistical and procedural robustness to biomarker discovery from blood. Methods: Carrier-protein–bound peptides were isolated from serum samples by affinity chromatography, and peptide mass spectra were acquired by a matrix-assisted laser desorption/ionization (MALDI) orthogonal time-of-flight (O-TOF) mass spectrometer capable of collecting data over a broad mass range (100 to >300 000 Da) in a single acquisition. Discriminatory analysis of mass spectra was used to process and analyze the raw mass spectral data. Results: Coupled with the biomarker enrichment protocol, the high-resolution MALDI O-TOF mass spectra provided informative, reproducible peptide signatures. The raw mass spectra were analyzed and used to build discriminant disease models that were challenged with blinded samples for classification. Conclusions: Carrier-protein enrichment of disease biomarkers coupled with high-resolution mass spectrometry and discriminant pattern analysis is a powerful technology for diagnostics and population screening. The mass fingerprint model successfully classified blinded AD patient and control samples with high sensitivity and specificity.

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Webber, Lucas C., Lindsey N. Anderson, Ines L. Paraiso, Thomas O. Metz, Ryan Bradley, Jan F. Stevens, and Aaron T. Wright. "Affinity- and activity-based probes synthesized from structurally diverse hops-derived xanthohumol flavonoids reveal highly varied protein profiling in Escherichia coli." RSC Advances 13, no. 42 (2023): 29324–31. http://dx.doi.org/10.1039/d3ra05296f.

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Xanthohumol, the principle prenylflavonoid found in hops (Humulus lupulus) and a reported anti-inflammatory agent, has great potential for pharmaceutical interventions related to inflammatory disorders in the gut.

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