Review
Immunology
Vincent Geoghegan, Jeremy C. Mottram, Nathaniel G. Jones
Summary: Proximity labelling is a powerful and rapidly developing technology that allows exploration of the interaction space and molecular environment of proteins at the nanometre scale. It can be performed in vivo without disrupting the normal functions of the proteins. This article highlights the applications of proximity labelling in kinetoplastid parasite research and provides an overview of experimental design and statistical analysis methods.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Francisco Zafra, Dolores Piniella
Summary: Membrane proteins play important roles in controlling cellular traffic and transmitting signals across the membrane. Interactions between membrane proteins and other cellular components form complex networks that regulate biological functions. Traditional methods for studying these interactomes may cause loss of components and non-native interactions. Proximity labelling techniques provide an alternative approach to identify interactors in a native cellular environment. This article reviews recent advances in proximity labelling for characterizing membrane interactomes.
JOURNAL OF PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Maik Pietzner, Eleanor Wheeler, Julia Carrasco-Zanini, Nicola D. Kerrison, Erin Oerton, Mine Koprulu, Jian'an Luan, Aroon D. Hingorani, Steve A. Williams, Nicholas J. Wareham, Claudia Langenberg
Summary: This study integrates two proteomic technologies to analyze the effects of protein quantitative trait loci, showing that each technique captures different aspects of protein biology. The results provide a benchmark for future cross-platform discoveries and highlight the inconsistency in genetically predicted effect directions between different assays.
NATURE COMMUNICATIONS
(2021)
Article
Food Science & Technology
Daniel Dashevsky, Kate Baumann, Eivind A. B. Undheim, Amanda Nouwens, Maria P. Ikonomopoulou, Justin O. Schmidt, Lilin Ge, Hang Fai Kwok, Juanita Rodriguez, Bryan G. Fry
Summary: Aculeate hymenopterans use venom for different purposes based on social behavior, with solitary species using it to paralyze prey and social species using it for colony defense. This study found that venom compositions and activities vary among species, with social species having higher presence of peptides causing damage and pain.
Article
Biochemical Research Methods
Li-Chun Cheng, Xi Zhang, Kanishk Abhinav, Julie A. Nguyen, Sabyasachi Baboo, Salvador Martinez-Bartolome, Tess C. Branon, Alice Y. Ting, Esther Loose, John R. Yates, Larry Gerace
Summary: By using engineered biotin ligase TurboID and quantitative proteomics, this study explored the neighborhoods of Emerin and LBR in cultured mouse embryonic fibroblasts. The analysis revealed 232 high confidence proximity partners interacting selectively with Emerin and/or LBR, with 49 shared by both.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Cell Biology
Yu Ding, Huibing Zhang, Yu-Ying Liao, Li-Nan Chen, Su-Yu Ji, Jiao Qin, Chunyou Mao, Dan-Dan Shen, Lin Lin, Hao Wang, Yan Zhang, Xiao-Ming Li
Summary: This article reports on the important role of cholecystokinin receptors in the brain-gut axis and how the receptors exhibit different affinities based on different posttranslational modification states. The study reveals key factors related to selectivity and activation in the receptor structure, providing multiple structural templates for drug design targeting the brain-gut axis.
Article
Multidisciplinary Sciences
Nadia Kamal, Nikos Tsardakas Renhuldt, Johan Bentzer, Heidrun Gundlach, Georg Haberer, Angela Juhasz, Thomas Lux, Utpal Bose, Jason A. Tye-Din, Daniel Lang, Nico van Gessel, Ralf Reski, Yong-Bi Fu, Peter Spegel, Alf Ceplitis, Axel Himmelbach, Amanda J. Waters, Wubishet A. Bekele, Michelle L. Colgrave, Mats Hansson, Nils Stein, Klaus F. X. Mayer, Eric N. Jellen, Peter J. Maughan, Nicholas A. Tinker, Martin Mascher, Olof Olsson, Manuel Spannagl, Nick Sirijovski
Summary: This study presents a high-quality reference genome of cultivated oat and its diploid and tetraploid progenitors. It reveals the structure of the oat genome and provides insights into the genetic factors influencing human health and agronomic traits. This resource will accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.
Article
Biochemistry & Molecular Biology
Giuliana Costanzo, Rita Turnaturi, Carmela Parenti, Salvatore Spoto, Silvia Piana, Maria Dichiara, Chiara Zagni, Anna Rita Galambos, Nariman Essmat, Agostino Marrazzo, Emanuele Amata, Mahmoud Al-Khrasani, Lorella Pasquinucci
Summary: In this study, we investigated the pharmacological properties of LP1 analogs both in vitro and in vivo to develop compounds with improved analgesic effects. By modifying the structure of the N-substituent of LP1, we found that compounds 3 and 7 displayed high binding affinity for the mu opioid receptor (MOR) and showed antagonist or agonist effects in different assays. Compound 7, as potent as LP1 and DAMGO, demonstrated analgesic effects in thermal and inflammatory pain models.
Article
Engineering, Environmental
Hillol Chakdar, Shobit Thapa, Amit Srivastava, Pratyoosh Shukla
Summary: Cyanobacteria have emerged as a potential option for bioremediation of heavy metals due to their unique adaptations and robust metabolic machineries. Understanding their physiological responses and regulation at the molecular level is necessary to identify candidate genes and proteins for improving bioremediation efficiency. These approaches might pave new possibilities of implementing genetic engineering strategies in the future.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Qiang Li, Minglong Li, Huiying Ma, Man Xue, Tong Chen, Xiaodong Ding, Shuzhen Zhang, Jialei Xiao
Summary: This study used quantitative phosphoproteomic analysis to investigate the phosphorylation events in soybean leaf and root tissues under sodium bicarbonate stress. The results revealed different responses and enriched pathways between leaf and root tissues. Protein kinase/phosphatase interactome analysis identified proteins involved in transporters/membrane trafficking, transcriptional level regulation, protein level regulation, signaling/stress response, and other functions.
Article
Biochemistry & Molecular Biology
Claudia Maria do Nascimento Moreira, Cristina D. Kelemen, Samson O. Obado, Farnaz Zahedifard, Ning Zhang, Fabiola B. Holetz, Laura Gauglitz, Bruno Dallagiovanna, Mark C. Field, Susanne Kramer, Martin Zoltner
Summary: The characterization of protein-protein interactions (PPIs) is important for understanding protein function. Two popular strategies, affinity capture and BioID, are used to identify PPIs in the cellular environment. A comparison of these methods using different trypanosome proteins as baits showed that BioID had fewer candidate interacting proteins with more confined bait protein localization, produced more false positives, and was less efficient in identifying low molecular weight proteins. These differences indicate the importance of using multiple methods to identify PPIs and suggest that BioID and affinity capture are complementary approaches.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Review
Immunology
Stephanie J. Hanna, Danijela Tatovic, Terri C. Thayer, Colin M. Dayan
Summary: In recent years, significant progress has been made in the analysis of individual cells using RNA sequencing techniques, leading to exciting discoveries in the immunology of type 1 diabetes (T1D). Single-cell RNA sequencing has revealed specific gene expression patterns in T1D patients, allowing for predictions of disease development and offering insights into potential immunotherapy targets for T1D.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Plant Sciences
Adriana Trifan, Andra-Cristina Bostanaru, Simon Vlad Luca, Veronika Temml, Muhammad Akram, Sonja Herdlinger, Lukasz Kulinowski, Krystyna Skalicka-Wozniak, Sebastian Granica, Monika E. Czerwinska, Aleksandra Kruk, Helene Greige-Gerges, Mihai Mares, Daniela Schuster
Summary: This study found that honokiol and magnolol have high activity against dermatophyte infections, acting as fungicidal agents through inhibition of ergosterol biosynthesis. Synergistic effects were observed when magnolol was combined with terbinafine, while honokiol only showed additive effects. Additionally, magnolol displayed inhibitory effects on pro-inflammatory cytokines released by stimulated human neutrophils.
Editorial Material
Multidisciplinary Sciences
Emily R. Liman
Summary: Insects use odorant receptor proteins to form membrane ion channels that open when binding to an odorant molecule, allowing them to detect and distinguish between smells.
Article
Cell Biology
Laura M. Szczesniak, Caden G. Bonzerato, Richard J. H. Wojcikiewicz
Summary: The study revealed the interactome of Bok with various proteins, particularly those related to mitochondrial fission and cellular structures. It also identified novel physical and functional interactions between Bok and Mcl-1.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Si Wu, Liu Hong, Yuqing Wang, Jieqiong Yu, Jie Yang, Jie Yang, Hong Zhang, Sarah Perrett
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Review
Biochemical Research Methods
Oliver M. Crook, Tom Smith, Mohamed Elzek, Kathryn S. Lilley
Article
Biochemistry & Molecular Biology
Christoph B. Messner, Vadim Demichev, Daniel Wendisch, Laura Michalick, Matthew White, Anja Freiwald, Kathrin Textoris-Taube, Spyros Vernardis, Anna-Sophia Egger, Marco Kreidl, Daniela Ludwig, Christiane Kilian, Federica Agostini, Aleksej Zelezniak, Charlotte Thibeault, Moritz Pfeiffer, Stefan Hippenstiel, Andreas Hocke, Christof von Kalle, Archie Campbell, Caroline Hayward, David J. Porteous, Riccardo E. Marioni, Claudia Langenberg, Kathryn S. Lilley, Wolfgang M. Kuebler, Michael Muelleder, Christian Drosten, Norbert Suttorp, Martin Witzenrath, Florian Kurth, Leif Erik Sander, Markus Ralser
Article
Biology
Siqi Fang, Paul D. W. Kirk, Marcus Bantscheff, Kathryn S. Lilley, Oliver M. Crook
Summary: Thermal proteome profiling is a method for monitoring protein thermal stability that can provide insights into protein function, drug targets, and off-targets. The use of Bayesian functional data analysis tools can improve sensitivity and identify new drug-protein associations.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rayner M. L. Queiroz, Sian C. Piper, Johanna S. Rees, Sam Strickson, Emmanuel Briend, Choon Pei Low, G. John Ferguson, Kathryn S. Lilley, Antony P. Jackson, Donna K. Finch
Summary: The ability of the cellular immune system to distinguish self from foreign antigens depends on the calibration of the T cell receptor signaling threshold, which can be affected by interleukin 7 (IL-7). In this study, the researchers investigated the early signaling events triggered by IL-7 and discovered previously unknown transduction events. They found that IL-7 leads to dephosphorylation of cytohesin interacting protein (CYTIP) and alters the co-localization of cytohesin-1 with the TCR and LFA-1 integrin. This study provides insights into the molecular mechanisms underlying TCR activation thresholds and has implications for autoimmune disease therapy and cancer immunotherapy.
BIOCHEMICAL JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Samantha C. Salvage, Zaki F. Habib, Hugh R. Matthews, Antony P. Jackson, Christopher L. -H. Huang
Summary: The activation of voltage-dependent Na+ channels plays a crucial role in cellular excitability through action potential generation. This review discusses the potential feedback actions of intracellular [Ca2+] on Na+ channel activity, highlighting their structural, genetic, cellular, and functional implications and their possible clinical importance. Studies on Na+ channel mutations associated with skeletal and cardiac muscle diseases, as well as the effects of cytoplasmic [Ca2+] on channel gating, provide insight into potential therapeutic strategies for arrhythmic conditions such as catecholaminergic polymorphic ventricular tachycardia.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Review
Biochemical Research Methods
Josie A. Christopher, Aikaterini Geladaki, Charlotte S. Dawson, Owen L. Vennard, Kathryn S. Lilley
Summary: The internal environment of cells is crowded with molecules, requiring spatial organization through subcellular compartmentalization. These compartments provide specific conditions for molecules to carry out their biological functions, and molecules traffic between these compartments. Aberrant localization of proteins or RNA species is associated with various pathological conditions. Differential expression studies often overlook the importance of subcellular information, and subcellular transcriptomics and proteomics data do not always overlap, highlighting their complementary nature.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Letter
Biotechnology & Applied Microbiology
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
Article
Multidisciplinary Sciences
Vadim Demichev, Lukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda, Daniela Ludwig, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S. Lilley, Michael Muelleder, Alexey Nesvizhskii, Markus Ralser
Summary: The dia-PASEF technology utilizes ion mobility separation to reduce signal interference and enhance sensitivity in proteomic experiments. This study introduces a novel algorithm and software solution that significantly improves proteomic depth in dia-PASEF experiments, particularly for fast experiments and those with limited sample sizes.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Clarissa Braccia, Josie A. Christopher, Oliver M. Crook, Lisa M. Breckels, Rayner M. L. Queiroz, Nara Liessi, Valeria Tomati, Valeria Capurro, Tiziano Bandiera, Simona Baldassari, Nicoletta Pedemonte, Kathryn S. Lilley, Andrea Armirotti
Summary: This study investigates the impact of pharmacological rescue treatment on the proteome of a CF model. The results suggest that VX-809 treatment induces extensive structural and functional remodeling of mitochondria and peroxisomes. These findings are important for further understanding the therapeutic mechanisms and drug research of CF.
Article
Multidisciplinary Sciences
Oliver M. Crook, Colin T. R. Davies, Lisa M. Breckels, Josie A. Christopher, Laurent Gatto, Paul D. W. Kirk, Kathryn S. Lilley
Summary: The steady-state localisation and re-localisation of proteins are crucial for understanding their function and cellular dynamics, with high-throughput methods like BANDLE using Bayesian principles to accurately compute differential protein localisation probabilities upon cellular perturbation, reducing errors compared to existing approaches.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Alistair R. Hines, Matthew Edgeworth, Paul W. A. Devine, Samuel Shepherd, Nicholas Chatterton, Claire Turner, Kathryn S. Lilley, Xiaoyu Chen, Nicholas J. Bond
Summary: Antibody-drug conjugates (ADCs) have been widely developed, leading to new approvals and improved standard of care for cancer patients. This study describes the development of a mass-spectrometry-based method that can simultaneously monitor four quality attributes of ADCs, providing new insights into their properties and manufacturing processes. The study identified variations in thiol state, N-linked glycosylation, reduction of disulfide bonds, and polypeptide fragmentation in ADCs. The method offers a high-throughput approach to support the development of engineered antibody scaffolds.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Nicola M. Moloney, Konstantin Barylyuk, Eelco Tromer, Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Ross F. Waller, Paula MacGregor
Summary: This study maps the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, providing insights into the molecular basis for diversity within and between these pathogen species. Comparative analysis reveals key routes of parasitic adaptation to different biological niches.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Qiong-Qiong Yao, Liu Hong, Si Wu, Sarah Perrett
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)