Review
Biochemical Research Methods
Rebecca Elizabeth Kattan, Deena Ayesh, Wenqi Wang
Summary: During intracellular signal transduction, protein-protein interactions (PPIs) play a critical role in regulating protein localization and function. Mass spectrometry-based interactome analysis has become a popular method for studying PPI networks, but the analysis of large datasets can be challenging. In this review, we discuss the methods and resources commonly used for analyzing large interactome-related proteomic data and propose a guideline for identifying novel interacting proteins.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Jianan Feng, Linlin Jiang, Yiqing Cao, Chunhui Deng, Yan Li
Summary: In this study, a tractable method was established for rapid quality assessment of a harvested cell culture fluid (HCCF) sample by differentially extracting IgG with different Fc gamma RIIIa affinity levels and determining the amount and monomer percentage of IgGs using size exclusion chromatography (SEC).
ANALYTICAL CHEMISTRY
(2022)
Article
Cell Biology
Thomas C. Panagiotou, Anan Chen, Andrew Wilde
Summary: Cell division is a crucial event in the life of a cell, and the mechanisms underlying the formation and maturation of intercellular bridges (ICBs) are poorly understood. This study identifies CIN85 as an important factor in ICB assembly and demonstrates its requirement for efficient and timely cytokinesis. Additionally, the study reveals the crucial role of Anillin's interaction with different septin units in the elongation and maturation of ICBs.
Article
Chemistry, Multidisciplinary
Samuel L. Scinto, Tyler R. Reagle, Joseph M. Fox
Summary: This study demonstrates a new method for site-selective functionalization of proteins using pyridyl-tetrazine tags, allowing for direct affinity purification on commonly used nickel-iminodiacetate (Ni-IDA) resins. The method is also applicable for protein purification from complex mixtures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Han Pan, Ruifang Guan, Ruixue Zhao, Guangshuo Ou, Zhucheng Chen
Summary: The central spindle in animal cells regulates the formation of the division plane during cytokinesis. The molecular backbone of centralspindlin has the propensity to undergo liquid-liquid phase separation, and the synergy between ZEN-4 and CYK-4 subunits is critical for its function in microtubule bundling and central spindle assembly. Charge-driven macromolecular condensation mediates the assembly of the central spindle by centralspindlin.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Hongxu Sun, Hongrui Wang, Qiwei Chen, Wenge Dong, Chao Gao, Haiyan Song, Hui Peng, Ren Li, Hao Wu, Liangyu Hou, Yanhong Chang, Hui Luo
Summary: Protein purification is a fundamental technique in biological research and industrial production, and there is a constant pursuit of efficient, convenient, economical, and environmentally friendly methods. This study discovered that certain cations, including alkaline earth metals, alkali metals, and even nonmetals, can precipitate multi-histidine-tagged proteins at low salts concentrations. Based on this finding, a novel cation affinity purification method was developed that requires only three centrifugal separations and achieves high purity similar to immobilized metal affinity chromatography. The study also provides insights into unexpected protein precipitation and highlights the importance of considering the influence of cations on experimental results. The interaction between histidine-tagged proteins and cations may have broad application prospects.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Shen Zhang, Brett Larsen, Karen Colwill, Cassandra J. Wong, Ji-Young Youn, Anne-Claude Gingras
Summary: In this study, a simple and robust approach called turboDDA was developed to improve interactome analysis of affinity-purified samples. By eliminating the dynamic exclusion step and optimizing acquisition parameters, turboDDA detected more interactors and provided better sensitivity compared to standard DDA methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Neurosciences
Jia-Hua Hu, Ying Liu, Dax A. Hoffman
Summary: Proteins in neurons form complexes to regulate signal transduction and synaptic function. A novel method combining lentiviral protein expression with tandem affinity purification followed by mass-spectrometry (TAP-MS) has been successfully used to identify protein complexes and post-translational modifications in neurons, shedding light on potential mechanisms underlying neurological diseases.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Article
Microbiology
Lien De Caluwe, Sandra Coppens, Katleen Vereecken, Simon Daled, Maarten Dhaenens, Xaveer Van Ostade, Dieter Deforce, Kevin K. Arien, Koen Bartholomeeusen
Summary: Researchers identified factors that facilitate the entry of CHIKV into human cells using an affinity purification mass spectrometry coupled approach, validating the CD147 protein complex as an entry factor for CHIKV. They also demonstrated the involvement of the CD147 complex in the replication cycle of related alphaviruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Analytical
Jundong Wang, Qiang Han, Kai Wang, Shurong Li, Wen Luo, Qionglin Liang, Jingming Zhong, Mingyu Ding
Summary: Protein separation plays a crucial role in proteomics research, as it enables early diagnosis of various diseases. Magnetic nanoparticles, with their excellent properties such as easy surface functionalization and high saturation magnetization, have been widely used for the isolation of proteins/peptides. The development of surface decoration strategies has led to the design and fabrication of functional magnetic adsorbents to meet the increasing demands in biological separation. This review provides recent information on the applications of magnetic adsorbents in selective protein/peptide separation and presents comprehensive prospects and challenges in the field of protein separation utilizing magnetic nanoparticles.
Article
Biochemical Research Methods
Zongqing Huang, Haoju Hua, Xiuzhen Du, Zipeng Zhen, Wei Zhao, Jun Feng, Ji-an Li
Summary: This study successfully isolated VHHs against the SUMO protein for the first time using biopanning of an immune camelid nanobody library. The VHHs were coupled to agarose resins to form affinity chromatography resins, allowing for one-step purification of various SUMO fusions.
JOURNAL OF CHROMATOGRAPHY A
(2024)
Article
Engineering, Chemical
D. Gomes, M. A. S. Correia, M. J. Romao, L. A. Passarinha, A. Sousa
Summary: Human papillomavirus (HPV) is a sexually transmissible virus linked to 5% of global human cancers, particularly cervical cancer. This study focuses on the purification of the E6 protein, a therapeutic target for anti-HPV drug development, in order to facilitate biointeraction studies and drug discovery. Recombinant dual-tagged E6 protein was successfully expressed and extracted using Escherichia coli (E. coli) cultures and sonication/ice cycles. Affinity chromatography followed by size exclusion or immobilized-metal affinity chromatography techniques allowed for the purification of highly pure and stable His6-MBP-E6 protein, which is required for subsequent research on protein-ligand interactions and structural characterization of protein-ligand complexes.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Jonas Schilz, Charlotte Clement, Franziska Greiner, Arne Skerra
Summary: A novel strategy for the efficient and gentle affinity purification of PASylated proteins is reported, which allows direct one-step purification from cell extracts or culture supernatants while avoiding harsh elution conditions. This method can improve the efficiency of biological drug development.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Sandra M. Kerbler, Roberto Natale, Alisdair R. Fernie, Youjun Zhang
Summary: AP-MS and PL-MS are two powerful techniques for studying protein-protein interactions, providing insights into the interactions between proteins in plant systems.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Developmental Biology
Pei Zhang, Jiwei Chen, Xiangchuan Wang, Yingchao Geng, Liangyu Sun, Hongjie Zhang
Summary: Organ morphogenesis requires coordination of cellular events, including cell division, shape change, rearrangement, and death. However, the regulatory mechanism of cytokinesis in organ size and shape remains unclear. This study demonstrates that the centralspindlin complex regulates cytokinesis and epithelial morphogenesis, affecting cell division and causing malformation in Caenorhabditis elegans spermatheca. Analysis shows that CYK-4 regulates cytokinesis of spermathecal cells in a GTPase activator activity-independent manner. Furthermore, the centralspindlin components CYK-4 and ZEN-4, along with RHO-1 and CDC-42, play crucial roles in a signaling network that guides spermathecal morphogenesis by enabling completion of cytokinesis.
Article
Biochemistry & Molecular Biology
Stacey J. Scott, Xiaodun Li, Sriganesh Jammula, Ginny Devonshire, Catherine Lindon, Rebecca C. Fitzgerald, Pier Paolo D'Avino
Summary: Polyloidy plays a significant role in promoting chromosomal instability, genome evolution, and heterogeneity in cancer cells. The study on esophageal adenocarcinoma (EAC) revealed that the likely origin of polyploidy is due to mitotic failure caused by problems in chromosomal attachments, shedding light on cancer evolution and diversification for potential classification and treatment improvements.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Cell Biology
Stefano Sechi, Angela Karimpour-Ghahnavieh, Anna Frappaolo, Laura Di Francesco, Roberto Piergentili, Eugenia Schinina, Pier Paolo D'Avino, Maria Grazia Giansanti
Summary: GOLPH3 is a highly conserved protein localized to the Golgi apparatus and cytosol, playing a crucial role in cell trafficking and proliferation. Analysis of the protein-protein interaction network of GOLPH3 in testes revealed enrichment for proteins involved in vesicle-mediated trafficking, cell proliferation, and cytoskeleton dynamics. The interaction of dGOLPH3 with Fragile X mental retardation protein and Ataxin-2 suggests a potential role in the pathophysiology of nervous system disorders.
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
Correction
Developmental Biology
Robert E. Ward, Pamela Reid, Arash Bashirullah, Pier Paolo D'Avino, Carl S. Thummel
DEVELOPMENTAL BIOLOGY
(2022)
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
Cell Biology
Ella F. J. Halcrow, Riccardo Mazza, Anna Diversi, Anton Enright, Pier Paolo D'Avino
Summary: This study investigates the temporal and spatial profiles of midbody proteins during mitotic exit, revealing two distinct classes of midbody proteins. The results highlight the importance of ubiquitination and phosphorylation in the dynamics and stability of midbody proteins during cytokinesis.
Article
Biochemistry & Molecular Biology
Gianluca Amadei, David M. M. Glover
Summary: Studies have found that stem cells can self-assemble in the culture dish to mimic early embryonic development. These stem cell-derived models can imitate cell movements and gene expression patterns of gastrulation, and even develop into different organs and tissues. This article explores the journey of discovering and understanding these stem cell capabilities.
Article
Biology
Levente Kovacs, Agnieszka Fatalska, David M. Glover
Summary: In this study, a 24-amino-acid sequence from the tail anchor domain of the Drosophila proapoptotic protein Hid was used to target exogenous proteins to the mitochondria in Drosophila cells. It was found that Drosophila Sas6 can bind both Drosophila Gorab and its human GORAB ortholog, whereas human SAS6 is unable to bind either GORAB or Gorab. These findings are discussed in relation to the evolutionary conservation of Gorab and the divergence of Sas6.
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)
Review
Biology
A. L. Sperling, D. M. Glover
Summary: Parthenogenesis is widely observed in animals, but remains understudied. In dipterans, it is of particular importance due to the presence of parthenogenetic species that are disease vectors and agricultural pests. This study presents a catalog of parthenogenetic dipterans, explores the genetic basis of parthenogenesis, and discusses the evolutionary significance of parthenogenesis in this order.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(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)