Review
Biochemical Research Methods
Huaming Chen, Fuyi Li, Lei Wang, Yaochu Jin, Chi-Hung Chi, Lukasz Kurgan, Jiangning Song, Jun Shen
Summary: This paper systematically evaluates machine learning-based computational methods for human-bacterium protein-protein interactions (HB-PPIs). By reviewing publicly available databases of HP-PPIs, identifying bacterium pathogens, summarizing existing models, and evaluating the performance of machine learning models, valuable insights are provided for predicting HB-PPIs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Dheeraj Chitara, Richa Anand, B. S. Sanjeev
Summary: RNA interference (RNAi) plays a role in genetic interference and is identified as an antiviral response mechanism in humans. The study on the interfaces between Ago, miRNA and Target RNA in the presence of molecular crowders through molecular dynamics simulations reveals that crowding changes dynamics, stabilizes the complex and aids in binding free energy. Conserved features and amino acid residues with crowding resilient interactions with RNA are identified in all three systems.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Kyle I. P. Le Huray, He Wang, Frank Sobott, Antreas C. Kalli
Summary: This study systematically simulated the interactions between 100 mammalian PH domains and PIP-containing membranes. The observed PIP interaction hotspots recapitulate crystallographic binding sites and provide insights into the mechanisms of PH domain/membrane association. The study offers a comprehensive view of the binding of PH domains to membranes.
Article
Multidisciplinary Sciences
Sheng Ye, Guozhen Zhang, Jun Jiang
Summary: This article presents a study on using machine learning and infrared spectroscopy to monitor the structural information of the SARS-CoV-2 and hACE2 protein complexes. The new technology can identify subtle changes in protein secondary structure variations at a much faster speed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Brendan M. Floyd, Kevin Drew, Edward M. Marcotte
Summary: Protein phosphorylation is a crucial regulatory mechanism in eukaryotic cellular processes, with the majority of phosphorylation sites still having unknown functions. A method called phospho-DIFFRAC was developed to systematically identify phosphorylation-dependent protein assemblies and found that these interactions are enriched in RNA-binding proteins.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Ludwig Geistlinger, Roger Vargas Jr, Tyrone Lee, Joshua Pan, Edward L. Huttlin, Robert Gentleman
Summary: The BioPlex project has created two proteome-scale, cell-line-specific protein-protein interaction networks, containing a large number of interactions among proteins in 293T and HCT116 cells. This project provides programmatic access to the networks and integration with related resources, facilitating downstream analysis in R and Python. The implemented functionality supports various analyses, such as sub-network analysis, protein domain-domain association analysis, protein structure mapping, and analysis of transcriptomic and proteomic data.
Article
Biochemistry & Molecular Biology
Filipe E. P. Rodrigues, Antonio J. Figueira, Claudio M. Gomes, Miguel Machuqueiro
Summary: Computational analysis revealed that Aβ-Lys28 plays a key role in stabilizing interactions with S100B, involving residues such as Met79, Thr82, and Glu86. Coulombic interactions, potentially involving the Lys28(Aβ)/Glu86(S100B) pair, are crucial for the holdase-type chaperone activity of S100B, and high ionic strength can reduce the anti-aggregation activity of the Aβ-S100B interaction through electrostatic perturbation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Gerard Duart, Brayan Grau, Ismael Mingarro, Luis Martinez-Gil
Summary: The study of protein-protein interactions is crucial for understanding cell processes, with transmembrane segments being able to participate in interactions. However, the hydrophobic nature of these segments and their environment pose challenges for studying intramembrane PPI, requiring specific approaches and techniques. This review explores strategies for studying intramembrane PPI in vitro, in vivo, and in silico, focusing on techniques suitable for standard molecular biology laboratories with experience in membrane proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Multidisciplinary Sciences
Rosa D. Hernansaiz-Ballesteros, Csenge Foldi, Luca Cardelli, Laszlo G. Nagy, Attila Csikasz-Nagy
Summary: Studying the kinase-phosphatase pair Wee1 and Cdc25 revealed their reversed action on CDK, which helps establish a stable G2 phase and add checkpoints to the cell cycle. This regulatory mechanism appeared in LECA and co-evolved in eukaryotes, indicating its crucial role at the emergence of eukaryotes.
SCIENTIFIC REPORTS
(2021)
Review
Psychology
Olga V. Burenkova, Tatiana A. Dolgorukova, Iuliia An, Tatiana A. Kustova, Aleksei A. Podturkin, Ekaterina M. Shurdova, Oksana I. Talantseva, Marina A. Zhukova, Elena L. Grigorenko
Summary: Studies investigating the relationship between endogenous oxytocin concentrations and human social interactions have shown inconsistent results. This systematic review and meta-analysis of 63 studies found that social interactions did not lead to expected hormone responses in causal designs, but there was a significant correlation between social interaction indicators and oxytocin concentrations in correlational designs. Subgroup analyses showed higher than zero mean effect sizes in studies involving parent-child interactions, the enzyme-linked immunosorbent assay method for oxytocin analysis, and unrestricted eating, drinking, or exercise before biofluid collection. Standardized and reliable approaches are needed to further study the neurochemical mechanisms of sociality in humans.
PSYCHOLOGICAL BULLETIN
(2023)
Article
Biochemistry & Molecular Biology
Silvia Gabbrielli, Luca Colnaghi, Gemma Mazzuoli-Weber, Alberto Cesare Luigi Redaelli, Alfonso Gautieri
Summary: Plastic pollution is a global threat to the environment and has raised concerns about the impact of plastic exposure on global health. Plastic nanoparticles have been found to affect protein folding and the formation of abnormal amyloid proteins, potentially leading to systemic and local amyloidosis. This study investigates the interaction between nanoplastics and beta-amyloid fibrils to gain a better understanding of the role of nanoplastics in the development of neurodegenerative disorders. Using molecular dynamics simulations, the study examines the interactions between neutral and charged nanoparticles made of common plastic materials and beta-amyloid fibrils, and identifies the factors that influence the interaction.
Article
Biotechnology & Applied Microbiology
Guobin Zhang, Zeyu Zhang, Shilei Luo, Xia Li, Jian Lyu, Zeci Liu, Zilong Wan, Jihua Yu
Summary: This study conducted a genome-wide investigation of the CsPP2C gene family in cucumber and identified 56 CsPP2C genes. Phylogenetic analysis revealed the classification of PP2C genes in cucumber and Arabidopsis into 13 groups. Different expression patterns of CsPP2C genes were observed under various abiotic treatments, and specific tissue expression patterns were also observed. Segmental duplication events played a key role in the expansion of the PP2C gene family in cucumber. Moreover, the presence of ABA and drought response elements in the promoter region of CsPP2C genes was detected. These findings provide a reference for the identification of the PP2C gene family in other species and lay the foundation for future studies on the function of PP2C genes in cucumber.
Article
Biochemistry & Molecular Biology
Wei Lim Chong, Koollawat Chupradit, Sek Peng Chin, Mai Mai Khoo, Sook Mei Khor, Chatchai Tayapiwatana, Piyarat Nimmanpipug, Weeraya Thongkum, Vannajan Sanghiran Lee
Summary: This study combined molecular dynamics simulations and nanoparticle tracking analysis to investigate protein-protein interactions. Results showed that a mutated protein had significantly lower binding free energy, indicating reduced affinity to the target protein. The possible mechanism of this decrease in affinity was explored through the analysis of crucial residues and hydrogen bonds.
Article
Biochemistry & Molecular Biology
Shuang Yang, WenJun Zhang
Summary: This study identified essential proteins in the olfactory system of Drosophila melanogaster and confirmed the key roles of specific proteins in fruit fly olfaction. These findings provide important protein information for further research on D. melanogaster olfaction.
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Review
Microbiology
Alison A. McBride
Summary: HPVs are a diverse group of viruses that replicate in specific anatomical niches of the stratified epithelia. Most infections are asymptomatic, but some can cause benign proliferative lesions or even cancer. These viruses have evolved to evade the host immune system and manipulate cellular processes to ensure their survival and replication.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Oncology
Julia Elzanowska, Laura Berrocal, Beatriz Garcia-Pelaez, Marta Vives-Usano, Beatriz Passos Sebo, Joana Maia, Silvia Batista, Jaakko Teppo, Markku Varjosalo, Maria Carolina Strano Moraes, Miguel Angel Molina-Vila, Bruno Costa-Silva
Summary: We conducted a comprehensive comparison of commonly used approaches for EV-DNA extraction and assessed their impact on DNA quantity, quality, and suitability for downstream analyses. Our findings suggest that different extraction methods can affect the detection of specific mutations by qPCR and the suitability of NGS, potentially influencing downstream clinical applications.
Article
Immunology
Elina A. Tuovinen, Sakari Poysti, Firas Hamdan, Kim My Le, Salla Keskitalo, Tanja Turunen, Lea Minier, Nanni Mamia, Kaarina Heiskanen, Markku Varjosalo, Vincenzo Cerullo, Juha Kere, Mikko R. J. Seppanen, Arno Hanninen, Juha Gronholm
Summary: This study investigated the function and phenotype of expanded gamma delta T cells in individuals with atypical SCID. The findings suggest that these cells have distinct characteristics in terms of IL2RG cell surface expression, signaling, cytotoxicity, and the presence of a novel IL2RG variant restricted to gamma delta T cells.
JOURNAL OF CLINICAL IMMUNOLOGY
(2023)
Article
Immunology
Elina A. Tuovinen, Outi Kuismin, Leila Soikkonen, Timi Martelius, Meri Kaustio, Sari Hamalainen, Hanna Viskari, Jaana Syrjanen, Ulla Wartiovaara-Kautto, Kari K. Eklund, Janna Saarela, Markku Varjosalo, Juha Kere, Timo Hautala, Mikko R. J. Seppanen
Summary: The NF-κB family of transcription factors is important in cellular signaling pathways, and NFKB1 variants have been associated with CVID and immunodeficiency. However, the penetrance and prevalence of CVID are relatively low, while inflammatory manifestations are more common.
CLINICAL IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Larisa Chernyaeva, Giorgio Ratti, Laura Teirila, Satoshi Fudo, Uni Rankka, Anssi Pelkonen, Paula Korhonen, Katarzyna Leskinen, Salla Keskitalo, Kari Salokas, Christina Gkolfinopoulou, Katrina E. Crompton, Matti Javanainen, Lotta Happonen, Markku Varjosalo, Tarja Malm, Ville Leinonen, Angeliki Chroni, Paivi Saavalainen, Seppo Meri, Tommi Kajander, Adam J. M. Wollman, Eija Nissila, Karita Haapasalo
Summary: By studying the interaction between apoE4 and FH, it was found that this interaction affects the neurotoxicity and clearance of A beta 1-42, which is related to AD pathogenesis. ApoE and FH reduce the binding of A beta 1-42 to CR3 and the subsequent phagocytosis by microglia, leading to changes in gene expression related to AD. FH forms complement-resistant oligomers with apoE/A beta 1-42 complexes, and the formation of these complexes is isoform specific, with apoE2 and apoE3 having higher affinity to FH than apoE4. These complexes reduce A beta 1-42 oligomerization and toxicity, and colocalize with C1q on A beta plaques in the brain, providing important insights into AD pathogenesis and how the strongest genetic risk factor for AD predisposes to neuroinflammation in the early stages of the disease pathology.
Article
Biochemistry & Molecular Biology
Yosuke Senju, Toiba Mushtaq, Helena Vihinen, Aki Manninen, Juha Saarikangas, Katharina Ven, Ulrike Engel, Markku Varjosalo, Eija Jokitalo, Pekka Lappalainen
Summary: The MTSS1 protein binds to the Arp2/3 and WAVE-2 protein complexes, promoting the formation of dynamic membrane folds at cell-cell junctions and enhancing the integrity of these junctions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Oncology
Sini Luoma, Philipp Sergeev, Komal Kumar Javarappa, Tiina J. Ohman, Markku Varjosalo, Marjaana Saily, Pekka Anttila, Marja Sankelo, Anu Partanen, Anne Nihtinen, Caroline A. A. Heckman, Raija Silvennoinen
Summary: The bone marrow microenvironment plays a significant role in cancer survival and immune evasion in multiple myeloma (MM). By analyzing longitudinal bone marrow samples, researchers found distinct immune profiles between patients with good and bad responses to specific treatment. These findings suggest that deep immune profiling could be a useful tool for treatment guidance and require further investigation.
Article
Multidisciplinary Sciences
Lisa Gawriyski, Eeva-Mari Jouhilahti, Masahito Yoshihara, Liangru Fei, Jere Weltner, Tomi T. Airenne, Ras Trokovic, Shruti Bhagat, Mari H. Tervaniemi, Yasuhiro Murakawa, Kari Salokas, Xiaonan Liu, Sini Miettinen, Thomas R. Burglin, Biswajyoti Sahu, Timo Otonkoski, Mark S. Johnson, Shintaro Katayama, Markku Varjosalo, Juha Kere
Summary: LEUTX, a transcription factor, is expressed in human preimplantation embryos at the 4-8 cell stages and silenced in somatic tissues. Through multiomic characterization, we found that LEUTX interacts with histone acetyltransferases, EP300 and CBP, via its 9 amino acid transactivation domain. It targets genomic cis-regulatory sequences overlapping with repetitive elements and functions as a transcriptional activator, upregulating genes involved in preimplantation development and 8-cell-like markers.
Editorial Material
Biochemical Research Methods
Salla Keskitalo, Markku Varjosalo
EXPERT REVIEW OF PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Svetlana Konovalova, Ruben Torregrosa-Munumer, Pooja Manjunath, Xiaonan Liu, Sundar Baral, Kaneez Fatima, Minna Holopainen, Jouni Kvist, Jayasimman Rajendran, Yang Yang, Markku Varjosalo, Reijo Kakela, Pentti Somerharju, Henna Tyynismaa
Summary: NERCLIN is a small mitochondrial protein that negatively regulates CL homeostasis and mitochondrial ultrastructure. It interacts with the CL synthesis and prohibitin complexes to regulate CL content and contributes to stress-induced adaptation of mitochondrial dynamics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Oncology
Matias Kinnunen, Xiaonan Liu, Elina Niemelae, Tiina Oehman, Lisa Gawriyski, Kari Salokas, Salla Keskitalo, Markku Varjosalo
Summary: Gene fusions can produce chimeric fusion proteins that have unpredictable properties, some of which can function as oncogenic drivers. ETV6-NTRK3 is a fusion gene that produces a constitutively active fusion kinase. Through proximity labeling, a study was conducted to analyze the interactomes of all four known ETV6-NTRK3 variants, revealing similarities and differences in their interacting proteins. These findings may explain the differences in reported frequencies and tissue specificities of the ETV6-NTRK3 variants.
Review
Oncology
Kari Salokas, Giovanna Dashi, Markku Varjosalo
Summary: Cancer-associated gene fusions, known as oncofusions, are driving forces in oncogenesis and have revolutionized cancer research through advanced sequencing technologies. They manipulate cellular signaling pathways and show promise as targets for therapy and diagnostic markers. Further research is needed to understand their functional impact and harness their potential for precision cancer treatment.
Article
Cell Biology
Emilia Piki, Alice Dini, Juuli Raivola, Kari Salokas, Kaiyang Zhang, Markku Varjosalo, Teijo Pellinen, Katja Valimaki, Kristina Tabor Veskimae, Synnove Staff, Sampsa Hautaniemi, Astrid Murumagi, Daniela Ungureanu
Summary: Dysregulation of the Wnt pathway, specifically the expression of the non-canonical receptor ROR1, is linked to ovarian cancer progression and drug resistance. ROR1 expression is enhanced by neoadjuvant chemotherapy, and its interaction with Wnt5a activates oncogenic signaling pathways in ovarian cancer cells. Furthermore, ROR1 and its downstream effector STAT3 are expressed at higher levels in stromal cells than in epithelial cancer cells in ovarian cancer tumors.
CELL DEATH DISCOVERY
(2023)
Article
Biochemistry & Molecular Biology
Liang Wang, Taru Hilander, Xiaonan Liu, Hoi Ying Tsang, Ove Eriksson, Christopher B. Jackson, Markku Varjosalo, Hongxia Zhao
Summary: This study identifies GTPBP8 as a crucial factor in the assembly of the mitoribosomal large subunit (mt-LSU) and mitochondrial translation. Depletion of GTPBP8 leads to abnormal accumulation of mt-LSU and compromised mitochondrial function.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Genetics & Heredity
Susanna Nousiainen, Outi Kuismin, Siiri Reinikka, Roosa Manninen, Sara Khamaiseh, Mari Kuivalainen, Anna Terho, Sari Koivurova, Maarit Niinimaki, Kari Salokas, Markku Varjosalo, Anne Ahtikoski, Ralf Butzow, Outi Lindgren, Outi Uimari, Pia Vahteristo
Summary: In this study, FGFR4, NALCN, and NAV2 were identified as novel high-risk candidate genes for familial endometriosis. The findings also support the association between endometriosis and high-grade serous carcinoma.
Meeting Abstract
Biotechnology & Applied Microbiology
Ganna Reint, Zhuokun Li, Kornel Labun, Salla Keskitalo, Inkeri Soppa, Katariina Mamia, Eero Tolo, Monika Szymanska, Leonardo Meza-Zepeda, Susanne Lorenz, Artur Cieslar-Pobuda, Xian Hu, Diana Bordin, Judith Staerk, Eivind Valen, Bernhard Schmierer, Markku Varjosalo, Jussi Taipale, Emma Haapaniemi
