Article
Biochemistry & Molecular Biology
Sonali Tayal, Venugopal Bhatia, Tanya Mehrotra, Sonika Bhatnagar
Summary: This study curated experimental host-pathogen and host-host protein-protein interactions, annotated the domains and motifs of these proteins, and proposed the concept of mimicry pairs. The results were organized in a web-based resource called ImitateDB, which allows for easy querying of a large number of identified mimicry pairs in interacting host and pathogen proteins.
Article
Multidisciplinary Sciences
Vinay Kumar Pathak, Itu Singh, Shoor Vir Singh, Utpal Sengupta
Summary: The study found that mimicking epitopes between Mycobacterium leprae and host components play a key role in inducing autoimmune response in leprosy, and may serve as biomarkers to predict inflammatory episodes. Antibodies against 8 linear B cell epitopes were significantly higher in Type 1 reaction leprosy patients compared to Non-reaction patients, while 5 linear T cell epitopes were associated with lymphocyte proliferation in the Type 1 reaction group.
SCIENTIFIC REPORTS
(2021)
Review
Microbiology
Vera Vozandychova, Pavla Stojkova, Kamil Hercik, Pavel Rehulka, Jiri Stulik
Summary: Ubiquitination, similar to phosphorylation and acetylation, plays a crucial role in regulating various cell processes. Understanding how pathogens manipulate host ubiquitination processes is important for vaccine development and disease treatment. Pathogenic bacteria encode effector proteins targeting the host ubiquitin machinery to disrupt host defense processes.
Article
Microbiology
Heidy Elkhaligy, Christian A. Balbin, Jessica Siltberg-Liberles
Summary: Protein-protein interactions in eukaryotes are driven by short linear motifs (SLiMs). Conserved SLiMs can help identify functional SLiMs in eukaryotic protein families. However, the simplicity of eukaryotic SLiMs makes them appear by chance not only in eukaryotes but also in pathogenic bacteria and viruses. Additionally, functional eukaryotic SLiMs often exist in disordered regions. Pathogenic bacteria and viruses have less disorder in their proteomes compared to eukaryotes, but their proteins can mimic and disrupt eukaryotic SLiMs. Finding important SLiMs in pathogens is challenging but essential for understanding host-pathogen interactions. A comparative analysis of SLiMs across viruses, bacteria, and eukaryotes showed that viral SLiMs and certain motifs found in both viruses and eukaryotes have less disorder. The analysis of structural features of equivalent SLiMs from pathogens and eukaryotes revealed that some motifs are more structured in pathogens while others are more structured in eukaryotes, suggesting a varied mechanism of interaction between pathogens and their eukaryotic hosts.
Review
Biochemistry & Molecular Biology
Saumyadeep Goswami, Dibyendu Samanta, Kheerthana Duraivelan
Summary: Viruses utilize molecular mimicry to hijack host cellular machinery, mimicking host sequences or structures to exploit host physiological interactions for their pathogenesis. Short linear motifs (SLiMs) are a common form of sequence mimicry, mediating transient interactions in host protein networks. Research on well-characterized SLiMs involved in viral entry can aid in the discovery of unknown cellular receptors used by viruses and inform the development of targeted therapeutics such as vaccines or inhibitors.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Jordi Gomez Borrego, Marc Torrent Burgas
Summary: Adhesion and colonization of host cells by pathogenic bacteria rely on protein-protein interactions (PPIs). This study developed a filtering process to obtain a reliable list of domains and motifs participating in PPIs between bacteria and human cells. Structural analysis revealed that human proteins involved in these interactions are rich in alpha helix and disordered regions. The most significant domain-domain interactions were validated, but verifying domain-motif interactions was more challenging. Post-translational modifications, especially phosphorylation, also play a role in these interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Asahiro Morishita, Kyoko Oura, Tomoko Tadokoro, Koji Fujita, Joji Tani, Tsutomu Masaki
Summary: The liver is a non-immunological organ involved in metabolic activities, nutrient storage, and detoxification. Resident immune cells in the liver drive immunological reactions and certain microRNAs are associated with the immune response to pathogens, although the exact mechanism of miRNA interference in these interactions remains unclear.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Anuja Jain, Shikha Mittal, Lokesh P. Tripathi, Ruth Nussinov, Shandar Ahmad
Summary: Recognition of pathogen-derived nucleic acids by host cells is crucial for detecting pathogenic invasion and triggering immune responses. Understanding the interactions between pathogen nucleic acids and host factors is essential for therapeutic intervention.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Biotechnology & Applied Microbiology
Paula M. Tribelli, Nancy Lopez
Summary: This review provides an overview of temperature-response mechanisms in Pseudomonas species and highlights their relevance to human and animal health as well as agricultural applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Environmental Sciences
Siddiq Akbar, Lei Gu, Yunfei Sun, Lu Zhang, Kai Lyu, Yuan Huang, Zhou Yang
Summary: Microbes play vital roles in healthy ecosystems, performing functions such as nutrient recycling, antibiotic production, and waste decomposition. In animals, microbes become part of the microbiome, defending the host against pathogens and providing essential nutrients. The microbiome is a polygenic trait influenced by host genotype and environmental factors. However, the effects of stress on microbiomes and their recovery are still poorly understood.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Oncology
Emine Sila Ozdemir, Ruth Nussinov
Summary: Host-pathogen interactions involve various mechanisms and disrupt homeostasis in host cells, leading to infections, diseases, and disorders. Understanding the 3D structures of host-pathogen complexes can provide insights for therapeutic development and preventive measures. However, structural studies face challenges in predicting protein-protein interactions and require computational approaches such as machine learning and artificial intelligence.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Medi Kori, Beste Turanli, Kazim Yalcin Arga
Summary: This study integrates interaction data with biological knowledge to identify potential drug targets for cervical cancer using HP-PPI networks. A novel bioinformatics framework is developed to select host proteins and perform drug repurposing analysis. Promising drug candidates for HPV16 and HPV18 subtypes are identified.
FRONTIERS IN ONCOLOGY
(2023)
Review
Cell Biology
Ana Katic, Dario Huesler, Francois Letourneur, Hubert Hilbi
Summary: This article introduces the haploid social amoeba Dictyostelium discoideum as a model organism for studying vesicle trafficking, motility and migration, cell division, and other biological processes, and discusses the crucial role of Dynamin superfamily proteins (DSPs) in these processes. Major progress has been made in elucidating the function and structure of mammalian and D. discoideum DSPs, and the potential of using the genetically tractable amoeba to further study the role of DSPs in cell and infection biology is emphasized.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Meshari Alazmi, N. Alshammari, Naimah A. Alanazi, Abdel Moneim E. Sulieman
Summary: Despite advancements in agricultural research, food safety remains a significant challenge. Scientists are utilizing systems biology tools to study the root causes of food safety issues and improve plant health and reliability.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Biochemistry & Molecular Biology
Cristian D. Loaiza, Naveen Duhan, Rakesh Kaundal
Summary: The Citrus genus faces a major threat from citrus greening disease, with limited knowledge on the mechanisms of infection by Liberibacter bacteria. Efforts to develop high-yield resistant cultivars are hindered by this lack of understanding. The GreeningDB database aims to provide a platform for HLB-related protein annotations and support the development of molecular-based strategies to combat this devastating disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Kevin M. Brown, Mai Xu, Michael Sargen, Hyunbum Jang, Mingzhen Zhang, Tongwu Zhang, Bin Zhu, Kristie Jones, Jung Kim, Laura Mendoza, Nicholas K. Hayward, Margaret A. Tucker, Alisa M. Goldstein, Xiaohong Rose Yang, Douglas R. Stewart, Belynda Hicks, Dario Consonni, Angela C. Pesatori, Maria Concetta Fargnoli, Ketty Peris, Alex Stratigos, Chiara Menin, Paola Ghiorzo, Susana Puig, Eduardo Nagore, Thorkell Andresson, Ruth Nussinov, Donato Calista, Maria Teresa Landi
Summary: A novel NRAS variant was identified in an Italian melanoma-prone family, absent in other populations, influencing signaling pathways differently than other RAS activating alterations. Further investigation into NRAS as a familial melanoma gene is warranted.
Article
Biochemical Research Methods
Damla Ovek, Ameer Taweel, Zeynep Abali, Ece Tezsezen, Yunus Emre Koroglu, Chung-Jung Tsai, Ruth Nussinov, Ozlem Keskin, Attila Gursoy
Summary: This web-based server provides navigation and visualization of possible interactions between SARS-CoV-2 and human host proteins. It catalogues all interactions, using an innovative interface mimicry strategy, allowing users to explore and view these interactions.
Article
Biochemistry & Molecular Biology
William Martin, Gloria Sheynkman, Felice C. Lightstone, Ruth Nussinov, Feixiong Cheng
Summary: The rapid increase in computing power has greatly enhanced the capabilities of molecular dynamics simulations. Integrating learning techniques into analysis pipelines can reveal the kinetics of protein aggregation in Alzheimer's disease, but there are limitations and potential solutions.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Review
Chemistry, Medicinal
Ruth Nussinov, Mingzhen Zhang, Ryan Maloney, Chung-Jung Tsai, Bengi Ruken Yavuz, Nurcan Tuncbag, Hyunbum Jang
Summary: Precision oncology benefits from early effective drug discovery decisions, with drugs targeting inactive protein conformations showing success. Cancer driver mutations mimic protein activation mechanisms, guiding target selection. Structural perturbations from double driver mutations may offer new insights for drug design.
MEDICINAL RESEARCH REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Kazi Lutful Kabir, Buyong Ma, Ruth Nussinov, Amarda Shehu
Summary: This paper investigates the application of Markov State Models (MSM) in the field of molecular dynamics and explores two important aspects in building the models: the selection of structure representation and the application of clustering algorithms. The results suggest that using fewer dimensions and including more structures leads to better models, which contribute to our understanding of antibody dynamics and antibody-antigen recognition.
Article
Biochemical Research Methods
Hansaim Lim, Chung-Jung Tsai, Ozlem Keskin, Ruth Nussinov, Attila Gursoy
Summary: HMI-PRED 2.0 is a publicly available web service that predicts host-microbe protein-protein interaction using interface mimicry. It aims to be user-friendly without requiring extensive computational experience.
Review
Oncology
Ruth Nussinov, Chung-Jung Tsai, Hyunbum Jang
Summary: This study examines driver mutations in cancer and questions whether activating mutations or signal strength play a larger role in tumor development. It suggests that signal strength, rather than the initial mutation, determines cell fate. Factors such as homeostatic mechanisms, additional mutations, and the expression levels of certain genes and regulators can impact signaling strength. Signal levels vary across cell types, states, and time windows due to chromatin structure. The study highlights the importance of determining signaling thresholds and predicting signal strength for improving patient outcomes.
Article
Biochemistry & Molecular Biology
Yonglan Liu, Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov
Summary: Bcr-Abl, a nonreceptor tyrosine kinase, plays a crucial role in leukemias, particularly chronic myeloid leukemia (CML). The fusion of Bcr and Abl leads to constitutive activation of Bcr-Abl. Oligomerization of Bcr-Abl is critical for its membrane clustering, MAPK signaling, and cell proliferation. Understanding the structural basis of Bcr-Abl oligomerization can guide the development of novel drugs targeting this process.
Letter
Oncology
Mingzhen Zhang, Ryan Maloney, Yonglan Liu, Hyunbum Jang, Ruth Nussinov
CANCER COMMUNICATIONS
(2023)
Review
Pharmacology & Pharmacy
Ruth Nussinov, Mingzhen Zhang, Yonglan Liu, Hyunbum Jang
Summary: Drug discovery is a highly challenging and significant interdisciplinary aim. The success of AlphaFold, an AI-powered technology, has raised hopes for drug discovery, but its limitations need to be considered. Improving AlphaFold's performance in active state models can enhance the success rate of rational drug design.
DRUG DISCOVERY TODAY
(2023)
Article
Chemistry, Physical
Mingzhen Zhang, Yonglan Liu, Hyunbum Jang, Ruth Nussinov
Summary: Kinase drug selectivity is a challenge in cancer research. Researchers propose a protocol to identify unique geometric features in the drug pocket that can distinguish one kinase from others. They analyze the structural principles of kinase drug selectivity using experimental structures and artificial intelligence. The results show that there are binary units in the kinome that can distinguish kinases from each other.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Biophysics
Ruth Nussinov, Bengi Ruken Yavuz, M. Kaan Arici, Habibe Cansu Demirel, Mingzhen Zhang, Yonglan Liu, Chung-Jung Tsai, Hyunbum Jang, Nurcan Tuncbag
Summary: Neurodevelopmental disorders (NDDs) and cancer have similarities in terms of proteins, pathways, and mutations, but have different clinical symptoms. However, individuals with NDDs have a higher likelihood of developing cancer later on. This review explores how shared features can result in different medical conditions and why having an NDD first can increase the chances of malignancy.
BIOPHYSICAL REVIEWS
(2023)
Article
Genetics & Heredity
Bengi Ruken Yavuz, M. Kaan Arici, Habibe Cansu Demirel, Chung-Jung Tsai, Hyunbum Jang, Ruth Nussinov, Nurcan Tuncbag
Summary: Epidemiological studies show that individuals with neurodevelopmental disorders are more likely to develop certain types of cancer. While these disorders and cancer share proteins, pathways, and mutations, they differ in clinical outcomes. The key factor determining clinical outcome is signaling strength, with strong signaling promoting cell proliferation in cancer and moderate signaling affecting differentiation in neurodevelopmental disorders.
NPJ GENOMIC MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Ruth Nussinov, Yonglan Liu, Wengang Zhang, Hyunbum Jang
Summary: The propensities of protein conformations can predict cell function and suggest drug efficiency.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Ruth Nussinov, Yonglan Liu, Wengang Zhang, Hyunbum Jang
Summary: The sequence-structure-function paradigm in molecular biology has been updated to include the concept of conformational ensembles, recognizing that proteins are dynamic and constantly transitioning between different conformational states. The number and stability of these states are crucial for protein function. Understanding conformational propensities is essential for studying diverse systems and can provide insights into the dynamics of protein ensembles in cells.
RSC CHEMICAL BIOLOGY
(2023)
Review
Cell Biology
Alyssa Kearly, Andrew D. L. Nelson, Aleksandra Skirycz, Monika Chodasiewicz
Summary: Stress Granules (SGs) and Processing-bodies (P-bodies) are important biomolecular condensates that play crucial roles in maintaining mRNA balance and regulating stress responses. They are composed of proteins and RNAs involved in translation, protein folding, and energy metabolism.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
P. Lemonnier, T. Lawson
Summary: Stomatal conductance plays a crucial role in determining CO2 uptake and water loss in plants, affecting overall water status and productivity. However, the signals coordinating mesophyll demands for CO2, the role of chloroplasts in stomatal function, and other GC metabolic processes in stomatal function remain poorly understood.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Matteo Gionfriddo, Timothy Rhodes, Spencer M. Whitney
Summary: Rubisco is a key enzyme that facilitates the entry of CO2 into the biosphere, but its catalytic properties are slow and error-prone. More effective Rubisco variants have been discovered in certain algae, offering the potential to significantly improve crop productivity. However, incompatibilities in protein folding have hindered the transplantation of these variants into plants. Directed evolution is now being explored to enhance Rubisco catalysis.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Vittoria Clapero, Stephanie Arrivault, Mark Stitt
Summary: The Calvin-Benson cycle has undergone massive selection and co-evolution with carbon-concentrating mechanisms due to changing environmental factors. Metabolite profiling reveals species-specific variations in the operation of the cycle, indicating the influence of different modes of photosynthesis. Connectivity analysis identifies constraints and driving factors for cross-species diversity in the cycle.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Sukhbir Kaur, David D. Roberts
Summary: Thrombospondin-1 modulates cell behavior by interacting with components of the extracellular matrix and cell surface receptors. Its release and expression are influenced by injuries and various diseases, while its sustained presence in the extracellular space is regulated by receptor-mediated clearance. Thrombospondin-1 plays important roles in immune responses.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Richard P. Tucker, Josephine C. Adams
Summary: Thrombospondins (TSPs) play diverse roles in animals and have been found to belong to a superfamily that includes different subgroups such as mega-TSPs, sushi-TSPs, and poriferan-TSPs. Invertebrates encode a greater diversity of TSP superfamily members than vertebrates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
James Petrik, Sylvia Lauks, Bianca Garlisi, Jack Lawler
Summary: Many cancers start with a small nest of transformed cells that can remain dormant. Thrombospondin-1 (TSP-1) initially promotes dormancy by suppressing angiogenesis, but over time, factors promoting angiogenesis become dominant and recruit various cells to form a complex tumor microenvironment. TSPs play a role in the proliferation, migration, and invasion of cells in the tumor microenvironment, as well as influencing the immune characteristics and phenotype of tumor-associated macrophages.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hana Fakim, Christine Vande Velde
Summary: There has been increasing attention to the role of phase-separated biomolecular condensates, specifically stress granules, in neurodegenerative diseases like ALS. ALS-associated mutations in genes involved in stress granule assembly have been found, and stress granule proteins have been detected in pathological inclusions in ALS patient neurons. However, protein components of stress granules are also present in other physiological biomolecular condensates, which have not been adequately discussed in relation to ALS. This review explores the functions of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites beyond stress granules, and discusses the impact of ALS-linked mutations on their ability to phase separate and perform their functions in stress-independent biomolecular condensates.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Alexander Lin, Yogambha Ramaswamy, Ashish Misra
Summary: Smooth muscle cells, endothelial cells, and macrophages in blood vessels display remarkable heterogeneity, and their developmental origins may influence their plasticity. Unbiased single cell whole transcriptome analysis techniques are revolutionizing the understanding of cellular diversity and plasticity, providing insights for therapeutic research.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Elton P. Hudson
Summary: The Calvin Benson cycle plays a crucial role in the ecological and biotechnological aspects of bacteria. Recent studies have shed light on the regulation of this cycle in bacteria, with post-transcriptional and post-translational regulation being important in phototrophic bacteria, and transcriptional regulation being prominent in chemolithoautotrophic bacteria. Understanding the regulation of the Calvin Benson cycle has implications for enhancing CO2 fixation and improving the synthesis of desired products. Non-canonical cycles may offer potential benefits for industrial applications.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Xin-Guang Zhu, Haim Treves, Honglong Zhao
Summary: This paper discusses the major regulatory mechanisms over the Calvin Benson Cycle (CBC) that maintain homeostasis of metabolite levels. These mechanisms include redox regulation of enzymes, metabolite regulations (especially allosteric regulations), and balanced activities of enzymes. These regulatory mechanisms are crucial for maintaining high flux and photosynthetic efficiency in CBC.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Hunter C. Herriage, Yi-Ting Huang, Brian R. Calvi
Summary: Apoptosis prevents the inappropriate acquisition of extra copies of the genome, known as polyploidy, but the polyploid state can suppress apoptosis. The mechanisms linking apoptosis and polyploid cell cycles are still largely unknown, and studying the regulation of apoptosis in development and cancer could lead to more effective therapies.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Daniel Campbell, Steven Zuryn
Summary: Mitochondrial dynamics play a crucial role in regulating cellular and organismal homeostasis, impacting various aspects of an organism's healthspan. By studying the nematode Caenorhabditis elegans, a comprehensive understanding of the impact of mitochondrial dynamics on homeostasis over a lifetime can be obtained.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Diba Borgmann, Henning Fenselau
Summary: Maintaining blood glucose at an appropriate physiological level requires coordination of multiple organs and tissues, with the vagus nerve playing a key role in central control. Recent studies have revealed the cellular identity, neuroanatomical organization, and functional contributions of vagal neurons in the regulation of systemic glucose metabolism. These findings provide new insights into the precise roles of vagal neurons in coordinating glucose levels and offer potential avenues for treating glucose metabolism disorders.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Tatiana C. Coverdell, Stephen B. G. Abbott, John N. Campbell
Summary: In this article, we review how genetic technology and single-cell genomics are revealing the organizational principles of the efferent vagus in unprecedented detail.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)