4.6 Review

Pathogen mimicry of host protein-protein interfaces modulates immunity

期刊

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
卷 58, 期 -, 页码 136-145

出版社

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.semcdb.2016.06.004

关键词

Molecular mimicry; Interface mimicry; Structure; Host-pathogen interactions; Protein-protein interactions; Multi-organism

资金

  1. Federal funds from the National Cancer Institute, National Institutes of Health [HHSN261200800001E]
  2. Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research

向作者/读者索取更多资源

Signaling pathways shape and transmit the cell's reaction to its changing environment; however, pathogens can circumvent this response by manipulating host signaling. To subvert host defense, they beat it at its own game: they hijack host pathways by mimicking the binding surfaces of host-encoded proteins. For this, it is not necessary to achieve global protein homology; imitating merely the interaction surface is sufficient. Different protein folds often interact via similar protein-protein interface architectures. This similarity in binding surfaces permits the pathogenic protein to compete with a host target protein. Thus, rather than binding a host-encoded partner, the host protein hub binds the pathogenic surrogate. The outcome can be dire: rewiring or repurposing the host pathways, shifting the cell signaling landscape and consequently the immune response. They can also cause persistent infections as well as cancer by modulating key signaling pathways, such as those involving Ras. Mapping the rewired host-pathogen 'superorganism' interaction network - along with its structural details - is critical for in-depth understanding of pathogenic mechanisms and developing efficient therapeutics. Here, we overview the role of molecular mimicry in pathogen host evasion as well as types of molecular mimicry mechanisms that emerged during evolution. (C) 2016 Elsevier Ltd. All rights reserved.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Oncology

Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family

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.

FAMILIAL CANCER (2022)

Article Biochemical Research Methods

SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions

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.

BIOINFORMATICS (2022)

Article Biochemistry & Molecular Biology

Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

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

Mechanism of activation and the rewired network: New drug design concepts

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

Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody

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.

BIOMOLECULES (2022)

Article Biochemical Research Methods

HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry

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.

BIOINFORMATICS (2022)

Review Oncology

A New View of Activating Mutations in Cancer

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.

CANCER RESEARCH (2022)

Article Biochemistry & Molecular Biology

Higher-order interactions of Bcr-Abl can broaden chronic myeloid leukemia (CML) drug repertoire

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.

PROTEIN SCIENCE (2023)

Letter Oncology

Activation mechanisms of clinically distinct B-Raf V600E and V600K mutants

Mingzhen Zhang, Ryan Maloney, Yonglan Liu, Hyunbum Jang, Ruth Nussinov

CANCER COMMUNICATIONS (2023)

Review Pharmacology & Pharmacy

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

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

Strategy toward Kinase-Selective Drug Discovery

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

Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK

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

Neurodevelopmental disorders and cancer networks share pathways, but differ in mechanisms, signaling strength, and outcome

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

Cell phenotypes can be predicted from propensities of protein conformations

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

Protein conformational ensembles in function: roles and mechanisms

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

Composition and function of stress granules and P-bodies in plants

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

Calvin cycle and guard cell metabolism impact stomatal function

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

Perspectives on improving crop Rubisco by directed evolution

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

Natural variation in metabolism of the Calvin-Benson cycle

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

Emerging functions of thrombospondin-1 in immunity

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

Molecular evolution of the Thrombospondin superfamily

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

Thrombospondins in the tumor microenvironment

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

The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis

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

Developmental heterogeneity of vascular cells: Insights into cellular plasticity in atherosclerosis?

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

The Calvin Benson cycle in bacteria: New insights from systems 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

Mechanisms controlling metabolite concentrations of the Calvin

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

The antagonistic relationship between apoptosis and polyploidy in development and cancer

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

The mechanisms and roles of mitochondrial dynamics in C. elegans

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

Vagal pathways for systemic regulation of glucose metabolism

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

Molecular cell types as functional units of the efferent vagus nerve

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)