scholarly journals Visualizing Human Protein‐Protein Interactions and Subcellular Localizations on Cell Images Through CellMap

2020 ◽  
Vol 69 (1) ◽  
Author(s):  
Christian Dallago ◽  
Tatyana Goldberg ◽  
Miguel Angel Andrade‐Navarro ◽  
Gregorio Alanis‐Lobato ◽  
Burkhard Rost
Keyword(s):  
Protein Interactions ◽  
Human Protein ◽  
Protein Protein Interactions

scholarly journals Inferring high-confidence human protein-protein interactions

2012 ◽  
Vol 13 (1) ◽  
pp. 79 ◽  
Author(s):  
Xueping Yu ◽  
Anders Wallqvist ◽  
Jaques Reifman
Keyword(s):  
Protein Interactions ◽  
Human Protein ◽  
Protein Protein Interactions ◽  
High Confidence

scholarly journals Predictions of Protein-Protein Interactions in Schistosoma Mansoni

2017 ◽  
Author(s):  
Javona White Bear ◽  
James H. McKerrow
Keyword(s):  
Schistosoma Mansoni ◽  
Language Processing ◽  
Protein Interactions ◽  
Species Interactions ◽  
Human Protein ◽  
Comparative Approach ◽  
Application Framework ◽  
Protein Protein Interactions ◽  
Protease Inhibition ◽  
Human Proteins

AbstractBackgroundSchistosoma mansoni invasion of the human host involves a variety of cross-species protein-protein interactions. The pathogen expresses a diverse arsenal of proteins that facilitate the breach of physical and biochemical barriers present in skin, evasion of the immune system, and digestion of human hemoglobin, allowing schistosomes to reside in the host for years. However, only a small number of specific interactions between S. mansoni and human proteins have been identified. We present and apply a protocol that generates testable predictions of S. mansoni-human protein interactions.MethodsIn this study, we first predict S. mansoni-human protein interactions based on similarity to known protein complexes. Putative interactions were then scored and assessed using several contextual filters, including the use of annotation automatically derived from literature using a simple natural language processing methodology. Our method predicted 7 out of the 10 previously known cross-species interactions.ConclusionsSeveral predictions that warrant experimental follow-up were presented and discussed, including interactions involving potential vaccine candidate antigens, protease inhibition, and immune evasion. The application framework provides an integrated methodology for investigation of host-pathogen interactions and an extensive source of orthogonal data for experimental analysis. We have made the predictions available online for community perusal.Author SummaryThe S. mansoni parasite is the etiological agent of the disease Schistomiasis. However, protein-protein interactions have been experimentally characterized that relate to pathogenesis and establishment of infection. As with many pathogens, the understanding of these interactions is a key component for the development of new vaccines. In this project, we have applied a computational whole-genome comparative approach to aid in the prediction of interactions between S. mansoni and human proteins and to identify important proteins involved in infection. The results of applying this method recapitulate several previously characterized interactions, as well as suggest additional ones as potential therapeutic targets.

scholarly journals Neuropsychiatric Symptoms of COVID-19 Explained by SARS-CoV-2 Proteins’ Mimicry of Human Protein Interactions

2021 ◽  
Vol 15 ◽  
Author(s):  
Hale Yapici-Eser ◽  
Yunus Emre Koroglu ◽  
Ozgur Oztop-Cakmak ◽  
Ozlem Keskin ◽  
Attila Gursoy ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Clinical Symptoms ◽  
Neuropsychiatric Symptoms ◽  
Data Bank ◽  
In Vitro Studies ◽  
Human Protein ◽  
Protein Protein Interactions ◽  
Human Proteins

The first clinical symptoms focused on the presentation of coronavirus disease 2019 (COVID-19) have been respiratory failure, however, accumulating evidence also points to its presentation with neuropsychiatric symptoms, the exact mechanisms of which are not well known. By using a computational methodology, we aimed to explain the molecular paths of COVID-19 associated neuropsychiatric symptoms, based on the mimicry of the human protein interactions with SARS-CoV-2 proteins.Methods: Available 11 of the 29 SARS-CoV-2 proteins’ structures have been extracted from Protein Data Bank. HMI-PRED (Host-Microbe Interaction PREDiction), a recently developed web server for structural PREDiction of protein-protein interactions (PPIs) between host and any microbial species, was used to find the “interface mimicry” through which the microbial proteins hijack host binding surfaces. Classification of the found interactions was conducted using the PANTHER Classification System.Results: Predicted Human-SARS-CoV-2 protein interactions have been extensively compared with the literature. Based on the analysis of the molecular functions, cellular localizations and pathways related to human proteins, SARS-CoV-2 proteins are found to possibly interact with human proteins linked to synaptic vesicle trafficking, endocytosis, axonal transport, neurotransmission, growth factors, mitochondrial and blood-brain barrier elements, in addition to its peripheral interactions with proteins linked to thrombosis, inflammation and metabolic control.Conclusion: SARS-CoV-2-human protein interactions may lead to the development of delirium, psychosis, seizures, encephalitis, stroke, sensory impairments, peripheral nerve diseases, and autoimmune disorders. Our findings are also supported by the previous in vivo and in vitro studies from other viruses. Further in vivo and in vitro studies using the proteins that are pointed here, could pave new targets both for avoiding and reversing neuropsychiatric presentations.

scholarly journals A review ofin silicoapproaches for analysis and prediction of HIV-1-human protein–protein interactions

2014 ◽  
Vol 16 (5) ◽  
pp. 830-851 ◽  
Author(s):  
Sanghamitra Bandyopadhyay ◽  
Sumanta Ray ◽  
Anirban Mukhopadhyay ◽  
Ujjwal Maulik
Keyword(s):  
Protein Interactions ◽  
Human Protein ◽  
Protein Protein Interactions ◽  
Hiv 1

scholarly journals An Mtb-Human Protein-Protein Interaction Map Reveals that Bacterial LpqN Antagonizes CBL, a Host Ubiquitin Ligase that Regulates the Balance Between Anti-Viral and Anti-Bacterial Responses

2017 ◽  
Author(s):  
Bennett H. Penn ◽  
Zoe Netter ◽  
Jeffrey R. Johnson ◽  
John Von Dollen ◽  
Gwendolyn M. Jang ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Protein Interactions ◽  
Human Protein ◽  
Viral Immunity ◽  
Protein Protein Interactions ◽  
Affinity Tag ◽  
Intrinsic Polarization ◽  
Protein Protein Interaction ◽  
Human Ubiquitin ◽  
Interaction Map

SUMMARYAlthough macrophages are armed with potent anti-bacterial functions, Mycobacterium tuberculosis (Mtb) replicates inside these innate immune cells. Determinants of macrophage-intrinsic bacterial control, and the Mtb strategies to overcome them are poorly understood. To further study these processes, we used a systematic affinity tag purification mass spectrometry (AP-MS) approach to identify 187 Mtb-human protein-protein interactions (PPIs) involving 34 secreted Mtb proteins. This interaction map revealed two new factors involved in Mtb pathogenesis - the secreted Mtb protein, LpqN, and its binding partner, the human ubiquitin ligase CBL. We discovered that an lpqN Mtb mutant is attenuated in macrophages, but growth is restored when CBL is removed. Conversely, Cbl-/- macrophages are resistant to viral infection, indicating that CBL regulates cell-intrinsic polarization between anti-bacterial and anti-viral immunity. Collectively, these findings illustrate the utility of this Mtb-human PPI map as a resource for developing a deeper understanding of the intricate interactions between Mtb and its host.

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