Genomes and Genes
protein interaction mapping
Summary: Methods for determining interaction between PROTEINS.
- Spinelli L, Gambette P, Chapple C, Robisson B, Baudot A, Garreta H, et al. Clust&See: a Cytoscape plugin for the identification, visualization and manipulation of network clusters. Biosystems. 2013;113:91-5 pubmed publisher..Importantly, tools for investigating the relationships between clusters and vertices as well as their organization within the whole graph are supplied. ..
- Zhu Y, Zhang X, Dai D, Wu M. Identifying spurious interactions and predicting missing interactions in the protein-protein interaction networks via a generative network model. IEEE/ACM Trans Comput Biol Bioinform. 2013;10:219-25 pubmed publisher..The experimental results show that the RIGNM is more effective and interpretable than the compared methods, which demonstrate that this approach has the potential to better describe the PPI networks and drive new discoveries. ..
- Meyer M, Das J, Wang X, Yu H. INstruct: a database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics. 2013;29:1577-9 pubmed publisher..INstruct is freely available on the web at http://instruct.yulab.org with all major browsers supported. ..
- Diss G, Dubé A, Boutin J, Gagnon Arsenault I, Landry C. A systematic approach for the genetic dissection of protein complexes in living cells. Cell Rep. 2013;3:2155-67 pubmed publisher..Our approach paves the way for studying the response of protein interactomes to mutations and enhances our understanding of genotype-phenotype maps. ..
- Hauri S, Wepf A, van Drogen A, Varjosalo M, Tapon N, Aebersold R, et al. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Mol Syst Biol. 2013;9:713 pubmed publisher..Collectively, our systematic analysis greatly enhances our insights into the biochemical landscape underlying human Hippo signaling and emphasizes multifaceted roles of cell polarity complexes in Hippo-mediated tissue growth control. ..
- Alkan F, Erten C. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. Bioinformatics. 2014;30:531-9 pubmed publisher..Supplementary material including code implementations in LEDA C++, experimental data and the results are available at http://webprs.khas.edu.tr/~cesim/BEAMS.tar.gz. ..
- Bissig C, Lenoir M, Velluz M, Kufareva I, Abagyan R, Overduin M, et al. Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell. 2013;25:364-73 pubmed publisher..We conclude that LBPA recruits ALIX onto late endosomes via the calcium-bound Bro1 domain, triggering a conformational change in ALIX to mediate the delivery of viral nucleocapsids to the cytosol during infection. ..
- Das A, Sharma O, Kumar M, Krishna R, Mathur P. PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics. 2013;11:241-6 pubmed publisher..These data indicate the importance of protein-peptide complexes in the regulation of cellular processes. ..
- Schaal W, Hammerling U, Gustafsson M, Spjuth O. Automated QuantMap for rapid quantitative molecular network topology analysis. Bioinformatics. 2013;29:2369-70 pubmed publisher..http://galaxy.predpharmtox.org firstname.lastname@example.org or email@example.com Supplementary data are available at Bioinformatics online. ..
- Labbé C, Laconde G, Kuenemann M, Villoutreix B, Sperandio O. iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. Drug Discov Today. 2013;18:958-68 pubmed publisher..This could assist scientists to design the next generation of PPI drugs. In this review, we describe iPPI-DB in the context of other low molecular weight molecule databases. ..
- Ruan P, Hayashida M, Maruyama O, Akutsu T. Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PLoS ONE. 2013;8:e65265 pubmed publisher..These results suggest that our proposed kernel considerably outperforms the naive Bayes-based method, which is the best existing method for predicting heterodimeric protein complexes. ..
- Mellacheruvu D, Wright Z, Couzens A, Lambert J, St Denis N, Li T, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. 2013;10:730-6 pubmed publisher..The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely accessible at http://www.crapome.org/. ..
- Jiang M, Chen Y, Zhang Y, Chen L, Zhang N, Huang T, et al. Identification of hepatocellular carcinoma related genes with k-th shortest paths in a protein-protein interaction network. Mol Biosyst. 2013;9:2720-8 pubmed publisher..05, and most of them have been reported to be involved in HCC tumorigenesis and development. The results also provide a new reference for research into HCC oncogenesis and for development of new strategies for HCC clinical therapies. ..
- Ivarsson Y, Arnold R, McLaughlin M, Nim S, Joshi R, Ray D, et al. Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. Proc Natl Acad Sci U S A. 2014;111:2542-7 pubmed publisher..The method can be extended to interrogate all potential eukaryotic, bacterial, and viral SLiMs and we suggest it will be a highly valuable approach for studying cellular and pathogen-host protein-protein interactions. ..
- Spratt D, Walden H, Shaw G. RBR E3 ubiquitin ligases: new structures, new insights, new questions. Biochem J. 2014;458:421-37 pubmed publisher..The present review discusses how three-dimensional structures of RBR (RING1-BRcat-Rcat) E3 ligases have provided new insights into our understanding of the biochemical mechanisms of these important enzymes in ubiquitin biology. ..
- Tripathi L, Kambara H, Chen Y, Nishimura Y, Moriishi K, Okamoto T, et al. Understanding the biological context of NS5A-host interactions in HCV infection: a network-based approach. J Proteome Res. 2013;12:2537-51 pubmed publisher..Our analysis builds upon the present understanding of the role of NS5A protein in HCV pathogenesis and provides potential targets for more effective anti-HCV therapeutic intervention. ..
- Jeong H, Yoon B. SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. BMC Syst Biol. 2017;11:20 pubmed publisher..The source code and datasets can be downloaded from http://www.ece.tamu.edu/~bjyoon/SEQUOIA . ..
- Hinow P, Rietman E, Omar S, TuszyÅ„ski J. Algebraic and topological indices of molecular pathway networks in human cancers. Math Biosci Eng. 2015;12:1289-302 pubmed..Beyond that, we provide a unifying framework to study protein-protein interaction networks of families of related diseases (e.g. neurodegenerative diseases, viral diseases, substance abuse disorders). ..
- Kang N, Koo J, Wang S, Hur S, Bahk Y. A systematic study of nuclear interactome of C-terminal domain small phosphatase-like 2 using inducible expression system and shotgun proteomics. BMB Rep. 2016;49:319-24 pubmed..This approach led to the identification of several interacting partners of CTDSPL2. This will provide a better understanding on CTDSPL2. [BMB Reports 2016; 49(6): 319-324]. ..
- Waraky A, Lin Y, Warsito D, Haglund F, Aleem E, Larsson O. Nuclear insulin-like growth factor 1 receptor phosphorylates proliferating cell nuclear antigen and rescues stalled replication forks after DNA damage. J Biol Chem. 2017;292:18227-18239 pubmed publisher..Unlike in cells expressing IGF-1R, externally induced DNA damage in IGF-1R-negative cells caused G1 cell cycle arrest and S phase fork stalling. Taken together, our results suggest a role of IGF-1R in DDT. ..
- Yan X, Kang H, Feng J, Yang Y, Tang K, Zhu R, et al. Identification of Toxic Pyrrolizidine Alkaloids and Their Common Hepatotoxicity Mechanism. Int J Mol Sci. 2016;17:318 pubmed publisher..In addition, all the strategies developed here could be extended to studies on toxicity mechanism of other toxins. ..
- Lu B, Chen L, Zhang Y, Shi Y, Zhou N. Quantitative analysis of G-protein-coupled receptor internalization using DnaE intein-based assay. Methods Cell Biol. 2016;132:293-318 pubmed publisher..These advantages may allow this assay to be used universally as a functional cell-based system for GPCR characterization and in the screening process of drug discovery. ..
- Zhao Z, Azadzoi K, Choi H, Jing R, Lu X, Li C, et al. LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer. Int J Mol Sci. 2017;18: pubmed publisher..Thus, LC-MS/MS analysis revealed multiple oxidative modifications of MNSOD at different amino acid residues that might mediate the regulation of the superoxide radicals, mitochondrial ROS scavenging and MNSOD activity in kidney cancer. ..
- Mo G, Ross B, Hertel F, Manna P, Yang X, Greenwald E, et al. Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nat Methods. 2017;14:427-434 pubmed publisher..Together, these findings suggest that biochemical activities of the cell are spatially organized into an activity architecture whose structural and functional characteristics can be revealed by these new biosensors. ..
- Das S, Gilchrist J, Bosmans F, Van Petegem F. Binary architecture of the Nav1.2-Î²2 signaling complex. elife. 2016;5: pubmed publisher..2 (912/918)Cys residues. The concepts emerging from this work will help to form a model reflecting the Î²-subunit location in a Nav channel complex. ..
- Rai S, Bhatnagar S. Hyperlipidemia, Disease Associations, and Top 10 Potential Drug Targets: A Network View. OMICS. 2016;20:152-68 pubmed publisher..These findings provide an integrative view of lipid-protein interactions leading to acquired hyperlipidemia and the associated diseases, and might prove useful in future translational pharmaceutical research. ..
- Gu J, Li T, Zhao L, Liang X, Fu X, Wang J, et al. Identification of Significant Pathways Induced by PAX5 Haploinsufficiency Based on Protein-Protein Interaction Networks and Cluster Analysis in Raji Cell Line. Biomed Res Int. 2017;2017:5326370 pubmed publisher..These changes hinted that the mechanism of PAX5 haploinsufficiency promoting tumorigenesis may be related to genomic instability, immune tolerance, and tumor pathways. ..
- Du X, Sun S, Hu C, Yao Y, Yan Y, Zhang Y. DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks. J Chem Inf Model. 2017;57:1499-1510 pubmed publisher..The source code of our approach can be available via http://ailab.ahu.edu.cn:8087/DeepPPI/index.html . ..
- Verma M, Charles R, Chakrapani B, Coumar M, Govindaraju G, Rajavelu A, et al. PRMT7 Interacts with ASS1 and Citrullinemia Mutations Disrupt the Interaction. J Mol Biol. 2017;429:2278-2289 pubmed publisher..We showed that ASS1 mutations linked to type I citrullinemia disrupt the ASS1-PRMT7 interaction, which might explain the molecular pathogenesis of the disease. ..
- Woolley M, Simms J, Uddin S, Poyner D, Conner A. Relative Antagonism of Mutants of the CGRP Receptor Extracellular Loop 2 Domain (ECL2) Using a Truncated Competitive Antagonist (CGRP8-37): Evidence for the Dual Involvement of ECL2 in the Two-Domain Binding Model. Biochemistry. 2017;56:3877-3880 pubmed publisher..This has implications for understanding family B GPCR activation and for drug design at the CGRP receptor. ..
- Kim S, Kim H, Chung S, Lee J. DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1. Biochem Biophys Res Commun. 2017;491:285-290 pubmed publisher..This study will serve as a platform to further understand more detailed action mechanism of DHU1 in UV-B response and DHU1-mediated core UV-B signaling in Arabidopsis. ..
- Lens Z, Cantrelle F, Peruzzini R, Hanoulle X, DeWitte F, Ferreira E, et al. Solution Structure of the N-Terminal Domain of Mediator Subunit MED26 and Molecular Characterization of Its Interaction with EAF1 and TAF7. J Mol Biol. 2017;429:3043-3055 pubmed publisher..This study provides molecular detail that will help to decipher the mechanistic basis for the initiation to elongation switch-function mediated by MED26-NTD. ..
- Maruyama O, Kuwahara Y. RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks. BMC Bioinformatics. 2017;18:491 pubmed publisher..This implies that the design of scoring functions including regularization terms is an effective approach for protein complex prediction. ..
- Li G, Liu L, Li P, Chen L, Song H, Zhang Y. Gene expression profiling of selenophosphate synthetase 2 knockdown in Drosophila melanogaster. Metallomics. 2016;8:354-65 pubmed publisher..Overall, our data provide new insights into the relationship between Se utilization and several fundamental cellular processes as well as diseases. ..
- Jafferali M, Figueroa R, Hallberg E. MCLIP Detection of Novel Protein-Protein Interactions at the Nuclear Envelope. Methods Enzymol. 2016;569:503-15 pubmed publisher..This chapter provides detailed protocols for MCLIP (membrane cross-linking immunoprecipitation) identification of novel protein-protein interactions in mammalian cells. ..
- Chimusa E, Mbiyavanga M, Mazandu G, Mulder N. ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations. Bioinformatics. 2016;32:549-56 pubmed publisher..The ancGWAS package and documents are available at http://www.cbio.uct.ac.za/~emile/software.html. ..
- Itoh Y, Fuchino H, Sanosaka M, Kako K, Hada K, Fukamizu A, et al. Pterosin B has multiple targets in gluconeogenic programs, including coenzyme Q in RORÎ±-SRC2 signaling. Biochem Biophys Res Commun. 2016;473:415-20 pubmed publisher..This was a site disrupted by pterosin B in gluconeogenic programs. ..
- Fish A, Riley S, Singh B, Riesbeck K, Martinez J. The Rickettsia conorii Adr1 Interacts with the C-Terminus of Human Vitronectin in a Salt-Sensitive Manner. Front Cell Infect Microbiol. 2017;7:61 pubmed publisher..In summary, elucidation of the mechanisms governing Adr1-Vn binding will be useful to specifically target this protein-protein interaction for therapeutic intervention. ..
- Xu H, Ma J, Wu J, Chen L, Sun F, Qu C, et al. Gene expression profiling analysis of lung adenocarcinoma. Braz J Med Biol Res. 2016;49: pubmed publisher..Our findings suggest that DEGs encoding subunits of NADH, PRIM1, MCM3, MAPK1, STAT3, RAF1, and JAK1 might be associated with the development of lung adenocarcinoma. ..
- Espinoza Fonseca L. Pathogenic mutation R959W alters recognition dynamics of dysferlin inner DysF domain. Mol Biosyst. 2016;12:973-81 pubmed publisher..In conclusion, these findings have important implications for our understanding of the structural aspects of muscular dystrophies in atomic-level resolution. ..
- He W, Gu J, Li C, Kuang Y, Kong B, Cheng L, et al. The PPI network and clusters analysis in glioblastoma. Eur Rev Med Pharmacol Sci. 2015;19:4784-90 pubmed..LYN, CD22 and LCP2 form a densely protein complex in the PPI network. Our results suggest that LYN, CD22 and LCP2 play important roles in the occurrence and progression of glioblastoma. ..
- Benitez P, Mascharak S, Proctor A, Heilshorn S. Use of protein-engineered fabrics to identify design rules for integrin ligand clustering in biomaterials. Integr Biol (Camb). 2016;8:50-61 pubmed publisher..Together, these two insights into the cellular responses to ligand clustering at the cell-matrix interface may serve as design principles when developing future generations of implantable biomaterials. ..
- Chen Y, Chan K. Differential effects of metal ions on TCDD-induced cytotoxicity and cytochrome P4501A1 gene expression in a zebrafish liver (ZFL) cell-line. Metallomics. 2016;8:236-51 pubmed publisher..A proteomic study showed that the toxic effects of As(3+) might be due to changes in cellular metabolic processes, the cellular stimulation response and the cellular redox state in ZFL cells. ..
- Andriamoratsiresy D, Piskunov A, Lutzing R, Rochette Egly C. PFN2a, a new partner of RAR? in the cytoplasm. Biochem Biophys Res Commun. 2018;495:846-853 pubmed publisher..Consequently, the actin filament network is altered and MEFs adhesion is decreased. This novel role opens novel avenues for the understanding of pathologies characterized by increased levels of cytoplasmic RAR?. ..
- Wu C, Chen B. Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. Int J Mol Sci. 2016;17:305 pubmed publisher..The results provide a more comprehensive understanding of stroke progression mechanisms from an immune perspective and shed light on acute stroke treatments. ..
- Ou Yang L, Wu M, Zhang X, Dai D, Li X, Yan H. A two-layer integration framework for protein complex detection. BMC Bioinformatics. 2016;17:100 pubmed publisher..Extensive experimental results demonstrate that TINCD performs much better than 21 state-of-the-art complex detection techniques, including ensemble clustering and data integration techniques. ..