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Article
Open AccessSystematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow
Cell-to-cell communications are critical determinants of pathophysiological phenotypes, but methodologies for their systematic elucidation are lacking. Herein, we propose an approach for the Systematic Elucida...
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Article
Bone vascular niche E-selectin induces mesenchymal–epithelial transition and Wnt activation in cancer cells to promote bone metastasis
How disseminated tumour cells engage specific stromal components in distant organs for survival and outgrowth is a critical but poorly understood step of the metastatic cascade. Previous studies have demonstra...
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Chapter
Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms o...
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Article
Open AccessAge-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes
Glaucoma is a chronic disease that shares many similarities with other neurodegenerative disorders of the central nervous system. This study was designed to evaluate the association between glaucoma and other ...
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Article
HIV–host interactome revealed directly from infected cells
Although genetically compact, HIV-1 commandeers vast arrays of cellular machinery to sustain and protect it during cycles of viral outgrowth. Transposon-mediated saturation linker scanning mutagenesis was used...
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Protocol
Identification of Sirtuin4 (SIRT4) Protein Interactions: Uncovering Candidate Acyl-Modified Mitochondrial Substrates and Enzymatic Regulators
Recent studies have highlighted the three mitochondrial human sirtuins (SIRT3, SIRT4, and SIRT5) as critical regulators of a wide range of cellular metabolic pathways. A key factor to understanding their impac...
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Protocol
Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy
In biological systems, proteins catalyze the fundamental reactions that underlie all cellular functions, including metabolic processes and cell survival and death pathways. These biochemical reactions are rare...
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Article
Systematic discovery of structural elements governing stability of mammalian messenger RNAs
Secondary structures, or pairing of complementary sequences within RNA, can regulate the binding of proteins that affect transcript stability, splicing, localization, and translation; a computational approach ...
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Protocol
Immunoisolation of Protein Complexes from Xenopus
The immunoaffinity isolation of protein complexes is an essential technique for the purification and concentration of protein complexes from cells and tissues. In this chapter we present the methodologies for...
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Protocol
Complementary Proteomic Analysis of Protein Complexes
Proteomic characterization of protein complexes leverages the versatile platform of liquid chromatography-tandem mass spectrometry to elucidate molecular and cellular signaling processes underlying the dynamic...
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Article
Integrating Lys-N proteolysis and N-terminal guanidination for improved fragmentation and relative quantification of singly-charged ions
Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA The study of isolated protein complexes has greatly benefited from recent advances in mass spectrometry instrumentation and qua...
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Protocol
The Identification of Protein S-Nitrosocysteine
Nitric oxide (NO•) bioactivity regulates cellular function in most major mammalian organ systems. NO signaling either through soluble guanylate cyclase activation and cGMP production, or S-nitrosylation, the modi...
