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Protein-protein interactions (PPIs) refer to the specific or functional associations formed between two or more protein molecules through non-covalent bonds, such as hydrogen bonds, hydrophobic interactions, ionic bonds, and van der Waals forces. These interactions underpin virtually all cellular processes, including signal transduction, gene expression regulation, metabolic pathway organization, cell cycle control, immune responses, and structural maintenance. The PPI network serves as a molecular map of cellular functional regulation, and its dysregulation is closely linked to cancer, neurodegenerative diseases, infectious diseases, and more, making PPIs a major focus in modern drug target discovery and precision medicine research. Technologies for studying PPIs have evolved from classical in vitro biochemical methods to advanced live-cell imaging techniques. Commonly used approaches include: affinity chromatography-based Pull-down assays (e.g., GST pull-down, His-tag pull-down, and biotin-streptavidin pull-down) for validating direct interactions in vitro; antibody-based Co-IP (including endogenous and tagged protein Co-IP) for detecting native protein complexes within cells; and various genetic and optical techniques such as Yeast Two-Hybrid (Y2H) for large-scale screening of interaction partners, bimolecular fluorescence complementation (BiFC), luciferase complementation (LUC), and fluorescence resonance energy transfer (FRET), which enable real-time, in situ visualization of PPI occurrence, localization, and dynamics in living cells. These methods each possess distinct strengths and complement one another, collectively forming a multi-dimensional technical framework for modern PPI research.

Protein-DNA interactions refer to the molecular associations formed between proteins (particularly transcription factors, chromatin remodeling complexes, DNA repair enzymes) and DNA molecules through specific sequence recognition or domain binding. These interactions constitute the core mechanism of gene expression regulation, determining the spatiotemporal specificity of transcription, DNA replication and repair, chromatin architecture maintenance, and the establishment and interpretation of epigenetic modifications. Aberrant protein-DNA interactions can lead to developmental defects, metabolic disorders, and cancer, making their in-depth characterization essential for understanding both normal biological processes and disease mechanisms. Key technologies for studying protein-DNA interactions fall into two categories: in vitro validation (DNA pull-down) and in vivo detection (Chromatin Immunoprecipitation, ChIP). These two methods provide complementary and powerful tools for dissecting protein-DNA interaction networks from both direct in vitro validation and native in situ detection perspectives.

Protein-RNA interactions are central mechanisms of gene expression regulation, governing RNA processing, transport, translation, and degradation. RNA-binding proteins control mRNA fate by recognizing specific sequences or structures, while non-coding RNAs dynamically engage with proteins in chromatin remodeling and signaling; dysregulation of these interactions is implicated in cancer, neurodegeneration, and viral infection, representing a critical frontier in functional genomics. The principal techniques for studying PRIs are RNA pull-down and RIP: RNA pull-down utilizes in vitro synthesized labeled RNA (e.g., biotinylated) as bait to capture interacting proteins from cell lysates for identification by mass spectrometry or Western blot, making it ideal for screening proteins bound to a specific RNA; RIP employs specific antibodies to immunoprecipitate a target protein and detects associated RNAs (by RT-qPCR or RIP-seq), reflecting endogenous physiological interactions within cells. These two approaches complement each other from “RNA-to-protein” and “protein-to-RNA” perspectives, collectively mapping the functional landscape of protein-RNA interaction networks.

Protein-small molecule interactions constitute the molecular foundation of cellular life and drug discovery, participating extensively in enzymatic catalysis, signal transduction, metabolic regulation, and gene expression. Small molecules, including endogenous metabolites, drug candidates, and natural products, modulate protein catalytic activity, conformational stability, and interaction networks by specifically binding to active sites or allosteric pockets, thereby influencing cellular phenotypes and physiological states. Systematic elucidation of these interactions is essential not only for uncovering the molecular mechanisms underlying metabolic diseases and signaling pathway dysregulation, but also for target identification, lead optimization, and mechanistic studies in drug development. A diverse array of methodologies is currently available, encompassing affinity-based pull-down approaches (such as small molecule pull-down and metabolite pull-down), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). Among these, pull-down methods have become particularly important tools for screening and identifying small-molecule target proteins from complex proteomes, owing to their experimental simplicity and strong compatibility with high-throughput workflows.

Spatial/proximity interaction studies aim to capture the physical proximity between spatially adjacent molecules (protein-protein, protein-nucleic acid, protein-small molecule, etc.) within living cells or tissues, thereby revealing their functional associations and regulatory networks in specific subcellular compartments or microenvironments. This approach is critical for understanding the spatial specificity of signal transduction, dynamic assembly of protein complexes, and spatiotemporal remodeling of disease-related interaction networks. Key technologies include DNA probe-based proximity ligation methods (Proximity Labeling and PLA/Proximity Ligation Assay), enabling in situ visualization and quantification at the single-molecule level; and cross-linking mass spectrometry (CL-MS), which covalently fixes spatially proximal amino acid residue pairs and, combined with mass spectrometry, precisely resolves protein three-dimensional structures and interaction interfaces.

Protein-macromolecule interactions serve as the fundamental basis for cellular signal transduction, metabolic regulation, immune responses, and gene expression, with their dysregulation frequently associated with cancer, autoimmune diseases, and neurodegenerative disorders. Consequently, investigating these interactions is of great significance for understanding disease mechanisms and identifying therapeutic targets. Commonly employed techniques include affinity purification-based pull-down assays (such as peptide pull-down, lipid pull-down, and glycan pull-down) and Co-IP (such as protein-peptide interaction Co-IP, protein-lipid interaction Co-IP, protein-glycan interaction Co-IP), which enable the elucidation of direct or indirect interactions between proteins and peptides, lipids, glycans, or other proteins at both in vitro and in vivo levels.