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At least 19 recordsLinked to original sources
PubMed1979

Drug-protein interaction: plasma protein binding of furocoumarins.

The binding of six furocoumarins (angelicin, psoralen, 8-methoxypsoralen, 5-methoxypsoralen, 8-methylpsoralen, 4,5'8-trimethylpsoralen) to human serum and human serum albumin was studied by equilibrium dialysis using tritium labelled compounds. The results indicated that in serum all furocoumarins are bound mostly by albumin, the extent of binding being related to the structure of the furocoumarins; at any rate, high values of the bound drug, ranging from 84 to 97% were observed. The percentage of binding is strictly related to the water solubility of the compounds. A limited number of binding sites, n = 1-2.4, were detected in the albumin molecule, indicating a high specificity in the binding process. The association constants of the furocoumarins to albumin. Ka, ranged from 1.2 X 10(4) M-1 (8-methoxypsoralen) to 1.9 X 10(5) M-1 (4,5'8-trimethylpsoralen).

Biological Availability↗
PubMed1976

Protein-protein interaction in transport: periplasmic histidine-binding protein J interacts with P protein.

A component of the high-affinity histidine transport system in Salmonella typhimurium, the periplasmic histidine-binding protein J, interacts with another transport component, the P protein. A mutant J protein, with a defective interaction site but intact histidine-binding site, can function in histidine transport if an appropriate compensating mutation is introduced in the P protein. The interaction between the J and P proteins is an obligatory step in transport. The significance of this interaction and of the involvement of the P protein in multiple transport functions is discussed.

Bacterial Proteins↗
PubMed1977

Cytochrome b5 and cytochrome b5 reductase-phospholipid vesicles. Intervesicle protein transfer and oreintation factors in protein-protein interactions.

NADH-cytochrome b5 reductase readily binds to preformed phospholipid vesicles either below or above the phase transition temperature of the lipid and in the absence of detergents. The isolated vesicles are free of unbound reductase, and the lipid is present as small, closed bilayers (250 to 400 A in diameter) as indicated by gel filtration, density gradient centrifugation, and internal volume measurements with [3H]glucose. The order of substrate specificity of the bound reductase is: ferricyanide = cytochrome b5 bound to reductase vesicles (100%) greater than cytochrome b5 heme peptide (13%) greater than unbound cytochrome b5 (4.5%) greater than cytochrome b5 vesicles (0.1%). This indicates that a specific orientation of cytochrome b5 and reductase in the bilayer is required for optimal interaction. Protein transfer occurs between reductase vesicles and cytochrome b5 vesicles. The transfer is time-dependent (40 to 70% complete in 2 h), does not involve vesicle fusion, is most rapid at the phase transition temperature of the phospholipid, and appears to require a fluid bilayer.

Animals↗
PubMed1979

Polynucleotide-protein interactions in the translation system. Identification of proteins interacting with tRNA in the A- and P-sites of E. coli ribosomes.

Ultraviolet irradiation (lambda = 254 nm) of ternary complexes of E. coli 70 S ribosomes with poly(U) and either Phe-tRNAPhe (in the A-site) or NAcPhe-tRNAPhe (in the P-site) effectively induces covalent linking of tRNA with a limited number of ribosomal proteins. The data obtained indicate that in both sites tRNA is in contact with proteins of both 30 S and 50 S subunits (S5, S7, S9, S10, L2, L6 and L16 proteins in the A-site and S7, S9, S11, L2, L4, L7/L12 and L27 proteins in the P-site). Similar sets of proteins are in contact with total aminoacyl-tRNA and N-acetylaminoacyl-tRNA. However, here no contacts of tRNA in the P-site with the S7 and L25/S17 proteins were revealed, whereas in the A-site total aminoacyl-tRNA contacts L7/L12. Proteins S9, L2 and, probably, S7 and L7/L12 are common to both sites.

Binding Sites↗
PubMed1978

The histone core complex: an octamer assembled by two sets of protein-protein interactions.

A protein complex, extracted from calf thymus chromatin with 2 M NaCl, pH 7.5, containing approximately equal molar ratios of histones H2A, H2B, H3, and H4, has been characterized in this study. Gel filtration, sedimentation velocity, and sedimentation equilibrium experiments demonstrate that this complex, known as the core complex, has a molecular weight near that expected for a histone octamer (108 000 for a unit containing two each of the four inner histones) and far exceeding that of a histone tetramer (54 400). This finding suggests that the histone octamer, postulated to be the fundamental histone unit in chromatin, is stable in 2 M NaCl, pH 7.5, in the absence of DNA or chemical cross-linking reagents. In the second part of this study, we demonstrate that the bonds maintaining the octameric complex in 2 M NaCl are weak and distinctly different from the forces stabilizing the H2A-H2B dimer or H3-H4 tetramer. The octamer is dissociated into two H2A-H2B dimers and one H3-H4 tetramer by (i) increasing temperature; (ii) decreasing NaCl concentration; (iii) adding low concentrations of urea or guanidine hydrochloride; and (iv) lowering the pH below 7 or raising it above 10. These findings indicate that the octamer is assembled by two sets-of protein-protein interactions. The first set involves mostly hydrophobic interactions and yields the H2A-H2B dimer and the H3-H4 tetramer subunits. The second set involves the weak association of one H3-H4 tetramer with two H2A-H2B dimers to form an octamer. We suggest that these weak interactions might be derived predominantly from histidine-lysine or histidine-tyrosine hydrogen bonds between the dimer and tetramer subunits.

Animals↗
PubMed2025

STUPPIT is a proximity labeling tool for labeling intermediary proteins that bridge two non-interacting proteins.

Decoding the complexities of signaling pathways is fundamental for deciphering the mechanisms underlying tissue development, homeostasis, and disease pathogenesis. Proximity labeling tools have been instrumental in identifying upstream or downstream effectors of specific proteins within signaling pathways. However, currently, there are no tools available to directly label and capture intermediary proteins that bridge two non-interacting proteins. Here, we developed Split-TurboID and PUP-IT based Protein Identification Tool (STUPPIT), a novel method combining split-TurboID and PUP-IT to biotinylate intermediary proteins of two non-interacting proteins through a two-step enzymatic reaction. STUPPIT was validated using three well-characterized protein triads, including YAP1/AMOT/β-actin, YAP1/LATS1/MOB1A, and β-catenin/α-catenin/β-actin using HEK293T human cell lines. Combining STUPPIT and proteomics, we identified novel intermediary proteins including ERC1 and USP7, which interacted both with β-catenin and SMAD4, key components of the Wnt and BMP signaling pathways. In conclusion, STUPPIT represents a powerful tool for labeling and capturing intermediary proteins between non-interacting partners, offering new insights into protein-protein interactions and advancing signal transduction research.

Humans↗
PubMed1991

Studying DNA-protein interactions using NMR.

NMR spectroscopy is emerging as a powerful tool in molecular biology and biotechnology; one aspect of which is the use of one- and two-dimensional NMR methodologies to investigate the interactions of proteins with DNA. The dynamic and structural information which NMR can provide, on the changes in conformation and molecular flexibility, complements X-ray crystallography data and enables mechanistic models of DNA-protein interactions to be formulated.

Base Sequence↗
PubMed1975

Microbiological determination of drug partitioning. IV. Drug-protein interactions.

The protein binding characteristics of chloramphenicol, furazolium chloride, benzalkonium chloride, and phenylmercuric nitrate were described from their partitioning behavior in gelatin-acacia complex coacervate systems. Although the partitioning was determined by two different methods (microbiological and chemical), the microbiological method was more reliable for this type of investigation. Drug-protein parameters were calculated for the four antimicrobials. The advantages of the coacervate systems over other models for protein binding studies of drugs are discussed.

Bacteria↗
PubMed2026

The Lipid Interactome: an interactive and open access platform for exploring cellular lipid-protein interactions.

SUMMARY: Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized lipid probes-equipped with photoactivatable crosslinkers, affinity handles, and photocleavable protecting groups-have enabled proteomics-based identification of lipid interacting proteins with unprecedented specificity and resolution. Despite the growing number of published lipid interactomes, there remains no centralized effort to harmonize, compare, or integrate these datasets. The Lipid Interactome addresses this gap by providing a structured, interactive web portal that adheres to FAIR data principles-ensuring that lipid interactome studies are Findable, Accessible, Interoperable, and Reusable. Through standardized data formatting, interactive visualizations, and direct cross-study comparisons, this resource enables researchers to systematically explore the protein-binding partners of diverse bioactive lipids. By consolidating and curating lipid interactome proteomics data from multiple studies, the Lipid Interactome database serves as a critical tool for deciphering the biological functions of lipids in cellularsystems. AVAILABILITY AND IMPLEMENTATION: This site can be viewed at LipidInteractome.org. All data are available for download. No user information is collected or necessary for data navigation, interaction, or download.

Proteins↗
PubMed1978

Effect of protein-protein interactions on binding of ligands by proteins.

In general, saturation curves for ligand binding by proteins are described by the Adair-equation. The approach to ligand binding with methods of statistical mechanics leads not only to expressions for the Adair-constants, but gives also the possibility of describing the effect of protein-protein interactions on the binding of ligands by proteins. Under the assumption of the superposition-approximation for the potential of mean force between proteins in a solution, which contains also ligand molecules, the variations of the second and third virial coefficient with ligand activity are calculated for several simple model-pontentials. Finally the pair potential of hemoglobin molecules known from X-ray measurements will be approximated by such a simple square-well potential. With that the effect of hemoglobin density on oxygenation will be estimated. One finds for our model system that at relatively high protein density a further increase in density should be accompanied by a decrease in affinity (hindrance of saturation) and an increasing steepness of the slope of the saturation curve.

Calorimetry↗
PubMed2025

Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.

Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.

Humans↗
PubMed2026

Library-based, multiplexed strategy for mapping protein interaction networks via crosslinking.

BACKGROUND: Protein-protein interactions are fundamental to cellular function, yet resolving their interaction interfaces and dynamic behaviors in native biological contexts remains challenging, particularly for weak or transient interactions. Crosslinking strategies based on noncanonical amino acids offer an effective means to capture such interactions; however, traditional single-site incorporation provides limited coverage and may overlook critical interaction hotspots. RESULTS: By employing a mutagenesis library, multiple interaction partners and cross-linking sites of a target protein can be simultaneously screened in a single experiment, without prior knowledge of its precise structural or functional features, enabling effective and unbiased analysis of its interaction network. In this study, we constructed an amber codon-scanning mutagenesis library of PSMD10, facilitating independent incorporation of the photocrosslinking ncAA p-azido-phenylalanine at multiple distinct residues. This approach allowed us to systematically interrogate and precisely map potential interaction regions across the protein surface. Coupled with crosslinking mass spectrometry, we identified multiple residues involved in intermolecular interactions, as well as previously unreported interaction partners, including T2FA, TBA1C, and ATRIP. CONCLUSIONS: These findings expand our understanding of PSMD10-associated proteasome interactome, demonstrate a multiplexed strategy for in situ mapping of protein interaction interfaces with broad coverage, and offer a valuable platform for developing therapeutics that target protein-protein interactions.

Protein Interaction Mapping↗
PubMed2026

SARS-CoV-2 Orf3a protein interaction mapping using unnatural amino acid incorporation.

Mapping transient protein-protein interactions remain a major challenge in studying viral host-pathogen interfaces. While some virus-host interactions are stable and readily captured, the majority are highly dynamic, reflecting the need for viral proteins to engage distinct host factors at different stages of the life cycle. Here, we employ a protein engineering strategy based on the site-specific incorporation of the unnatural acid p-azido-L-phenylalanine (AzF) to enable photo-crosslinking proteomic analysis of the SARS-CoV-2 accessory protein Orf3a in live cells. Genetic installation of AzF at residue K198 of Orf3a permitted UV-induced covalent capture of proximal host interacting proteins, overcoming challenges associated with membrane localization and limited protein abundance. A total of 248 high-confidence Orf3a-interacting proteins were reproducibly identified and subjected to gene ontology analysis, revealing enrichment in innate immune signaling, antiviral defense, RNA processing, and viral replication-associated pathways. Orf3a is an accessory protein that functions as a viroporin and traffics across multiple cellular compartments, and was found to interact with host RNA helicases, RNA-binding proteins, immune regulators, and metabolic enzymes implicated in SARS-CoV-2 infection. Together, these results demonstrate that genetically encoded, site-specific photo-crosslinking enables selective capture of transient interactions that are often missed by nonspecific 254 nm UV crosslinking approaches and highlights Orf3a as a multifunctional protein that engages diverse host pathways. More broadly, this study establishes a generalizable framework for leveraging unnatural amino acid-based protein engineering approaches to interrogate dynamic host-pathogen interactions.

Humans↗
PubMed2025

The signed two-space proximity model for learning representations in protein-protein interaction networks.

MOTIVATION: Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally expensive. Thus, attention has been recently drawn to machine learning approaches. Furthermore, insufficient effort has been made toward analyzing signed PPI networks, which capture both activating (positive) and inhibitory (negative) interactions. To accurately represent biological relationships, we present the Signed Two-Space Proximity Model (S2-SPM) for signed PPI networks, which explicitly incorporates both types of interactions, reflecting the complex regulatory mechanisms within biological systems. This is achieved by leveraging two independent latent spaces to differentiate between positive and negative interactions while representing protein similarity through proximity in these spaces. Our approach also enables the identification of archetypes representing extreme protein profiles. RESULTS: S2-SPM's superior performance in predicting the presence and sign of interactions in SPPI networks is demonstrated in link prediction tasks against relevant baseline methods. Additionally, the biological prevalence of the identified archetypes is confirmed by an enrichment analysis of Gene Ontology (GO) terms, which reveals that distinct biological tasks are associated with archetypal groups formed by both interactions. This study is also validated regarding statistical significance and sensitivity analysis, providing insights into the functional roles of different interaction types. Finally, the robustness and consistency of the extracted archetype structures are confirmed using the Bayesian Normalized Mutual Information (BNMI) metric, proving the model's reliability in capturing meaningful SPPI patterns. AVAILABILITY: S2-SPM is implemented and freely available under the MIT license at https://github.com/Nicknakis/S2SPM.

Protein Interaction Mapping↗
PubMed2004

Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks.

Calcium signals mediate a multitude of plant responses to external stimuli and regulate a wide range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, represent important relays in plant calcium signaling. These proteins form a complex network with their target kinases being the CBL-interacting protein kinases (CIPKs). Here, we present a comparative genomics analysis of the full complement of CBLs and CIPKs in Arabidopsis and rice (Oryza sativa). We confirm the expression and transcript composition of the 10 CBLs and 25 CIPKs encoded in the Arabidopsis genome. Our identification of 10 CBLs and 30 CIPKs from rice indicates a similar complexity of this signaling network in both species. An analysis of the genomic evolution suggests that the extant number of gene family members largely results from segmental duplications. A phylogenetic comparison of protein sequences and intron positions indicates an early diversification of separate branches within both gene families. These branches may represent proteins with different functions. Protein interaction analyses and expression studies of closely related family members suggest that even recently duplicated representatives may fulfill different functions. This work provides a basis for a defined further functional dissection of this important plant-specific signaling system.

Amino Acid Sequence↗
PubMed1975

DNA-protein interactions of the rat liver non-histone chromosomal protein.

Native rat liver NHC protein-DNA interactions have been investigated by use of a nitrocellulose filter assay sensitive in detection of protein-DNA complexes. Optimal conditions for DNA-protein interactions occurs at low ionic strength conditions (110 mM phosphate buffer). A fraction of NHC proteins was enriched 25-fold by their affinity for rat DNA immobilized on cellulose columns under these conditions. At higher ionic strength (260 mM-0.04M phosphate buffer and 0.15 M sodium chloride), this fraction binds approximately sevenfold less to rat DNA but with a substantial increase in stability of the complexes. Equilibrium competition experiments indicate that at the higher ionic strength there is a considerable DNA sequence specificity of the rat DNA binding NHC protein. Since rat DNA contains three components as defined by their reassociation kinetics: single copy DNA (C0t1/2pure = 1.6 times 103); middle repetitive DNA (C0t1?1PURE = 1.1); and highly repetitive (C0t1/2pure smaller than 0.02). The two former were isolated and employed in the DNA binding assays. At the high ionic strength criterion, the rat DNA binding NHC proteins showed a substantial preference for a subset of middle repetitive DNA sequences. This suggests a preferential interaction between a class of NHC proteins and a class of middle repetitive DNA sequences.

Animals↗