Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes Using a Single-Step Affinity Purification

Cellular protein-metabolite interactions (PMI), for decades relatively overlooked, are seeing a golden age in recent years. To facilitate simultaneous characterization of PMI and protein-protein interactions (PPI) of a given protein ("bait"), we developed a protocol that utilizes antibody-assisted affinity purification (AP) followed by liquid chromatography-mass spectrometry (LC-MS). Aside from its speed, simplicity, and adaptability to a variety of biological systems, its main strength lies in the parallel identification, in a near-physiological environment, of a given protein's protein and small-molecule partners.

Antimicrobial Titanium Surface via Click-Immobilization of Peptide and Its in Vitro/Vivo Activity

The use of antimicrobial peptides (AMPs)-functionalized titanium implants is an efficient method for preventing bacterial infection. However, the attachment of AMPs to the surface of titanium implants remains a challenge. In this study, a "clickable" titanium surface was developed by using a silane coupling agent with an alkynyl group. The antimicrobial titanium implant was then constructed through the reaction between the "clickable" surface and azido-AMPs (PEG-HHC36:N₃-PEG₁₂-KRWWKWWRR) via click chemistry of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Such an antimicrobial titanium implant, with an AMP density of 897.4 ± 67.3 ng/cm² (2.5 ± 0.2 molecules per nm²) on the surface, exhibited good and stable antimicrobial activity, inhibited 90.2% of Staphylococcus aureus and 88.1% of Escherichia coli after 2.5 h of incubation, and even inhibited 69.5% of Staphylococcus aureus after 4 days of degradation. The CCK-8 assay indicated that the antimicrobial titanium implant exhibited negligible cytotoxicity to mouse bone mesenchymal stem cells. In vivo assay illustrated that this implant could kill 78.8% of Staphylococcus aureus after 7 days. This method has great potential for the preparation of antimicrobial titanium implants and the prevention of infections in the clinic.

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Cellular processes are regulated by interactions between biological molecules such as proteins, metabolites, and nucleic acids. While the investigation of protein-protein interactions (PPI) is no novelty, experimental approaches aiming to characterize endogenous protein-metabolite interactions (PMI) constitute a rather recent development. Herein, we present a protocol that allows simultaneous characterization of the PPI and PMI of a protein of choice, referred to as bait. Our protocol was optimized for Arabidopsis cell cultures and combines affinity purification (AP) with mass spectrometry (MS)-based protein and metabolite detection. In short, transgenic Arabidopsis lines, expressing bait protein fused to an affinity tag, are first lysed to obtain a native cellular extract. Anti-tag antibodies are used to pull down protein and metabolite partners of the bait protein. The affinity-purified complexes are extracted using a one-step methyl tert-butyl ether (MTBE)/methanol/water method. Whilst metabolites separate into either the polar or the hydrophobic phase, proteins can be found in the pellet. Both metabolites and proteins are then analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS or UPLC-MS/MS). Empty-vector (EV) control lines are used to exclude false positives. The major advantage of our protocol is that it enables identification of protein and metabolite partners of a target protein in parallel in near-physiological conditions (cellular lysate). The presented method is straightforward, fast, and can be easily adapted to biological systems other than plant cell cultures.

Enantiodifferential Approach for the Target Protein Detection of the Jasmonate Glucoside That Controls the Leaf Closure of Samanea saman

The synthetic photoaffinity probe designed to mimic bioactive molecules is one of the powerful tools for the identification of the target protein in living organisms. However, nonspecific interaction between the probe and nontargets would cause a misleading result in many cases of the photoaffinity labeling. In this chapter, we describe an enantiodifferential approach as a reliable method for the detection of the specific target protein of the bioactive natural product, jasmonate glucoside, a chemical factor that controls the nyctinastic leaf movement of the leguminous plants.

Affinity purification with metabolomic and proteomic analysis unravels diverse roles of nucleoside diphosphate kinases

Interactions between metabolites and proteins play an integral role in all cellular functions. Here we describe an affinity purification (AP) approach in combination with LC/MS-based metabolomics and proteomics that allows, to our knowledge for the first time, analysis of protein-metabolite and protein-protein interactions simultaneously in plant systems. More specifically, we examined protein and small-molecule partners of the three (of five) nucleoside diphosphate kinases present in the Arabidopsis genome (NDPK1-NDPK3). The bona fide role of NDPKs is the exchange of terminal phosphate groups between nucleoside diphosphates (NDPs) and triphosphates (NTPs). However, other functions have been reported, which probably depend on both the proteins and small molecules specifically interacting with the NDPK. Using our approach we identified 23, 17, and 8 novel protein partners of NDPK1, NDPK2, and NDPK3, respectively, with nucleotide-dependent proteins such as actin and adenosine kinase 2 being enriched. Particularly interesting, however, was the co-elution of glutathione S-transferases (GSTs) and reduced glutathione (GSH) with the affinity-purified NDPK1 complexes. Following up on this finding, we could demonstrate that NDPK1 undergoes glutathionylation, opening a new paradigm of NDPK regulation in plants. The described results extend our knowledge of NDPKs, the key enzymes regulating NDP/NTP homeostasis.

Functional importance of the sugar moiety of jasmonic acid glucoside for bioactivity and target affinity

Importance of the d-glycopyranoside structure for the bioactivity and target affinity of jasmonic acid glucoside.

Affinity-based target identification for bioactive small molecules

A variety of new approaches of affinity-based target identification for bioactive small molecules are being developed, facilitating drug development and understanding complicated biological processes.

Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry

Photoaffinity labeling has a longstanding history as a powerful biochemical technique. However, photoaffinity labeling has significantly evolved over the past decade principally due to its coupling with bioorthogonal/click chemistry reactions. This review aims to highlight tandem photoaffinity labeling-bioorthogonal conjugation as a chemical approach in medicinal chemistry and chemical biology. In particular, recent examples of using this strategy for affinity-based protein profiling (AfBPP), drug target identification, binding ensemble profiling, studying endogenous biological molecules, and imaging applications will be presented. Additionally, recent advances in the development of 'all-in-one' compact moieties possessing a photoreactive group and clickable handle will be discussed.

Diazirine based photoaffinity labeling

Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.

The high performance of 3XFLAG for target purification of a bioactive metabolite: a tag combined with a highly effective linker structure

Affinity purification using immunoprecipitation (IP) is an extremely useful method for target profiling of bioactive natural products. We examined IP purification of CMetE, which is a molecular target for potassium isolespedezate (1), a leaf-opening factor of Cassia plant. We studied IP efficiency using a panel of FLAG-connected molecular probes (2-8), including probes with varying structures and lengths of the linker moiety. The results suggest that not only the length, but the chemical nature of the linker moiety, strongly affect the IP efficiency. 3XFLAG, a tag combined with a linker moiety of charged amino acids, gave the best results and was most useful for IP purification of the molecular target.

Recent advances on bioorganic chemistry of plant metabolites controlling nyctinasty

Leguminous plants open their leaves during the daytime and close them at night as if sleeping, a type of movement that follows circadian rhythms, and is known as nyctinastic movement. This phenomenon is controlled by two endogenous bioactive substances that exhibit opposing activities: Leaf-Opening Factor (LOF), which opens the leaves, and Leaf-Closing Factor (LCF), which closes them. The authors have carried out chemical biological research using these bioactive substances as molecular probes in order to clarify the mechanisms of nyctinastic movement. Here, we report on the detection and identification of the target proteins of these compounds using original methodology.