BLI-MS: Combining biolayer interferometry and mass spectrometry

Generating robust aptamers for food analysis by sequence-based configuration optimization

Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.

Novel Umami Peptides from Mushroom (Agaricus bisporus) and Their Umami Enhancing Effect via Virtual Screening and Molecular Simulation

This study aimed to identify novel umami peptides in Agaricus bisporus and investigate their umami enhancing effect. We virtually screened 155 potential umami peptides from the ultrasound-assisted A. bisporus hydrolysate according to Q values, iUmami-SCM, Umami_YYDS, and Tastepeptides_DM models, and molecular docking. Five peptides (AGKNTNGSQF, DEAVARGATF, REESDFQSSF, SEETTTGVHH, and WNNDAFQSSTN) were synthesized for sensory evaluation and kinetic analysis. The result showed that the umami thresholds of the five peptides were in the range of 0.21-0.40 mmol/L. Notably, REESDFQSSF, SEETTTGVHH, and WNNDAFQSSTN had low dissociation constant (KD) values and high affinity for the T1R1-VFT receptor. The enhancing effect of the three peptides with MSG or IMP was investigated by sensory evaluation, kinetic analysis, and molecular dynamics simulations. In stable complexes, ARG_277 in T1R1 played a major role in umami peptide binding to T1R1-VFT. These results provide a theoretical basis for future screening of umami peptides and improving the umami taste of food containing mushrooms.

Microprobe-Capture In-Emitter Elution: An Affinity Capture Technique to Directly Couple a Label-Free Optical Sensing Technology with Mass Spectrometry for Protein Analysis

Affinity capture of an analyte by a capture agent is one of the most effective sample preparation approaches in mass spectrometry (MS), especially top-down MS. We describe a new affinity capture technique for protein targets, called microprobe-capture in-emitter elution (MPIE), which can directly couple a label-free optical sensing technology (next-generation biolayer interferometry, BLI) with MS. To implement MPIE, an analyte is first captured on the surface of a microprobe and subsequently eluted from the microprobe inside an electrospray emitter. The capture process is monitored in real-time via BLI. When electrospray is established from the emitter to a mass spectrometer, the analyte is immediately ionized via electrospray ionization (ESI) for MS analysis. By this means, BLI and MS are directly coupled in the form of MPIE-ESI-MS. The performance of MPIE-ESI-MS was demonstrated by the analysis of β-amyloid 1-40 and transferrin using both standard samples and human specimens. In comparison to conventional affinity capture techniques such as bead-based immunoprecipitation, MPIE innovates the affinity capture methodology by introducing real-time process monitoring and providing binding characteristics of analytes, offering more information-rich experiment results. Thus, MPIE is a valuable addition to the top-down MS sample preparation toolbox, and MPIE-ESI-MS can be useful for identification and characterization of targets of interest.

Relationships of Matrix Metalloproteinase 1 and a Tissue Inhibitor of Metalloproteinase to Collagen Metabolism in Haliotis discus hannai

In response to physical, chemical, and/or biological stimuli, considerable tissue self-degradation occurs in abalone, causing severe post-harvest quality loss. During this process, the extracellular matrix (ECM) is greatly degraded by endogenous proteases. The main component of the ECM is collagen, primarily type I collagen. Although the activity of matrix metalloproteinases (MMPs), which can specifically degrade collagen, is precisely regulated by tissue inhibitors of MPs (TIMPs), indicating that MMPs and TIMPs play crucial roles in the regulation of tissue self-degradation, few studies have reported the interaction between MMPs and TIMPs. In this study, we reveal collagenases to participate in postmortem tissue self-degradation of Haliotis discus hannai by degrading type I collagen. The recombinant MMP-1 catalytic domain (rMMP1c) of abalone with high purity and enzyme activity is expressed using a prokaryotic expression system. The optimum temperature and pH for rMMP1c are 37 °C and 7.0, respectively. The thermal denaturation temperature of rMMP1c is 67.0 ± 0.9 °C. Ethylenediamine tetraacetic acid (EDTA) and 1,10-phenanthroline can completely inhibit rMMP1c activity, while Ba²⁺, Ca²⁺, and Mg²⁺ can significantly elevate it. TIMP is also expressed using HEK 293F cells. Recombinant TIMP (rTIMP) shows good inhibitory activity toward rMMP1c. Inhibition kinetics analyses reveal rTIMP to be a competitive inhibitor of rMMP1c. Biolayer interferometry reveals that rTIMP can effectively bind with rMMP1c, with an equilibrium dissociation constant value of 263 nM. rMMP1c effectively degrades type I collagen γ-β-α chains in turn, and rTIMP can significantly inhibit rMMP1c degradation activity. These results provide a theoretical basis for the study of MMP and TIMP interaction and elucidate the possible mechanism for abalone tissue self-degradation.