Fluorescence imaging opens a new window for the diagnosis of early-stage Alzheimer's disease.

As the global population ages, the incidence and prevalence of Alzheimer's disease (AD) continues to rise, posing a serious threat to human health. Butyrylcholinesterase (BChE), which is overexpressed in the brains of patients with AD, is a potential drug target and biomarker. However, the molecular mechanism underlying BChE's role in the AD process remains unclear.

Expression, purification, and characterization of transmembrane protein homogentisate solanesyltransferase.

Homogentisate solanesyltransferase (HST) is a crucial enzyme in the plastoquinone biosynthetic pathway and has recently emerged as a promising target for herbicides. In this study, we successfully expressed and purified a stable and highly pure form of seven times transmembrane protein Chlamydomonas reinhardtii HST (CrHST). The final yield of CrHST protein obtained was 12.

Rational Design of Esterase-Insensitive Fluorogenic Probes for In Vivo Imaging.

Small-molecule fluorogenic probes are indispensable tools for performing research in biomedical fields and chemical biology. Although numerous cleavable fluorogenic probes have been developed to investigate various bioanalytes, few of them meet the baseline requirements for in vivo biosensing for disease diagnosis due to their insufficient specificity resulted from the remarkable esterase interferences. To address this critical issue, we developed a general approach called fragment-based fluorogenic probe discovery (FBFPD) to design esterase-insensitive probes for in vitro and in vivo applications.

Protein-nucleic acid thermodynamic databases for specific uses.

In response to Gromiha and Harini, we review the currently available thermodynamic databases for protein-nucleic acid interactions. These databases are designed for particular uses. We give general comments on them to facilitate browsing and exploration.

Engineered Metallacycle-Based Supramolecular Photosensitizers for Effective Photodynamic Therapy.

Although metallacycle-based supramolecular photosensitizers (PSs) have attracted increasing attention in biomedicine, their clinical translation is still hindered by their inherent dark toxicity. Herein, we report what to our knowledge is the first example of a molecular engineering approach to building blocks of metallacycles for constructing a series of supramolecular PSs (RuA-RuD), with the aim of simultaneously reducing dark toxicity and enhancing phototoxicity, and consequently obtaining high phototoxicity indexes (PI). Detailed in vitro investigations demonstrate that RuA-RuD display high cancer cellular uptake and remarkable antitumor activity even under hypoxic conditions.

Web tools support predicting protein-nucleic acid complexes stability with affinity changes.

Numerous biological processes, such as transcription, replication, and translation, rely on protein-nucleic acid interactions (PNIs). Demonstrating the binding stability of protein-nucleic acid complexes is vital to deciphering the code for PNIs. Numerous web-based tools have been developed to attach importance to protein-nucleic acid stability, facilitating the prediction of PNIs characteristics rapidly.

Thermodynamic database supports deciphering protein-nucleic acid interactions.

The thermodynamics of protein-nucleic acid interactions (PNIs) is crucial for elucidating the mechanisms of molecular recognition and pathological consequences. The Protein-Nucleic Acid Thermodynamics Database (PNATDB) is a database containing experimentally determined thermodynamic parameters along with sequence, structural, and function data, which is available free online.

In vivo diagnostics of abiotic plant stress responses via in situ real-time fluorescence imaging.

A hydroxyphenylpyruvate dioxygenase-targeted fluorescent biosensor enables the early diagnostics of abiotic stresses in plants.

Pesticide Informatics Platform (PIP): An International Platform for Pesticide Discovery, Residue, and Risk Evaluation.

Pesticides are widely used agrochemicals for crop protection. The need for novel pesticides becomes urgent as a result of the emergence of resistance and environmental toxicity. Pesticide informatics has been applied in different phase processes of pesticide target identification, active ingredient design, and impact evaluation.

Computational methods for predicting hotspots at protein-RNA interfaces.

Protein-RNA interactions play essential roles in many critical biological events. A comprehensive understanding of the mechanisms underlying these interactions is helpful when studying cellular activities and therapeutic applications. Hotspots are a small portion of residues contributing much toward protein-RNA binding affinity.

Multienzyme-Targeted Fluorescent Probe as a Biosensing Platform for Broad Detection of Pesticide Residues.

Pesticide residues, significantly hampering the overall environmental and human health, have become an increasingly severe issue. Thus, developing rapid, cost-effective, and sensitive tools for monitoring the pesticide residues in food and water is extremely important. Compared to the conventional and chromatographic techniques, enzyme inhibition-based biosensors conjugated with the fluorogenic probes provide effective alternative methods for detecting pesticide residues due to the inherent advantages including high selectivity and sensitivity, simple operation, and capability of providing in situ and real-time information.

Web resources facilitate drug discovery in treatment of COVID-19.

The infectious disease Coronavirus 2019 (COVID-19) continues to cause a global pandemic and, thus, the need for effective therapeutics remains urgent. Global research targeting COVID-19 treatments has produced numerous therapy-related data and established data repositories. However, these data are disseminated throughout the literature and web resources, which could lead to a reduction in the levels of their use.

Protocol for hit-to-lead optimization of compounds by auto ligand directing evolution (AILDE) approach.

Hit-to-lead (H2L) optimization is crucial for drug design, which has become an increasing concern in medicinal chemistry. A virtual screening strategy of auto ligand directing evolution (AILDE) has been developed to yield promising lead compounds rapidly and efficiently. The protocol includes instructions for fragment compound library construction, conformational sampling by molecular dynamics simulation, ligand modification by fragment growing, as well as the binding free energy prediction.

HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study.

Protein-nucleic acid interactions play essential roles in many biological processes, such as transcription, replication and translation. In protein-nucleic acid interfaces, hotspot residues contribute the majority of binding affinity toward molecular recognition. Hotspot residues are commonly regarded as potential binding sites for compound molecules in drug design projects.

PIIMS Server: A Web Server for Mutation Hotspot Scanning at the Protein-Protein Interface.

Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other residues. Research on the mutational effects of hotspots is important for understanding basic aspects of protein association.

Bioinformatics toolbox for exploring protein phosphorylation network.

A clear systematic delineation of the interactions between phosphorylation sites on substrates and their effector kinases plays a fundamental role in revealing cellular activities, understanding signaling modulation mechanisms and proposing novel hypotheses. The emergence of bioinformatics tools contributes to studying phosphorylation network. Some of them feature the visualization of network, enabling more effective trace of the underlying biological problems in a clear and succinct way.

Spreading of benquitrione droplets on superhydrophobic leaves through pillar[5]arene-based host-guest chemistry.

Spreading of agricultural sprays on plant surfaces is a significant task as it helps decrease pesticide usage and thereby reduces the risk of environmental pollution. Here, we report a method of increasing the spreading of herbicide benquitrione droplets on superhydrophobic surfaces through its selective dynamic self-assembly with amino pillar[5]arenes. Supramolecular interaction such as host-guest interaction was utilized for the complete diffusion of benquitrione over the hydrophobic plant surface.

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations.

A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration.