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1. Binding equations for the lipid composition dependence of peripheral membrane-binding proteins

   https://doi.org/10.1016/j.bpj.2024.02.031  

   Kerr, Daniel; Suwatthee, Tiffany; Maltseva, Sofiya; Lee, Ka_Yee C (April 2024, Biophysical Journal)
2. The binding and specificity of chemokine binding proteins, through the lens of experiment and computation

   https://doi.org/10.1016/j.bj.2021.07.004  

   Stark, Lauren E.; Guan, Wenyan; Colvin, Michael E.; LiWang, Patricia J. (June 2022, Biomedical Journal)
3. Binding behavior of receptor binding domain of the SARS-CoV-2 virus and ivermectin

   https://doi.org/10.1038/s41598-024-53086-0  

   Gossen, Kasidy R; Zhang, Meiyi; Nikolov, Zivko L; Fernando, Sandun D; King, Maria D (December 2024, Scientific Reports)

   Abstract The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), sparked an international debate on effective ways to prevent and treat the virus. Specifically, there were many varying opinions on the use of ivermectin (IVM) throughout the world, with minimal research to support either side. IVM is an FDA-approved antiparasitic drug that was discovered in the 1970s and was found to show antiviral activity. The objective of this study is to examine the binding behavior and rates of association and dissociation between SARS-CoV-2 receptor binding domain (RBD), IVM, and their combination using aminopropylsilane (APS) biosensors as surrogates for the hydrophobic interaction between the viral protein and human angiotensin-converting enzyme 2 (ACE2) receptors to determine the potential of IVM as a repurposed drug for SARS-CoV-2 prevention and treatment. The IVM, RBD, and combination binding kinetics were analyzed using biolayer interferometry (BLI) and validated with multiple in silico techniques including protein–ligand docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA), and principal component analysis (PCA). Our results suggest that with increasing IVM concentrations the association rate with the hydrophobic biosensor increases with a simultaneous decrease in dissociation. Significant kinetic changes to RBD, when combined with IVM, were found only at a concentration a thousand times the approved dosage with minimal changes found over a 35-min time period. Our study suggests that IVM is not an effective preventative or treatment method at the currently approved dosage. 

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4. Binding-promoted chemical reaction in the nanospace of a binding site: effects of environmental constriction

   https://doi.org/10.1039/C8OB00590G  

   Xing, Xiaoyu; Zhao, Yan (January 2018, Organic & Biomolecular Chemistry)

   Chemical reactions in a confined nanospace can be very different from those in solution. Imine formation between molecular amines and an aldehyde inside a molecularly imprinted receptor was promoted strongly by the binding. Although how well the amine fit in the binding pocket and its electronic nature both influenced the reaction, the freedom of movement for the amine was the most important factor determining the binding-normalized reactivity. 

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5. The Binding Problem 2.0: Beyond Perceptual Features

   https://doi.org/10.1111/cogs.13244  

   Yu, Xinchi; Lau, Ellen (February 2023, Cognitive Science)

   Abstract The “binding problem” has been a central question in vision science for some 30 years: When encoding multiple objects or maintaining them in working memory, how are we able to represent the correspondence between a specific feature and its corresponding object correctly? In this letter we argue that the boundaries of this research program in fact extend far beyond vision, and we call for coordinated pursuit across the broader cognitive science community of this central question for cognition, which we dub “Binding Problem 2.0”. 

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