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1. Aquaglyceroporin AQP7's affinity for its substrate glycerol. Have we reached convergence in the computed values of glycerol-aquaglyceroporin affinity?

   https://doi.org/10.1039/D1RA07367B  

   Falato, Michael; Chan, Ruth; Chen, Liao Y. (January 2022, RSC Advances)

   AQP7 is one of the four human aquaglyceroporins that facilitate glycerol transport across the cell membrane, a biophysical process that is essential in human physiology. Therefore, it is interesting to compute AQP7's affinity for its substrate (glycerol) with reasonable certainty to compare with the experimental data suggesting high affinity in contrast with most computational studies predicting low affinity. In this study aimed at computing the AQP7-glycerol affinity with high confidence, we implemented a direct computation of the affinity from unbiased equilibrium molecular dynamics (MD) simulations of three all-atom systems constituted with 0.16 M, 4.32 M, and 10.23 M atoms, respectively. These three sets of simulations manifested a fundamental physics law that the intrinsic fluctuations of pressure in a system are inversely proportional to the system size (the number of atoms in it). These simulations showed that the computed values of glycerol-AQP7 affinity are dependent upon the system size (the inverse affinity estimations were, respectively, 47.3 mM, 1.6 mM, and 0.92 mM for the three model systems). In this, we obtained a lower bound for the AQP7-glycerol affinity (an upper bound for the dissociation constant). Namely, the AQP7-glycerol affinity is stronger than 1087/M (the dissociation constant is less than 0.92 mM). Additionally, we conducted hyper steered MD (hSMD) simulations to map out the Gibbs free-energy profile. From the free-energy profile, we produced an independent computation of the AQP7-glycerol dissociation constant being approximately 0.18 mM. 

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2. Analysis of drug interactions with serum proteins and related binding agents by affinity capillary electrophoresis: A review

   https://doi.org/10.1002/elps.202200191  

   Sharmeen, Sadia; Kyei, Isaac; Hatch, Arden; Hage, David_S (November 2022, ELECTROPHORESIS)

   Abstract Biomolecules such as serum proteins can interact with drugs in the body and influence their pharmaceutical effects. Specific and precise methods that analyze these interactions are critical for drug development or monitoring and for diagnostic purposes. Affinity capillary electrophoresis (ACE) is one technique that can be used to examine the binding between drugs and serum proteins, or other agents found in serum or blood. This article will review the basic principles of ACE, along with related affinity‐based capillary electrophoresis (CE) methods, and examine recent developments that have occurred in this field as related to the characterization of drug–protein interactions. An overview will be given of the various formats that can be used in ACE and CE for such work, including the relative advantages or weaknesses of each approach. Various applications of ACE and affinity‐based CE methods for the analysis of drug interactions with serum proteins and other binding agents will also be presented. Applications of ACE and related techniques that will be discussed include drug interaction studies with serum agents, chiral drug separations employing serum proteins, and the use of CE in hybrid methods to characterize drug binding with serum proteins. 

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3. Characterization of cerium (III) ion binding to surface‐immobilized EF‐hand loop I of calmodulin

   https://doi.org/10.1002/pep2.24133  

   Xu, MingYuan; Su, Zihang; Renner, Julie N. (August 2019, Peptide Science)

   Abstract Cerium has a wide range of current and emerging applications, and the binding of cerium ions to solid substrates is important for cerium recovery, or in advanced material synthesis. In this study, we investigate the affinity of a surface‐bound peptide derived from the EF‐hand loop I of calmodulin for cerium (III) ions and compare the results to a scrambled control. Results obtained via quartz crystal microbalance with dissipation are used to estimate the dissociation constant between the bound EF‐hand loop I peptide and cerium (III) ions (1.3 ± 0.1 μM), which is comparable with other dissociation constants measured for EF‐hand peptides and cerium ions in solution reported this work and in literature (0.95‐5.8 μM). Circular dichroism also suggests that the peptide binds to cerium (III) ions in solution, and undergoes a secondary structural change upon binding. Overall, this study shows that EF‐hand loop peptides are capable of binding cerium (III) ions in solution and when attached to a solid substrate. 

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4. An octahedral coordination cage with six Fe( iii ) centers as a T ₁ MRI probe

   https://doi.org/10.1039/d4cc03681f  

   Dissanayake, Aruni; Spernyak, Joseph A; Morrow, Janet R (October 2024, Chemical Communications)

   A coordination cage containing six high-spin Fe(iii) centers is an effectiveT₁relaxation agent through second-sphere water interactions. The cage is robust towards dissociation and binds avidly to serum albumin through electrostatic interactions. 

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5. Thermodynamic non-ideality in charge regulation of weak polyelectrolytes

   https://doi.org/10.1039/D1SM00848J  

   Gallegos, Alejandro; Ong, Gary M.; Wu, Jianzhong (October 2021, Soft Matter)

   Polymer ionization differs from that for their monomeric counterparts due to intramolecular correlations. Such effects are conventionally described in terms of the site-binding model that accounts for short-range interactions between neighboring sites. With an apparent equilibrium constant for each ionizable group and the nearest-neighbor energy as adjustable parameters, the site-binding method is useful to correlate experimental titration curves when the site–site interactions are insignificant at long ranges. This work aims to describe the electrostatic behavior of weak polyelectrolytes in aqueous solutions on the basis of the intrinsic equilibrium constants of the individual ionizable groups and solution conditions underlying the thermodynamic non-ideality. A molecular thermodynamic model is proposed for the protonation of weak polyelectrolytes by incorporating classical density functional theory into the site-binding model to account for the effects of the local ionic environment on both inter-chain and intra-chain correlations. By an extensive comparison of theoretical predictions with experimental titration curves, we demonstrate that the thermodynamic model is able to quantify the ionization behavior of weak polyelectrolytes over a broad range of molecular architectures and solution conditions. 

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