Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data

Enantiomeric analysis of chiral phenyl aromatic compounds by coated capillary electrochromatography based on a MOF-on-MOF stationary phase

Chiral phenyl aromatic compounds (CPACs) are widely used in drug development, food/cosmetic production, and other organic synthesis processes, and their different enantiomers have distinct physiological activities and application differences. A double-layer metal-organic framework composite (MOF-on-MOF) was obtained by in situ synthesis of chiral metal-organic framework (CMOM-3S) on the surface of an iron-based metal-organic framework (NH2-MIL-101(Fe)). According to our investigation, MOF-on-MOF composite was for the first time applied to the stationary phase of capillary electrochromatography (CEC), and enantioseparations of eight CPACs were accomplished. Compared with single CMOM-3S, the enantioseparation performance of the coated capillary columns based on NH2-MIL-101(Fe)@CMOM-3S was improved by 34.07 ~ 720.0%. The R-/S-mandelic acid in actual sample (apricot leaves) was detected by the newly CEC system to be 0.0118 mg mL-1 and 0.0523 mg mL-1, respectively. The spike recoveries were 96.60 ~ 104.7%, indicating its good stability and accuracy. In addition, the selective adsorption capacity of MOF-on-MOF composites was verified by adsorption experiments.

Crowding revisited: Open questions and future perspectives

Although biophysical studies have traditionally been performed in diluted solutions, it was pointed out in the late 1990s that the cellular milieu contains several other macromolecules, creating a condition of molecular crowding. How crowding affects protein stability is an important question heatedly discussed over the past 20 years. Theoretical estimations have suggested a 5-20°C effect of fold stabilisation. This estimate, however, is at variance with what has been verified experimentally that proposes only a limited increase of stability, opening the question whether some of the assumptions taken for granted should be reconsidered. The present review critically analyses the causes of this discrepancy and discusses the limitations and implications of the current concept of crowding.

Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing

The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be applied to complex systems and limits the reliability of such calculations. Supramolecular sensor systems include many interactions that make such chemical systems complicated. The challenges in creating sensing molecules can be significantly decreased through the availability of detailed mathematical models of such systems. Here, we propose uncovering accurate thermodynamic parameters of chemical reactions using better-defined mathematical modeling-fitting analysis is the key to understanding molecular assemblies and developing new bio/sensing agents. The supramolecular example we chose for this investigation is a self-assembled sensor consists of a synthesized receptor, DPA (DPA = dipicolylamine)-appended phenylboronic acid (1) in combination with Zn2+(1.Zn) that forms various assemblies with a fluorophore like alizarin red S (ARS). The self-assemblies can detect multi-phosphates like pyrophosphate (PPi) in aqueous solutions. We developed a mathematical model for the simultaneous quantitative analysis of twenty-seven intertwined interactions and reactions between the sensor (1.Zn-ARS) and the target (PPi) for the first time, relying on the Newton-Raphson algorithm. Through analyzing simulated potentiometric titration data, we describe the concurrent determination of thermodynamic parameters of the different guest-host bindings. Various values of temperatures, initial concentrations, and starting pHs were considered to predict the required measurement conditions for thermodynamic studies. Accordingly, we determined the species concentrations of different host-guest bindings in a generalized way. This way, the binding capabilities of a set of species can be quantitatively examined to systematically measure the power of the sensing system. This study shows analyzing supramolecular self-assemblies with solid mathematical models has a high potential for a better understanding of molecular interactions within complex chemical networks and developing new sensors with better sensing effects for bio-purposes.

An "Onion-like" Model of Protein Unfolding: Collective versus Site Specific Approaches

Approximating protein unfolding by an all-or-none cooperative event is a convenient assumption that can provide precious global information on protein stability. It is however quickly emerging that the scenario is far more complex and that global denaturation curves often hide a rich heterogeneity of states that are largely probe dependent. In this review, we revisit the importance of gaining site-specific information on the unfolding process. We focus on nuclear magnetic resonance, as this is the main technique able to provide site-specific information. We review historical and most modern approaches that have allowed an appreciable advancement of the field of protein folding. We also demonstrate how unfolding is a reporter dependent event, suggesting the outmost importance of selecting the reporter carefully.