KINETIC HETEROGENEITY OF POLYMER PRODUCTS OBTAINED IN THE PRESENCE OF MICROHETEROGENIC CATALYTIC SYSTEMS BASED ON GEL CHROMATOGRAMS

Background: the polymer product obtained in the presence of microheterogeneous catalytic systems is characterized by fairly molecular weight distribution (MWD), resulted from kinetically nonequivalent active centers (ACs) in the system that initiate the polymerization process. The nature and composition of ACs are determined by setting and solving an inverse problem on the formation of MWD. This problem is acute because revealing the nature of the kinetic heterogeneity explains changes in the molecular and consumer parameters of the product for different catalyst compositions and propagation modes in polymerizations. Aim: This study aimed to develop methods and algorithms for interpreting gel chromatograms to analyze the kinetic heterogeneity of a polymer product obtained industrially in microheterogeneous catalytic systems. Methods: the solution method is based on the assumption that the formed MWD is a superposition of distributions inherent in each type of ACs. Since the problem in the final formulation refers to the Fredholm integral equations of the first kind, the regularization method of A. N. Tikhonov is used for its numerical solution, with the original problem being preliminary discretized. This methodology and the developed software algorithms were used to determine the kinetic heterogeneity of titanium- and neodymium-containing catalytic systems. Results and discussion: The MWD analysis revealed two types of ACs with an average molecular weight of ATi-lnM = 11.3 and BTi-lnM = 13.2 in the titanium catalyst and three types of ACs ANd-lnM = 11.1, BNd-lnM = 12.7 and CNd-lnM = 14 for the neodymium catalyst, respectively. Conclusions: repeated computational experiments under different polymerization conditions and requirements for the preparation of a catalytic system make it possible to reveal a relationship with the resulting heterogeneity of ACs. It allows us to set and solve problems of controlling the molecular characteristics of the resulting polymer product.

Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts

The fidelity of group II intron self-splicing and retrohoming relies on long-range tertiary interactions between the intron and its flanking exons. By single-molecule FRET, we explore the binding kinetics of the most important, structurally conserved contact, the exon and intron binding site 1 (EBS1/IBS1). A comparison of RNA-RNA and RNA-DNA hybrid contacts identifies transient metal ion binding as a major source of kinetic heterogeneity which typically appears in the form of degenerate FRET states. Molecular dynamics simulations suggest a structural link between heterogeneity and the sugar conformation at the exon-intron binding interface. While Mg2+ ions lock the exon in place and give rise to long dwell times in the exon bound FRET state, sugar puckering alleviates this structural rigidity and likely promotes exon release. The interplay of sugar puckering and metal ion coordination may be an important mechanism to balance binding affinities of RNA and DNA interactions in general.

Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity

ABSTRACTSingle-molecule kinetic experiments allow the reaction trajectories of individual biomolecules to be directly observed, eliminating the effects of population averaging and providing a powerful approach for elucidating the kinetic mechanisms of biomolecular processes. A major challenge to the analysis and interpretation of these experiments, however, is the kinetic heterogeneity that almost universally complicates the recorded single-molecule signal versus time trajectories (i.e., signal trajectories). Such heterogeneity manifests as changes and/or differences in the transition rates that are observed within individual signal trajectories or across a population of signal trajectories. Although characterizing kinetic heterogeneity can provide critical mechanistic information, there are currently no computational methods available that effectively and/or comprehensively enable such analysis. To address this gap, we have developed a computational algorithm and software program, hFRET, that uses the variational approximation for Bayesian inference to estimate the parameters of a hierarchical hidden Markov model, thereby enabling robust identification and characterization of kinetic heterogeneity. Using simulated signal trajectories, we demonstrate the ability of hFRET to accurately and precisely characterize kinetic heterogeneity. In addition, we use hFRET to analyze experimentally recorded signal trajectories reporting on the conformational dynamics of ribosomal pre-translocation (PRE) complexes. The results of our analyses demonstrate that PRE complexes exhibit kinetic heterogeneity, reveal the physical origins of this heterogeneity, and allow us to expand the current model of PRE complex dynamics. The methods described here can be applied to signal trajectories generated using any type of signal and can be easily extended to the analysis of signal trajectories exhibiting more complex kinetic behaviors. Moreover, variations of our approach can be easily developed to integrate kinetic data obtained from different experimental constructs and/or from molecular dynamics simulations of a biomolecule of interest. The hFRET source code, graphical user interface, and user manual can be downloaded as freeware at https://github.com/GonzalezBiophysicsLab/hFRET.