Search

Recent advancements in single‐molecule methods have not only made it possible to obtain precise measurements for complex biological processes but also to produce simple mathematical models for intricate biochemical mechanisms, which would otherwise be speculative. These developments have strengthened our ability to respond through mathematical modeling to concepts of protein‒protein and protein‒DNA interactions on a nanometer level and address‐related questions. In this article, we examine an intriguing biological phenomenon in which a protein and an enzyme co‐jointly encounter carcinogenic adducts during transcription. We are focusing mainly on the dysregulation of the protein involved and the possible consequences that may arise. By providing a quantum mechanical model, we have demonstrated that the presence of carcinogenic adducts in a transcriptional bubble deregulates the protein that could cause lethal mutations. Next, we present a case study to explore carcinogenesis by suggesting an alternative experimental design. Our quantum mechanical model emphasizes the use of a quantized energies approach for specific mechanisms within the living cells. Radiation‐induced carcinogenicity can be prevented if radiation interacting with tissue is not given the energies that satisfy the quantization conditions. [ABSTRACT FROM AUTHOR]

Chromatin homeostasis mediates essential processes in eukaryotes, where histone chaperones have emerged as major regulatory factors during DNA replication, repair, and transcription. The dynamic nature of these processes, however, has severely impeded their characterization at the molecular level. Here, fluorescence optical tweezers are applied to follow histone chaperone dynamics in real time. The molecular action of SET/template-activating factor-l/β and nucleophosmin 1-representing the two most common histone chaperone folds-are examined using both nucleosomes and isolated histones. It is shown that these chaperones present binding specificity for fully dismantled nucleosomes and are able to recognize and disrupt non-native histone-DNA interactions. Furthermore, the histone eviction process and its modulation by cytochrome c are scrutinized. This approach shows that despite the different structures of these chaperones, they present conserved modes of action mediating nucleosome remodeling. [ABSTRACT FROM AUTHOR]

Abstract: Monosaccharides, such as d‐glucose and d‐fructose, exist in aqueous solution as an equilibrium mixture of cyclic isomers and can be detected with boronic acids by the reversible formation of boronate esters. The engineering of accurate, discriminating and continuous monitoring devices relies on knowledge of which cyclic isomer of a sugar binds to a boronic acid receptor. Herein, by monitoring fluctuations in ionic current, we show that an engineered α‐hemolysin (αHL) nanopore modified with a boronic acid reacts reversibly with d‐glucose as the pyranose isomer (α‐ d‐glucopyranose) and d‐fructose as either the furanose (β‐ d‐fructofuranose) or the pyranose (β‐ d‐fructopyranose). Both of these binding modes contradict current binding models. With this knowledge, we distinguished the individual sugars in a mixture of d‐maltose, d‐glucose, and d‐fructose. [ABSTRACT FROM AUTHOR]

Artificial nanopores have recently emerged as versatile tools for analyzing and sorting single molecules at high speed. However, the biological cell has already developed a large set of sophisticated protein nanopores that are able to selectively translocate all types of molecules through membranes. Therefore, hybrid devices combining artificial solid-state with biomimetic protein nanopores appear to us as a particularly promising approach to the creation of powerful diagnostic, preparative and therapeutic devices. Here, we discuss a technique, optical single-transporter recording (OSTR), in which arrays of artificial micropores and nanopores are employed to analyze protein nanopores of cellular membranes. After briefly summarizing some salient features of OSTR, the technique is compared with the electrical patch clamp method and the first results of our efforts to amalgamate optical and electrical recording are described. Finally, prospects for combining OSTR with 4Pi microscopy, single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy are discussed. [ABSTRACT FROM AUTHOR]