Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level

Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease

A hallmark of tightly regulated high-fidelity enzymes is that they become activated only after encountering cognate substrates, often by an induced-fit mechanism rather than conformational selection. Upon analysis of molecular dynamics trajectories, we recently discovered that the Cas9 HNH domain exists in three conformations: 1) Y836 (which is two residues away from the catalytic D839 and H840 residues) is hydrogen bonded to the D829 backbone amide, 2) Y836 is hydrogen bonded to the backbone amide of D861 (which is one residue away from the third catalytic residue N863), and 3) Y836 is not hydrogen bonded to either residue. Each of the three conformers differs from the active state of HNH. The conversion between the inactive and active states involves a local unfolding-refolding process that displaces the Cα and side chain of the catalytic N863 residue by ∼5 Å and ∼10 Å, respectively. In this study, we report the two largest principal components of coordinate variance of the HNH domain throughout molecular dynamics trajectories to establish the interconversion pathways of these conformations. We show that conformation 2 is an obligate step between conformations 1 and 3, which are not directly interconvertible without conformation 2. The loss of hydrogen bonding of the Y836 side chain in conformation 3 likely plays an essential role in activation during local unfolding-refolding of an α-helix containing the catalytic N863. Three single Lys-to-Ala mutants appear to eliminate this substrate-independent activation pathway of the wild-type HNH nuclease, thereby enhancing the fidelity of HNH cleavage.

Microbe‐Mediated Biosynthesis of Multidimensional Carbon‐Based Materials for Energy Storage Applications

Biosynthesis methods are considered to be a promising technology for engineering new carbon‐based materials or redesigning the existing ones for specific purposes with the aid of synthetic biology. Lots of biosynthetic processes including metabolism, fermentation, biological mineralization, and gene editing have been adopted to prepare novel carbon‐based materials with exceptional properties that cannot be realized by traditional chemical methods, because microbes evolved to possess special abilities to modulate components/structure of materials. In this review, the recent development on carbon‐based materials prepared via different biosynthesis methods and various microbe factories (such as bacteria, yeasts, fungus, viruses, proteins) are systematically reviewed. The types of biotechniques and the corresponding mechanisms for the synthesis of carbon‐based materials are outlined. This review also focuses on the structural design and compositional engineering of carbon‐based nanostructures (e.g., metals, semiconductors, metal oxides, metal sulfides, phosphates, Mxenes) derived from biotechnology and their applications in electrochemical energy storage devices. Moreover, the relationship of the architecture–composition–electrochemical behavior and performance enhancement mechanism is also deeply discussed and analyzed. Finally, the development perspectives and challenges on the biosynthetic carbons are proposed and may pave a new avenue for rational design of advanced materials for the low‐carbon economy.

Principles of Resonance Energy Transfer

This unit describes the basic principles of Förster resonance energy transfer (FRET). Beginning with a brief summary of the history of FRET applications, the theory of FRET is introduced in detail using figures to explain all the important parameters of the FRET process. After listing various approaches for measuring FRET efficiency, several pieces of advice are given on choosing the appropriate instrumentation. The unit concludes with a discussion of the limitations of FRET measurements followed by a few examples of the latest FRET applications, including new developments such as spectral flow cytometric FRET, single-molecule FRET, and combinations of FRET with super-resolution or lifetime imaging microscopy and with molecular dynamics simulations. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.