Atomic and Electronic Structure of Pilus from Geobacter sulfurreducens through QM/MM Calculations: Evidence for Hole Transfer in Aromatic Residues

Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning

Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex molecular environment of biomolecular building blocks, however, it is unclear which chemical and structural dynamic features support electronic conductivity. Here, we investigate the role of finite temperature fluctuations on the electronic structure and its implications for conductivity in a peptide-based fiber material composed of an antiparallel coiled coil hexamer, ACC-Hex, building block. All-atom classical molecular dynamics (MD) and first-principles density functional theory (DFT) are combined with interpretable machine learning (ML) to understand the relationship between physical and electronic structure of the peptide dimer subunit of ACC-Hex. For 1101 unique MD "snapshots" of the ACC peptide dimer, hybrid DFT calculations predict a significant variation of near-gap orbital energies among snapshots, with an increase in the predicted number of nearly degenerate states near the highest occupied molecular orbital (HOMO), which suggests improved conductivity. Interpretable ML is then used to investigate which nuclear conformations increase the number of nearly degenerate states. We find that molecular conformation descriptors of interphenylalanine distance and orientation are, as expected, highly correlated with increased state density near the HOMO. Unexpectedly, we also find that descriptors of tightly coiled peptide backbones, as well as those describing the change in the electrostatic environment around the peptide dimer, are important for predicting the number of hole-accessible states near the HOMO. Our study illustrates the utility of interpretable ML as a tool for understanding complex trends in large-scale ab initio simulations.

Engineering nanowires in bacteria to elucidate electron transport structural-functional relationships

Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells' bioenergetic programming. Their role is thought to be linked to facilitating electron transfer between cells and the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineered Cupriavidus necator H16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using a Cupriavidus necator chassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.

Comparative antibacterial analysis of the anthraquinone compounds based on the AIM theory, molecular docking, and dynamics simulation analysis

BACKGROUND

Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components.

METHODS

Comparison of structure characteristics and antibacterial effect of these compounds was performed by applying quantum chemical calculations, atoms in molecules theory, molecular docking, and dynamics simulation procedure. Density functional theory calculation with B3LYP using 6-31G (d, p) basis set has been used to determine ground state molecular geometries.

RESULTS

The molecular geometric stability, electrostatic potential, frontier orbital energies, and topological properties were analyzed at the active site. Once glucose ring is introduced into the hydroxyanthraquinone rings, almost all of the positive molecular potentials are distributed among the hydroxyl hydrogen atoms of the glucose rings. In addition, low electron density ρ (r) and positive Laplacian value of the O-H bond of the anthraquinone glucoside are the evidences of the highly polarized and covalently decreased bonding interactions. The anthraquinone glucoside compounds have generally higher intermolecular binding energies than the corresponding aglycones due to the strong interaction between the glucose rings and the surrounding amino acids. Molecular dynamics simulations further explored the stability and dynamic behavior of the anthraquinone compound and protein complexes through RMSD, RMSF, SASA, and Rg.

CONCLUSION

The type of carboxyl, hydroxyl, and hydroxymethyl groups on phenyl ring and the substituent glucose rings is important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire

A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨H_mn⟩), reaction free energies (ΔG_mn), reorganization energies (λ_mn), and activation energies (E_a) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔG_mn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.

Electronic Structure of de Novo Peptide ACC-Hex from First Principles

Proteins are promising components for bioelectronic devices due in part to their biocompatibility, flexibility, and chemical diversity, which enable tuning of material properties. Indeed, an increasingly broad range of conductive protein supramolecular materials have been reported. However, due to their structural and environmental complexity, the electronic structure, and hence conductivity, of protein assemblies is not well-understood. Here we perform an all-atom simulation of the physical and electronic structure of a recently synthesized self-assembled peptide antiparallel coiled-coil hexamer, ACC-Hex. Using classical molecular dynamics and first-principles density functional theory, we examine the interactions of each peptide, containing phenylalanine residues along a hydrophobic core, to form a hexamer structure. We find that while frontier electronic orbitals are composed of phenylalanine, the peptide backbone and remaining residues, including those influenced by solvent, also contribute to the electronic density. Additionally, by studying dimers extracted from the hexamer, we show that structural distortions due to atomic fluctuations significantly impact the electronic structure of the peptide bundle. These results indicate that it is necessary to consider the full atomistic picture when using the electronic structure of supramolecular protein complexes to predict electronic properties.

Microbial nanowires

In this Quick guide, Derek Lovley introduces microbial nanowires-conductive extracellular appendages made by some bacteria and archaea.