Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models

Intra-strand phosphate-mediated pathways in microsolvated double-stranded DNA

We argue that dry DNA charge transport in molecular junctions, over distances of tens of nanometers, can take place via independent intra-strand pathways involving the phosphate groups. Such pathways explain recent single-molecule experiments that compare currents in intact and nicked 100 base-pair double-stranded DNA. We explore the conditions that favor independent intra-strand transport channels with the participation of the phosphate groups, as opposed to purely base-mediated transport involving the pi-stacked bases and inter-strand transitions. Our computations demonstrate how long-distance transport pathways in DNA are tuned by the degree of solvation, which affects the level of dynamic disorder in the pi-stacking, and the energies of phosphate-group molecular orbitals.

Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency

Interferon regulatory factor 4 (IRF4) is a transcription factor that regulates the development and function of immune cells. Recently, a new multimorphic mutation T95R was identified in the IRF4 DNA-binding domain (DBD) in patients with autosomal dominant combined immune deficiency. Here, we characterized the interactions of the wild-type IRF4-DBD (IRF4-DBDWT) and T95R mutant (IRF4-DBDT95R) with a canonical DNA sequence and several noncanonical DNA sequences. We found that compared to IRF4-DBDWT, IRF4-DBDT95R exhibits higher binding affinities for both canonical and noncanonical DNAs, with the highest preference for the noncanonical GATA sequence. The crystal structures of IRF4-DBDWT in complex with the GATA sequence and IRF4-DBDT95R in complexes with both canonical and noncanonical DNAs were determined, showing that the T95R mutation enhances the interactions of IRF4-DBDT95R with the canonical and noncanonical DNAs to achieve higher affinity and specificity. Collectively, our data provide the molecular basis for the gain-of-function and new function of IRF4T95R.

Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid-amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

Local electronic structure analysis by ab initio elongation method: A benchmark using DNA block polymers

The ab initio elongation (ELG) method based on a polymerization concept is a feasible way to perform linear-scaling electronic structure calculations for huge aperiodic molecules while maintaining computational accuracy. In the method, the electronic structures are sequentially elongated by repeating (1) the conversion of canonical molecular orbitals (CMOs) to region-localized MOs (RLMOs), that is, active RLMOs localized onto a region close to an attacking monomer or frozen RLMOs localized onto the remaining region, and the subsequent (2) partial self-consistent-field calculations for an interaction space composed of the active RLMOs and the attacking monomer. For each ELG process, one can obtain local CMOs for the interaction space and the corresponding local orbital energies. Local site information, such as the local highest-occupied/lowest-unoccupied MOs, can be acquired with linear-scaling efficiency by correctly including electronic effects from the frozen region. In this study, we performed a local electronic structure analysis using the ELG method for various DNA block polymers with different sequential patterns. This benchmark aimed to confirm the effectiveness of the method toward the efficient detection of a singular local electronic structure in unknown systems as a future practical application. We discussed the high-throughput efficiency of our method and proposed a strategy to detect singular electronic structures by combining with a machine learning technique.

Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions

The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an increased efficiency. In particular, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain, including the effect of double mutation, and compare the results with the wild type. We have recently developed a method of calculating the amino-acid-amino-acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant finding is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.

Voltage-induced long-range coherent electron transfer through organic molecules

Biological structures rely on kinetically tuned charge transfer reactions for energy conversion, biocatalysis, and signaling as well as for oxidative damage repair. Unlike man-made electrical circuitry, which uses metals and semiconductors to direct current flow, charge transfer in living systems proceeds via biomolecules that are nominally insulating. Long-distance charge transport, which is observed routinely in nucleic acids, peptides, and proteins, is believed to arise from a sequence of thermally activated hopping steps. However, a growing number of experiments find limited temperature dependence for electron transfer over tens of nanometers. To account for these observations, we propose a temperature-independent mechanism based on the electric potential difference that builds up along the molecule as a precursor of electron transfer. Specifically, the voltage changes the nature of the electronic states away from being sharply localized so that efficient resonant tunneling across long distances becomes possible without thermal assistance. This mechanism is general and is expected to be operative in molecules where the electronic states densely fill a wide energy window (on the scale of electronvolts) above or below the gap between the highest-occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). We show that this effect can explain the temperature-independent charge transport through DNA and the strongly voltage-dependent currents that are measured through organic semiconductors and peptides.

Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA

We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.

Complex interplay of interatomic bonding in a multi-component pyrophosphate crystal: K2Mg (H2P2O7)2·2H2O

The electronic structure and interatomic bonding of pyrophosphate crystal K₂Mg (H₂P₂O₇)₂·2H₂O are investigated for the first time showing complex interplay of different types of bindings. The existing structure from single-crystal X-ray diffraction is not sufficiently refined, resulting in unrealistic short O─H bonds which is rectified by high-precision density functional theory (DFT) calculation. K₂Mg (H₂P₂O₇)₂·2H₂O has a direct gap of 5.22 eV and a small electron effective mass of 0.14 m_e. Detailed bond analysis between every pair of atoms reveals the complexity of various covalent, ionic, hydrogen bonding and bridging bonding and their sensitive dependence on structural differences. The K--O bonds are much weaker than Mg--O bonds and contributions from the hydrogen bonds are non-negligible. Quantitative analysis of internal cohesion in terms of total bond order density and partial bond order density divulges the relative importance of different types of bonding. The calculated optical absorptions show multiple peaks and a sharp Plasmon peak at 23 eV and a refractive index of 1.44. The elastic and mechanical properties show features unique to this low-symmetry crystal. Phonon calculation gives vibrational frequencies in agreement with reported Raman spectrum. These results provide new insights indicating that acidic pyrophosphates could have a variety of unrealized applications in advanced technology.

Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA

MS2 presents a well-studied example of a single-stranded RNA virus for which the genomic RNA plays a pivotal role in the virus assembly process based on the packaging signal-mediated mechanism. Packaging signals (PSs) are multiple dispersed RNA sequence/structure motifs varying around a central recognition motif that interact in a specific way with the capsid protein in the assembly process. Although the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimental protocols, we approach this problem using large-scale ab initio computation centered on critical aspects of the consensus protein-RNA interactions recognition motif. DFT calculations are carried out on two nucleoprotein complexes: wild-type and mutated (PDB IDs: 1ZDH and 5MSF ). The calculated partial charge distribution of residues and the strength of hydrogen bonding (HB) between them enabled us to locate the exact binding sites with the strongest HBs, identified to be LYS43-A^-4, ARG49-C^-13, TYR85-C^-5, and LYS61-C^-5, due to the change in the sequence of the mutated RNA.

Designing the Interface of Carbon Nanotube/Biomaterials for High-Performance Ultra-Broadband Photodetection

Inorganic/biomolecule nanohybrids can combine superior electronic and optical properties of inorganic nanostructures and biomolecules for optoelectronics with performance far surpassing that achievable in conventional materials. The key toward a high-performance inorganic/biomolecule nanohybrid is to design their interface based on the electronic structures of the constituents. A major challenge is the lack of knowledge of most biomolecules due to their complex structures and composition. Here, we first calculated the electronic structure and optical properties of one of the cytochrome c (Cyt c) macromolecules (PDB ID: 1HRC ) using ab initio OLCAO method, which was followed by experimental confirmation using ultraviolet photoemission spectroscopy. For the first time, the highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels of Cyt c, a well-known electron transport chain in biological systems, were obtained. On the basis of the result, pairing the Cyt c with semiconductor single-wall carbon nanotubes (s-SWCNT) was predicted to have a favorable band alignment and built-in electrical field for exciton dissociation and charge transfer across the s-SWCNT/Cyt c heterojunction interface. Excitingly, photodetectors based on the s-SWCNT/Cyt c heterojunction nanohybrids demonstrated extraordinary ultra-broadband (visible light to infrared) responsivity (46-188 A W^-1) and figure-of-merit detectivity D* (1-6 × 10¹⁰ cm Hz^1/2 W^-1). Moreover, these devices can be fabricated on transparent flexible substrates by a low-lost nonvacuum method and are stable in air. These results suggest that the s-SWCNT/biomolecule nanohybrids may be promising for the development of CNT-based ultra-broadband photodetectors.

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence

The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

van der Waals Interactions on the Mesoscale: Open-Science Implementation, Anisotropy, Retardation, and Solvent Effects

The self-assembly of heterogeneous mesoscale systems is mediated by long-range interactions, including van der Waals forces. Diverse mesoscale architectures, built of optically and morphologically anisotropic elements such as DNA, collagen, single-walled carbon nanotubes, and inorganic materials, require a tool to calculate the forces, torques, interaction energies, and Hamaker coefficients that govern assembly in such systems. The mesoscale Lifshitz theory of van der Waals interactions can accurately describe solvent and temperature effects, retardation, and optically and morphologically anisotropic materials for cylindrical and planar interaction geometries. The Gecko Hamaker open-science software implementation of this theory enables new and sophisticated insights into the properties of important organic/inorganic systems: interactions show an extended range of magnitudes and retardation rates, DNA interactions show an imprint of base pair composition, certain SWCNT interactions display retardation-dependent nonmonotonicity, and interactions are mapped across a range of material systems in order to facilitate rational mesoscale design.