Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.

The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes

Vacancies in graphene: an application of adiabatic quantum optimization

Quantum annealers have grown in complexity to the point that quantum computations involving few thousands of qubits are now possible. In this paper, \textcolor{black}{with the intentions to show the feasibility of quantum annealing to tackle problems of physical relevance, we used a simple model, compatible with the capability of current quantum annealers, to study} the relative stability of graphene vacancy defects. By mapping the crucial interactions that dominate carbon-vacancy interchange onto a quadratic unconstrained binary optimization problem, our approach exploits \textcolor{black}{the ground state as well the excited states found by} the quantum annealer to extract all the possible arrangements of multiple defects on the graphene sheet together with their relative formation energies. This approach reproduces known results and provides a stepping stone towards applications of quantum annealing to problems of physical-chemical interest

The Enactive Didactics for Enactive Mind:The Evolution of a Learning Model

The term "enactive mind " comes from the Varela work and the concept of "activation " underlines. Approach you enactive involves two concepts: from a side than the perception he consists in an action to his time driven by the perception coming from that action date and from the other but the cognitive structures they emerge from the recurring sensory- motor schemes which allow the action to be perceptively driven. In the specific one, approach him EM places like a frame to frame a series of phenomena considered essential for the comprehension of the concept of adaptation as social as the necessity of considering the relation world complexity as, the importing time constraints present in it, the nature and the modes in which mechanisms of this adaptation allow the formation of the social knowledge. In the EM approach the child "activates the social world " selectively perceiving it in the terms of what which is immediately essential for a social action, while the mental representations (the social knowledge) of this individualized world build themselves based on the repeated experiences ripened by these actions driven by the perception, become then deeply you root in the history of relational actions of the child to be tools for the adaptation to the world in which alive. The enactive vision, although it recalls in the meaning the concept of representation as mode to know, tries to exceed it in favor of the corporeality, that is an incorporate mind (embodied mind). A corollary of this theory is that subject

Investigating the Chinese Postman Problem on a Quantum Annealer

The recent availability of quantum annealers has fueled a new area of information technology where such devices are applied to address practically motivated and computationally difficult problems with hardware that exploits quantum mechanical phenomena. D-Wave annealers are promising platforms to solve these problems in the form of quadratic unconstrained binary optimization. Here we provide a formulation of the Chinese postman problem that can be used as a tool for probing the local connectivity of graphs and networks. We treat the problem classically with a tabu algorithm and using a D-Wave device. We systematically analyze computational parameters associated with the specific hardware. Our results clarify how the interplay between the embedding due to limited connectivity of the Chimera graph, the definition of logical qubits, and the role of spin-reversal controls the probability of reaching the expected solution

Unraveling the Mechanism of Tip-Enhanced Molecular Energy Transfer

Electronic Energy Transfer (EET) between chromophores is fundamental in many natural light-harvesting complexes, serving as a critical step for solar energy funneling in photosynthetic plants and bacteria. The complicated role of the environment in mediating this process in natural architectures has been addressed by recent scanning tunneling microscope (STM) experiments involving EET between two molecules supported on a solid substrate [Cao, S. et al., Nat. Chem. 2021, 13, 766-770]. These measurements demonstrated that EET in such conditions has peculiar features, such as a steep dependence on the donor-acceptor distance, reminiscent of a short-range mechanism more than of a Forster-like process. By using state of the art hybrid ab initio electromagnetic modeling, here we provide a comprehensive theoretical analysis of tip-enhanced EET. In particular, we show that this process can be understood as a complex interplay of electromagnetic-based molecular plasmonic processes, whose result may effectively mimic short range effects. Therefore, the established identification of an exponential decay with Dexter-like effects does not hold for tip-enhanced EET, and accurate electromagnetic modeling is needed to identify the EET mechanism

the interaction of peptides and proteins with nanostructures surfaces a challenge for nanoscience

Abstract The impact of nanotechnologies in biomedicine and biotechnology is becoming more and more evident. It imposes practical challenges, for instance, raising specific issues on the biocompatibility of nanostructures. Nanoparticles are characterized by a high surface-to-volume ratio, which makes them reactive to foreign species. Thus, when proteins or peptides approach an inorganic nanoparticle, as well as a flat surface, they are likely to interact with the substrate to some extent. This interaction is crucial for applications in drug delivery, imaging, diagnostics, implants, and other medical devices. Specifically, gold nanoparticles are highly versatile and particularly appealing. It is widely accepted that the surfaces of nanoparticles adsorb proteins either transiently in the soft corona layer or permanently in the hard corona layer. As a consequence, the protein structure and/or function may undergo profound adjustments or remain conserved. Detailing the interaction of different inorganic substrates with proteins and peptides at the atomic level, and designing ways to control the interaction, is the key for biomedical applications of nanoparticles, both from a fundamental viewpoint and for practical implementations. In the last decade, we have addressed protein–nanoparticle interactions, focusing on interfaces of gold surfaces and nanoparticles with amyloidogenic peptides and protein models. We have developed classical force fields, performed advanced molecular dynamics simulations, and compared computational outcomes with data from nuclear magnetic resonance experiments. Protein–gold complexes with differently coated gold nanoparticles have been modeled to explore the effects of charge and size on the protein structure. Our work unravels that a complex interplay between surface properties and characteristics of the biological adsorbate determines whether peptide conformation is influenced and whether protein aggregation is accelerated or inhibited by the presence of the substrate. General guidelines to cope with amyloidogenic proteins could be inferred: these can be essentially summarized with the necessity of balancing the hydrophobic and electrostatic interactions that the amyloidogenic proteins establish with the coating moieties