Editorial: Structural and Dynamic Aspects of Protein Function and Allostery

Editorial on the Research Topi

Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways

Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids. In this work, we establish the eigenvector centrality metric in terms of the mutual information, as a mean of elucidating the allosteric mechanism that regulates the enzymatic activity of proteins. Moreover, we propose a strategy to characterize the range of the physical interactions that underlie the allosteric process. In particular, the well known enzyme, imidazol glycerol phosphate synthase (IGPS), is utilized to test the proposed methodology. The eigenvector centrality measurement successfully describes the allosteric pathways of IGPS, and allows to pinpoint key amino acids in terms of their relevance in the momentum transfer process. The resulting insight can be utilized for refining the control of IGPS activity, widening the scope for its engineering. Furthermore, we propose a new centrality metric quantifying the relevance of the surroundings of each residue. In addition, the proposed technique is validated against experimental solution NMR measurements yielding fully consistent results. Overall, the methodologies proposed in the present work constitute a powerful and cost effective strategy to gain insight on the allosteric mechanism of proteins

The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations

A computational protocol based on the complete and restricted active space self-consistent field (CASSCF/RASSCF) methods and their second-order perturbation theory extensions (CASPT2/RASPT2) is employed to benchmark the highly excited-state manifold of the DNA/RNA canonical purine nucleobase guanine in vacuo. Several RASPT2 schemes are tested, displaying a steady convergence of electronic transition energies and dipole moments upon active space enlargement toward the reference values. The outcome allows calibrating and optimizing computational efforts by considering cheaper and more approximate RAS schemes that could enable the characterization of the excited-state manifolds of multi-chromophoric systems, such as DNA/RNA nucleobase dimers or multimers. Simulations of two-dimensional electronic spectra show similar trends to those observed on the other purine nucleobase adenine, deviating from this and other pyrimidine nucleobases in featuring its main excited-state absorption signal, embodied by sizable double HOMO to LUMO excitation contributions, in the UV probing window

Elucidating the activation mechanism of AMPK by direct pan-activator PF-739

Adenosine monophosphate-activated protein kinase (AMPK) is a key energy sensor regulating the cell metabolism in response to energy supply and demand. The evolutionary adaptation of AMPK to different tissues is accomplished through the expression of distinct isoforms that can form up to 12 heterotrimeric complexes, which exhibit notable differences in the sensitivity to direct activators. To comprehend the molecular factors of the activation mechanism of AMPK, we have assessed the changes in the structural and dynamical properties of b1- and b2-containing AMPK complexes formed upon binding to the pan-activator PF-739. The analysis revealed the molecular basis of the PF-739-mediated activation of AMPK and enabled us to identify distinctive features that may justify the slightly higher affinity towards the b1-isoform, such as the b1-Asn111 to b2-Asp111 substitution, which seems to be critical for modulating the dynamical sensitivity of b1- and b2 isoforms. The results are valuable in the design of selective activators to improve the tissue specificity of therapeutic treatment

Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9

CRISPR-Cas9 is a genome editing technology with major impact in life sciences. In this system, the endonuclease Cas9 generates double strand breaks in DNA upon RNA-guided recognition of a complementary DNA sequence, which strictly requires the presence of a protospacer adjacent motif (PAM) next to the target site. Although PAM recognition is essential for cleavage, it is unknown whether and how PAM binding activates Cas9 for DNA cleavage at spatially distant sites. Here, we find evidence of a PAM-induced allosteric mechanism revealed by microsecond molecular dynamics simulations. PAM acts as an allosteric effector and triggers the interdependent conformational dynamics of the Cas9 catalytic domains (HNH and RuvC), responsible for concerted cleavage of the two DNA strands. Targeting such an allosteric mechanism should enable control of CRISPR-Cas9 functionality

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy

By comparing two-dimensional electronic spectroscopy (2DES) and Pump-Probe (PP) measurements on xanthorhodopsin (XR) and reduced-xanthorhodopsin (RXR) complexes, the ultrafast carotenoid-to-retinal energy transfer pathway is revealed, at very early times, by an excess of signal amplitude at the associated cross-peak and by the carotenoid bleaching reduction due to its ground state recovery. The combination of the measured 2DES and PP spectroscopic data with theoretical modelling allows a clear identification of the main experimental signals and a comprehensive interpretation of their origin and dynamics. The remarkable velocity of the energy transfer, despite the non-negligible energy separation between the two chromophores, and the analysis of the underlying transport mechanism, highlight the role played by the ground state carotenoid vibrations in assisting the process

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations