Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides.

Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational exchange. Here, a framework is presented that predicts Raman spectra using mixtures of sub-spectra corresponding to major conformers calculated using classical and ab initio molecular dynamics. Experimental optimization allowed purines and pyrimidines to be characterized as predominantly syn and anti, respectively, and ribose into exchange between equivalent south and north populations. These measurements are in excellent agreement with Raman spectroscopy of ribonucleosides, and previous experimental and computational results. This framework provides a measure of ribonucleoside solution populations and conformational exchange in RNA subunits. It complements other experimental techniques and could be extended to other molecules, such as proteins and carbohydrates, enabling biological insights and providing a new analytical tool.

Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase.

Catechol-O-methyltransferase (COMT) is a model S-adenosyl-l-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal-derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site "compaction", which is driven by electrostatic stabilization between the transferring methyl group and "equatorial" active site residues that are orthogonal to the donor-acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor-acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via "equatorial" H-bonding and electrostatic interactions orthogonal to the donor-acceptor coordinate.

Does the Intra-atomic Deformation Energy of Interacting Quantum Atoms Represent Steric Energy?

Invited for this month's cover picture is the group of Paul L. A. Popelier from Manchester Institute of Biotechnology (UK). The cover picture shows the quantum topological atoms in a configuration of the complex HF⋅⋅⋅OH2, where F is green and O is red. Read the full text of their Full Paper at 10.1002/open.201800275.

Does the Intra-Atomic Deformation Energy of Interacting Quantum Atoms Represent Steric Energy?

We show that the mutual, through-space compression of atomic volume experienced by approaching topological atoms causes an exponential increase in the intra-atomic energy of those atoms, regardless of approach orientation. This insight was obtained using the modern energy partitioning method called interacting quantum atoms (IQA). This behaviour is consistent for all atoms except hydrogen, which can behave differently depending on its environment. Whilst all atoms experience charge transfer when they interact, the intra-atomic energy of the hydrogen atom is more vulnerable to these changes than larger atoms. The difference in behaviour is found to be due to hydrogen's lack of a core of electrons, which, in heavier atoms, consistently provide repulsion when compressed. As such, hydrogen atoms do not always provide steric hindrance. In accounting for hydrogen's unusual behaviour and demonstrating the exponential character of the intra-atomic energy in all other atoms, we provide evidence for IQA's intra-atomic energy as a quantitative description of steric energy.

Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models.

A new type of model, FFLUX, to describe the interaction between atoms has been developed as an alternative to traditional force fields. FFLUX models are constructed by applying the kriging machine learning method to the topological energy partitioning method, interacting quantum atoms (IQA). The effect of varying parameters in the construction of the FFLUX models is analyzed, with the most dominant effects found to be the structure of the molecule and the number of conformations used to build the model. Using these models, the optimization of a variety of small organic molecules is performed, with sub kJ mol-1 accuracy in the energy of the optimized molecules. The FFLUX models are also evaluated in terms of their performance in describing the potential energy surfaces (PESs) associated with specific degrees of freedoms within molecules. While the accurate description of PESs presents greater challenges than individual minima, FFLUX models are able to achieve errors of <2.5 kJ mol-1 across the full C-C-C-C dihedral PES of n-butane, indicating the future possibilities of the technique.

Exponential Relationships Capturing Atomistic Short-Range Repulsion from the Interacting Quantum Atoms (IQA) Method.

A topological atom is a quantum object with a well-defined intra-atomic energy, which includes kinetic energy, Coulomb energy, and exchange energy. In the context of intermolecular interactions, this intra-atomic energy is calculated from supermolecular wave functions, by using the topological partitioning. This partitioning is parameter-free and invokes only the electron density to obtain the topological atoms. In this work, no perturbation theory is used; instead, a single wave function describes the behavior of all van der Waals complexes studied. As the monomers approach each other, frontier atoms deform, which can be monitored through a change in their shape and volume. Here we show that the corresponding atomic deformation energy is very well described by an exponential function, which matches the well-known Buckingham repulsive potential. Moreover, we recover a combination rule that enables the interatomic repulsion energy between topological atoms A and B to be expressed as a function of the interatomic repulsion energy between A and A on one hand, and between B and B on the other hand. As a result a link is established between quantum topological atomic energies and classical well-known interatomic repulsive potentials.