A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds

This work was financially supported by ETH Zürich, University of Minnesota, the Swiss National Science Foundation (grant nos. 31003A_149512 and 200021–159713), Wellcome Trust (094476/Z/10/Z), ERC (NCB-TNT 339367), and BBSRC (BB/R018189/1).The peptide bond, the defining feature of proteins, governs peptide chemistry by abolishing nucleophilicity of the nitrogen. This and the planarity of the peptide bond arise from the delocalization of the lone pair of electrons on the nitrogen atom into the adjacent carbonyl. While chemical methylation of an amide bond uses a strong base to generate the imidate, OphA, the precursor protein of the fungal peptide macrocycle omphalotin A, self-hypermethylates amides at pH 7 using S-adenosyl methionine (SAM) as cofactor. The structure of OphA reveals a complex catenane-like arrangement in which the peptide substrate is clamped with its amide nitrogen aligned for nucleophilic attack on the methyl group of SAM. Biochemical data and computational modeling suggest a base-catalyzed reaction with the protein stabilizing the reaction intermediate. Backbone N-methylation of peptides enhances their protease resistance and membrane permeability, a property that holds promise for applications to medicinal chemistry.Publisher PDFPeer reviewe

Standardized Definitions for Bioprosthetic Valve Dysfunction Following Aortic or Mitral Valve Replacement: JACC State-of-the-Art Review.

peer reviewedBioprosthetic valve dysfunction (BVD) and bioprosthetic valve failure (BVF) may be caused by structural or nonstructural valve dysfunction. Both surgical and transcatheter bioprosthetic valves have limited durability because of structural valve deterioration. The main objective of this summary of experts participating in a virtual workshop was to propose standardized definitions for nonstructural and structural BVD and BVF following aortic or mitral biological valve replacement with the goal of facilitating research reporting and implementation of these terms in clinical practice. Definitions of structural BVF, based on valve reintervention or death, underestimate the true incidence of BVF. However, definitions solely based on the presence of high transprosthetic gradient at a given echocardiogram during follow-up overestimate the incidence of structural BVD and BVF. Definitions of aortic or mitral structural BVD must therefore include the confirmation by imaging of permanent structural changes to the leaflets alongside evidence of deterioration in valve hemodynamic function at echocardiography follow-up

Efficient self-consistent treatment of electron correlation within the random phase approximation

A self-consistent Kohn-Sham (KS) method is presented that treats correlation on the basis of the adiabatic-connection dissipation-fluctuation theorem employing the direct random phase approximation (dRPA), i.e., taking into account only the Coulomb kernel while neglecting the exchange-correlation kernel in the calculation of the Kohn-Sham correlation energy and potential. The method, denoted self-consistent dRPA method, furthermore treats exactly the exchange energy and the local multiplicative KS exchange potential. It uses Gaussian basis sets, is reasonably efficient, exhibiting a scaling of the computational effort with the forth power of the system size, and thus is generally applicable to molecules. The resulting dRPA correlation potentials in contrast to common approximate correlation potentials are in good agreement with exact reference potentials. The negatives of the eigenvalues of the highest occupied molecular orbitals are found to be in good agreement with experimental ionization potentials. Total energies from self-consistent dRPA calculations, as expected, are even poorer than non-self-consistent dRPA total energies and dRPA reaction and non-covalent binding energies do not significantly benefit from self-consistency. On the other hand, energies obtained with a recently introduced adiabatic-connection dissipation-fluctuation approach (EXXRPA+, exact-exchange random phase approximation) that takes into account, besides the Coulomb kernel, also the exact frequency-dependent exchange kernel are significantly improved if evaluated with orbitals obtained from a self-consistent dRPA calculation instead of an exact exchange-only calculation. Total energies, reaction energies, and noncovalent binding energies obtained in this way are of the same quality as those of high-level quantum chemistry methods, like the coupled cluster singles doubles method which is computationally more demanding

Resolution of identity approach for the Kohn-Sham correlation energy within the exact-exchange random-phase approximation

Two related methods to calculate the Kohn-Sham correlation energy within the framework of the adiabatic-connection fluctuation-dissipation theorem are presented. The required coupling-strength-dependent density-density response functions are calculated within exact-exchange time-dependent density-functional theory, i.e., within time-dependent density-functional response theory using the full frequency-dependent exchange kernel in addition to the Coulomb kernel. The resulting resolution-of-identity exact-exchange random-phase approximation (RI-EXXRPA) methods in contrast to previous EXXRPA methods employ an auxiliary basis set (RI basis set) to improve the computational efficiency, in particular, to reduce the formal scaling of the computational effort with respect to the system size N from N6 to N5. Moreover, the presented RI-EXXRPA methods, in contrast to previous ones, do not treat products of occupied times unoccupied orbitals as if they were linearly independent. Finally, terms neglected in previous EXXRPA methods can be included, which leads to a method designated RI-EXXRPA+, while the method without these extra terms is simply referred to as RI-EXXRPA. Both EXXRPA methods are shown to yield total energies, reaction energies of small molecules, and binding energies of noncovalently bonded dimers of a quality that is similar and in some cases even better than that obtained with quantum chemistry methods such as Møller-Plesset perturbation theory of second order (MP2) or with the coupled cluster singles doubles method. In contrast to MP2 and to conventional density-functional methods, the presented RI-EXXRPA methods are able to treat static correlation

Beyond the Rosenfeld Equation: Computation of Vibrational Circular Dichroism Spectra for Anisotropic Solutions

ISSN:1549-9618ISSN:1549-962

Correction to “Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations”

Correction to “Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations

Milk supply problems in tropical Africa - Economic trends

Data on milk production, and consumption and import of dairy products in tropical Africa, w. ref. to development constraints of dairy industry, milk prices and development policies

Correction to “Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations”

Correction to “Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations

Hydrogen storage on metal oxide model clusters using density-functional methods and reliable van der Waals corrections

We investigate the capability of low-coordinated sites on small model clusters to act as active centers for hydrogen storage. A set of small magic clusters with the formula (XY)6 (X = Mg, Ba, Be, Zn, Cd, Na, Li, B and Y = O, Se, S, F, I, N) and a “drumlike” hexagonal shape showing a low coordination number of three was screened. Oxide clusters turned out to be the most promising candidates for hydrogen storage. For these ionic compounds we explored the suitability of different van der Waals (vdW) corrections to density-functional calculations by comparing the respective H2 physisorption profile to highly accurate CCSD(T) (Coupled Cluster Singles Doubles with perturbative Triples) calculations. The Grimme D3 vdW correction in combination with the Perdew–Burke–Ernzerhof exchange–correlation functional was found to be the best approach compared to CCSD(T) hydrogen physisorption profiles and is, therefore, suited to study these and other light metal oxide systems. H2 adsorption on sites of oxide model clusters is found to meet the adsorption energy criteria for H2 storage, with bond strengths ranging from 0.15 to 0.21 eV. Energy profiles and estimates of kinetic constants for the H2 splitting reaction reveal that H2 is likely to be adsorbed molecularly on sites of (MgO)6, (BaO)6, and (BeO)6 clusters, suggesting a rapid H2 uptake/release at operating temperatures and moderate pressures. The small mass of beryllium and magnesium makes such systems appealing for meeting the gravimetric criterion for H2 storage

Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations

Parametrization of small organic molecules for classical molecular dynamics simulations is not trivial. The vastness of the chemical space makes approaches using building blocks challenging. The most common approach is therefore an individual parametrization of each compound by deriving partial charges from semiempirical or ab initio calculations and inheriting the bonded and van der Waals (Lennard-Jones) parameters from a (bio)­molecular force field. The quality of the partial charges generated in this fashion depends on the level of the quantum-chemical calculation as well as on the extraction procedure used. Here, we present a machine learning (ML) based approach for predicting partial charges extracted from density functional theory (DFT) electron densities. The training set was chosen with the goal to provide a broad coverage of the known chemical space of druglike molecules. In addition to the speed of the approach, the partial charges predicted by ML are not dependent on the three-dimensional conformation in contrast to the ones obtained by fitting to the electrostatic potential (ESP). To assess the quality and compatibility with standard force fields, we performed benchmark calculations for the free energy of hydration and liquid properties such as density and heat of vaporization