Rotamer libraries of spin labelled cysteines for protein studies

Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.     

The colorful Helly theorem and colorful resolutions of ideals

We demonstrate that the topological Helly theorem and the algebraic Auslander-Buchsbaum theorem may be viewed as different versions of the same phenomenon. Using this correspondence we show how the colorful Helly theorem of I. Barany and its generalizations by G. Kalai and R. Meshulam translate to the algebraic side. Our main results are algebraic generalizations of these translations, which in particular give a syzygetic version of Helly’s theorem.     

The classical Wigner method with an effective quantum force: application to the collinear H + H2 reaction

To improve the classical Wigner (CW) model, we recently proposed the classical Wigner model with an effective quantum force (CWEQF). The results of the CWEQF model are more accurate than those of the CW model. Still the simplicity of the CW model is retained. The quantum force was obtained by defining a characteristic distance η(0) between two Feynman paths that enter the expression for the flux-flux correlation function. η(0) was considered independent of the position along the reaction path. The CWEQF leads to a lowering of the effective potential barrier. Here we develop the method to use position dependent η(0) values. The method is also generalized to two dimensions. Applications are carried out on one-dimensional model problems and the two-dimensional H + H(2) collinear reaction.     

Adsorption of trimethyl phosphate on maghemite, hematite, and goethite nanoparticles

Adsorption of trimethyl phosphate (TMP) on well-characterized hematite, maghemite and goethite nanoparticles was studied by in situ DRIFT spectroscopy as a model system for adsorption of organophosphorous (OP) compounds on iron minerals. The iron minerals were characterized by X-ray diffraction (XRD), Raman spectroscopy, transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), specific surface area, and pore size distribution. The minerals were found to consist of stoichimetrically and morphologically well-defined maghemite, hematite, and goethite nanoparticles. Analysis of in situ diffuse reflectance Fourier transform (DRIFT) spectroscopy shows that TMP bonds mainly to Lewis acid Fe sites through the O phosphoryl atom (-P═O-Fe) on hematite and maghemite. On goethite most TMP molecules bond to Br?nstedt acid surface OH groups and form hydrogen bonded surface complexes. The vibrational mode analysis and uptake kinetics suggest two main reasons for the observed trend of reactivity toward TMP (hematite > maghemite > goethite): (i) larger number of accessible Lewis acid adsorption sites on hematite; (ii) stronger interaction between the Lewis acid Fe sites and the phosphoryl O atom on TMP for hematite and maghemite compared to goethite with concomitant formation of surface coordinated TMP and dimethyl phosphate intermediates. As a result, on the oxides a surface oxidation pathway dominates during the initial adsorption, which results in the formation of surface methoxy and formate. In contrast, on goethite a slower hydrolysis pathway is identified, which eventually yields phosphoric acid. The observed trends of the reactivity and analysis of the corresponding surface structure and particle morphology suggest an intimate relation between the surface chemistry of exposed crystal facets on the iron minerals. These results are important to understand OP surface chemistry on iron minerals.     

Haloperoxidase activity of oxovanadium(V) thiobisphenolates

By employing the 2,2'-thiobis(2,4-di-tert-butylphenolate) ligand ((S)L(2-)) a novel oxovanadium(V) complex, (PPh(4))(2)[(S)LV(O)(μ(2)-O)(2)V(O)(S)L] (1), was synthesised that exhibits haloperoxidase activity: on addition of H(2)O(2) a sequence of successive peroxide formation and intramolecular thioether oxidation events (sulfoxide and sulfone) led to a mixture of five products, which were all identified unambiguously, partly through an independent synthesis and characterisation. It was shown that internal thioether oxidation proceeds through peroxide formation, but the sulfoxidation of external thioether functions requires further activation of the peroxide function by protons or alkyl cations. Consistently, the employment of tBuOOH instead of H(2)O(2) led to a very active system for the catalytic sulfoxidation of thioethers.     

Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal dali alignments for the very first time.     

A short and efficient error correcting code for polarization coded photonic qubits in a dissipative channel

We propose a short and efficient non-degenerate quantum error correcting code that is adapted for qubits encoded on two orthogonal, single-photon states (e.g., horizontally and vertically polarized) subject to a dissipative channel.The proposed code draws its strength from the fact that it is adapted to the physical characteristics of the information-carrying basis states under the action of the channel. The code combines different energy manifolds and consists of only 3 spatio-temporal modes and on average 2 photons per code word.     

On column generation approaches for approximate solutions of quadratic programs in intensity-modulated radiation therapy

This paper deals with numerical behavior of a recently presented column generation approach for optimization of so called step-and-shoot radiotherapy treatment plans. The approach and variants of it have been reported to be efficient in practice, finding near-optimal solutions by generating only a low number of columns. The impact of different restrictions on the columns in a column generation method is studied, and numerical results are given for quadratic programs corresponding to three patient cases. In particular, it is noted that with a bound on the two-norm of the columns, the method is equivalent to the conjugate-gradient method. Further, the above-mentioned column generation approach for radiotherapy is obtained by employing a restriction based on the infinity-norm and non-negativity. The column generation method has weak convergence properties if restricted to generating feasible step-and-shoot plans, with a “tailing-off” effect for the objective values. However, the numerical results demonstrate that, like the conjugate-gradient method, a rapid decrease of the objective value is obtained in the first few iterations. For the three patient cases, the restriction on the columns to generate feasible step-and-shoot plans has small effect on the numerical efficiency.     

The review of advances in interfacial electrochemistry in Estonia: electrochemical double layer and adsorption studies for the development of electrochemical devices

The electrochemistry nowadays has many faces and challenges. Although the focus has shifted from fundamental electrochemistry to applied electrochemistry, one needs to acknowledge that it is impossible to develop and design novel green energy transition devices without a comprehensive understanding of the electrochemical processes at the electrode and electrolyte interface that define the performance mechanisms. The review gives an overview of the systematic research in the field of electrochemistry in Estonia which reflects on the excellent collaboration between fundamental and applied electrochemistry.

     

Design of Drug Efficacy Guided by Free Energy Simulations of the β2-Adrenoceptor

G-protein-coupled receptors (GPCRs) play important roles in physiological processes and are modulated by drugs that either activate or block signaling. Rational design of the pharmacological efficacy profiles of GPCR ligands could enable the development of more efficient drugs, but is challenging even if high-resolution receptor structures are available. We performed molecular dynamics simulations of the β₂ adrenergic receptor in active and inactive conformations to assess if binding free energy calculations can predict differences in ligand efficacy for closely related compounds. Previously identified ligands were successfully classified into groups with comparable efficacy profiles based on the calculated shift in ligand affinity upon activation. A series of ligands were then predicted and synthesized, leading to the discovery of partial agonists with nanomolar potencies and novel scaffolds. Our results demonstrate that free energy simulations enable design of ligand efficacy and the same approach can be applied to other GPCR drug targets.