RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited – bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure

BACKGROUND: Escherichia coli guanine-N2 (m(2)G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-terminus. Their C-terminal domain is related to the YbiN family of hypothetical MTases, but nothing is known about the structure or function of the N-terminal domain. RESULTS: Using a combination of sequence database searches and fold recognition methods it has been demonstrated that the N-termini of RsmC and RsmD are related to each other and that they represent a "degenerated" version of the C-terminal MTase domain. Novel members of the YbiN family from Archaea and Eukaryota were also indentified. It is inferred that YbiN and both domains of RsmC and RsmD are closely related to a family of putative MTases from Gram-positive bacteria and Archaea, typified by the Mj0882 protein from M. jannaschii (1dus in PDB). Based on the results of sequence analysis and structure prediction, the residues involved in cofactor binding, target recognition and catalysis were identified, and the mechanism of the guanine-N2 methyltransfer reaction was proposed. CONCLUSIONS: Using the known Mj0882 structure, a comprehensive analysis of sequence-structure-function relationships in the family of genuine and putative m(2)G MTases was performed. The results provide novel insight into the mechanism of m(2)G methylation and will serve as a platform for experimental analysis of numerous uncharacterized N-MTases

Construction of analytical many body wave functions for correlated bosons in a harmonic trap

We develop an analytical many-body wave function to accurately describe the crossover of a one-dimensional bosonic system from weak to strong interactions in a harmonic trap. The explicit wave function, which is based on the exact two-body states, consists of symmetric multiple products of the corresponding parabolic cylinder functions, and respects the analytically known limits of zero and infinite repulsion for arbitrary number of particles. For intermediate interaction strengths we demonstrate, that the energies, as well as the reduced densities of first and second order, are in excellent agreement with large scale numerical calculations.Comment: 4 pages, 2 Figure

mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships

BACKGROUND: The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis. However, a crystal structure is not available and cap 0 MTases are too diverged from other MTases of known structure to allow straightforward homology-based interpretation of these data. RESULTS: We report a 3D model of cap 0 MTase, developed using sequence-to-structure threading and comparative modeling based on coordinates of the glycine N-methyltransferase. Analysis of the predicted structural features in the phylogenetic context of the cap 0 MTase family allows us to rationalize most of the experimental data available and to propose potential binding sites. We identified a case of correlated mutations in the cofactor-binding site of viral MTases that may be important for the rational drug design. Furthermore, database searches and phylogenetic analysis revealed a novel subfamily of hypothetical MTases from plants, distinct from "orthodox" cap 0 MTases. CONCLUSIONS: Computational methods were used to infer the evolutionary relationships and predict the structure of Eukaryotic cap MTase. Identification of novel cap MTase homologs suggests candidates for cloning and biochemical characterization, while the structural model will be useful in designing new experiments to better understand the molecular function of cap MTases

3D-Fun: predicting enzyme function from structure

The ‘omics’ revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/

Explicitly correlated trial wave functions in Quantum Monte Carlo calculations of excited states of Be and Be-

We present a new form of explicitly correlated wave function whose parameters are mainly linear, to circumvent the problem of the optimization of a large number of non-linear parameters usually encountered with basis sets of explicitly correlated wave functions. With this trial wave function we succeeded in minimizing the energy instead of the variance of the local energy, as is more common in quantum Monte Carlo methods. We applied this wave function to the calculation of the energies of Be 3P (1s22p2) and Be- 4So (1s22p3) by variational and diffusion Monte Carlo methods. The results compare favorably with those obtained by different types of explicitly correlated trial wave functions already described in the literature. The energies obtained are improved with respect to the best variational ones found in literature, and within one standard deviation from the estimated non-relativistic limitsComment: 19 pages, no figures, submitted to J. Phys.

Expanding the set of rhodococcal Baeyer–Villiger monooxygenases by high-throughput cloning, expression and substrate screening

To expand the available set of Baeyer–Villiger monooxygenases (BVMOs), we have created expression constructs for producing 22 Type I BVMOs that are present in the genome of Rhodococcus jostii RHA1. Each BVMO has been probed with a large panel of potential substrates. Except for testing their substrate acceptance, also the enantioselectivity of some selected BVMOs was studied. The results provide insight into the biocatalytic potential of this collection of BVMOs and expand the biocatalytic repertoire known for BVMOs. This study also sheds light on the catalytic capacity of this large set of BVMOs that is present in this specific actinomycete. Furthermore, a comparative sequence analysis revealed a new BVMO-typifying sequence motif. This motif represents a useful tool for effective future genome mining efforts.

The closest elastic tensor of arbitrary symmetry to an elasticity tensor of lower symmetry

The closest tensors of higher symmetry classes are derived in explicit form for a given elasticity tensor of arbitrary symmetry. The mathematical problem is to minimize the elastic length or distance between the given tensor and the closest elasticity tensor of the specified symmetry. Solutions are presented for three distance functions, with particular attention to the Riemannian and log-Euclidean distances. These yield solutions that are invariant under inversion, i.e., the same whether elastic stiffness or compliance are considered. The Frobenius distance function, which corresponds to common notions of Euclidean length, is not invariant although it is simple to apply using projection operators. A complete description of the Euclidean projection method is presented. The three metrics are considered at a level of detail far greater than heretofore, as we develop the general framework to best fit a given set of moduli onto higher elastic symmetries. The procedures for finding the closest elasticity tensor are illustrated by application to a set of 21 moduli with no underlying symmetry.Comment: 48 pages, 1 figur

Reflexive adaptation for resilient water services: lessons for theory and practice

‘Adaptive management’ concern attempts to manage complex social-ecological and socio-technical systems in nimble ways to enhance their resilience. In this paper, three forms of adaptive management are identified, ‘scientific’ forms focused on collation of scientific data in response to management experiments, but more recent developments adding processes of collaboration as well as emphasising the need for reflexivity, that is, conscious processes of opening up debates to different perspectives and values. While reflexive adaptive management has been increasingly discussed in theory, there is a lack of examples of what its application means in practice. As a response, this paper examines an ‘Adaptive Planning Process’ (APP), seeking to apply reflexive adaptive management as a means to improve climate resilience in the UK water sector. The APP’s three inter linked workshops – Aspiration, Scenario and Roadmapping – were co-developed and trialled in a water utility. By describing and justifying the choices made in the development of the APP, the paper aims to reveal some of the challenges that arise when trying to design processes that achieve reflexive adaptation. The paper concludes that, if applied to planning for climate change, reflexive adaptation has the potential to explore multiple value positions, highlight different potential futures and acknowledge (and hence, partly address) power differentials, and therefore to offer the possibility of real change. On the basis of the trial, we argue that through tapping the depth and breadth of internal knowledge the APP process created the potential for decision making to be joined up across different parts of the utility, and hence offering new strategies and routes for addressing uncertainties and delivering more resilient water services

Considering scores between unrelated proteins in the search database improves profile comparison

<p>Abstract</p> <p>Background</p> <p>Profile-based comparison of multiple sequence alignments is a powerful methodology for the detection remote protein sequence similarity, which is essential for the inference and analysis of protein structure, function, and evolution. Accurate estimation of statistical significance of detected profile similarities is essential for further development of this methodology. Here we analyze a novel approach to estimate the statistical significance of profile similarity: the explicit consideration of background score distributions for each database template (subject).</p> <p>Results</p> <p>Using a simple scheme to combine and analytically approximate query- and subject-based distributions, we show that (i) inclusion of background distributions for the subjects increases the quality of homology detection; (ii) this increase is higher when the distributions are based on the scores to all known non-homologs of the subject rather than a small calibration subset of the database representatives; and (iii) these all known non-homolog distributions of scores for the subject make the dominant contribution to the improved performance: adding the calibration distribution of the query has a negligible additional effect.</p> <p>Conclusion</p> <p>The construction of distributions based on the complete sets of non-homologs for each subject is particularly relevant in the setting of structure prediction where the database consists of proteins with solved 3D structure (PDB, SCOP, CATH, etc.) and therefore structural relationships between proteins are known. These results point to a potential new direction in the development of more powerful methods for remote homology detection.</p