17 research outputs found
MODOMICS: a database of RNA modification pathways
MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data. The current list of modifications and pathways is comprehensive, while the dataset of enzymes is limited to Escherichia coli and Saccharomyces cerevisiae and sequence alignments are presented only for tRNAs from these organisms. RNAs and enzymes from other organisms will be included in the near future. MODOMICS can be queried by the type of nucleoside (e.g. A, G, C, U, I, m(1)A, nm(5)s(2)U, etc.), type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.) and name or sequence of an enzyme of interest. Options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literature data. The contents of MODOMICS can be accessed through the World Wide Web at
MetaMQAP: A meta-server for the quality assessment of protein models
Abstract Background Computational models of protein structure are usually inaccurate and exhibit significant deviations from the true structure. The utility of models depends on the degree of these deviations. A number of predictive methods have been developed to discriminate between the globally incorrect and approximately correct models. However, only a few methods predict correctness of different parts of computational models. Several Model Quality Assessment Programs (MQAPs) have been developed to detect local inaccuracies in unrefined crystallographic models, but it is not known if they are useful for computational models, which usually exhibit different and much more severe errors. Results The ability to identify local errors in models was tested for eight MQAPs: VERIFY3D, PROSA, BALA, ANOLEA, PROVE, TUNE, REFINER, PROQRES on 8251 models from the CASP-5 and CASP-6 experiments, by calculating the Spearman's rank correlation coefficients between per-residue scores of these methods and local deviations between C-alpha atoms in the models vs. experimental structures. As a reference, we calculated the value of correlation between the local deviations and trivial features that can be calculated for each residue directly from the models, i.e. solvent accessibility, depth in the structure, and the number of local and non-local neighbours. We found that absolute correlations of scores returned by the MQAPs and local deviations were poor for all methods. In addition, scores of PROQRES and several other MQAPs strongly correlate with 'trivial' features. Therefore, we developed MetaMQAP, a meta-predictor based on a multivariate regression model, which uses scores of the above-mentioned methods, but in which trivial parameters are controlled. MetaMQAP predicts the absolute deviation (in Ångströms) of individual C-alpha atoms between the model and the unknown true structure as well as global deviations (expressed as root mean square deviation and GDT_TS scores). Local model accuracy predicted by MetaMQAP shows an impressive correlation coefficient of 0.7 with true deviations from native structures, a significant improvement over all constituent primary MQAP scores. The global MetaMQAP score is correlated with model GDT_TS on the level of 0.89. Conclusion Finally, we compared our method with the MQAPs that scored best in the 7th edition of CASP, using CASP7 server models (not included in the MetaMQAP training set) as the test data. In our benchmark, MetaMQAP is outperformed only by PCONS6 and method QA_556 – methods that require comparison of multiple alternative models and score each of them depending on its similarity to other models. MetaMQAP is however the best among methods capable of evaluating just single models. We implemented the MetaMQAP as a web server available for free use by all academic users at the URL https://genesilico.pl/toolkit/</p
FILTREST3D: discrimination of structural models using restraints from experimental data
Summary: Automatic methods for macromolecular structure prediction (fold recognition, de novo folding and docking programs) produce large sets of alternative models. These large model sets often include many native-like structures, which are often scored as false positives. Such native-like models can be more easily identified based on data from experimental analyses used as structural restraints (e.g. identification of nearby residues by cross-linking, chemical modification, site-directed mutagenesis, deuterium exchange coupled with mass spectrometry, etc.). We present a simple server for scoring and ranking of models according to their agreement with user-defined restraints
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
Intrinsically disordered proteins
(IDPs) are notoriously challenging
to study both experimentally and computationally. The structure of
IDPs cannot be described by a single conformation but must instead
be described as an ensemble of interconverting conformations. Atomistic
simulations are increasingly used to obtain such IDP conformational
ensembles. Here, we have compared the IDP ensembles generated by eight
all-atom empirical force fields against primary small-angle X-ray
scattering (SAXS) and NMR data. Ensembles obtained with different
force fields exhibit marked differences in chain dimensions, hydrogen
bonding, and secondary structure content. These differences are unexpectedly
large: changing the force field is found to have a stronger effect
on secondary structure content than changing the entire peptide sequence.
The CHARMM 22* ensemble performs best in this force field comparison:
it has the lowest error in chemical shifts and J-couplings and agrees
well with the SAXS data. A high population of left-handed α-helix
is present in the CHARMM 36 ensemble, which is inconsistent with measured
scalar couplings. To eliminate inadequate sampling as a reason for
differences between force fields, extensive simulations were carried
out (0.964 ms in total); the remaining small sampling uncertainty
is shown to be much smaller than the observed differences. Our findings
highlight how IDPs, with their rugged energy landscapes, are highly
sensitive test systems that are capable of revealing force field deficiencies
and, therefore, contributing to force field development
Structural Basis for Efficient Chromophore Communication and Energy Transfer in a Constructed Didomain Protein Scaffold
The construction of useful functional biomolecular components
not
currently part of the natural repertoire is central to synthetic biology.
A new light-capturing ultra-high-efficiency energy transfer protein
scaffold has been constructed by coupling the chromophore centers
of two normally unrelated proteins: the autofluorescent protein enhanced
green fluorescent protein (EGFP) and the heme-binding electron transfer
protein cytochrome <i>b</i><sub>562</sub> (cyt <i>b</i><sub>562</sub>). Using a combinatorial domain insertion strategy,
a variant was isolated in which resonance energy transfer from the
donor EGFP to the acceptor cyt <i>b</i><sub>562</sub> was
close to 100% as evident by virtually full fluorescence quenching
on heme binding. The fluorescence signal of the variant was also sensitive
to the reactive oxygen species H<sub>2</sub>O<sub>2</sub>, with high
signal gain observed due to the release of heme. The structure of
oxidized holoprotein, determined to 2.75 Ã… resolution, revealed
that the two domains were arranged side-by-side in a V-shape conformation,
generating an interchromophore distance of ∼17 Å (14 Å
edge-to-edge). Critical to domain arrangement is the formation of
a molecular pivot point between the two domains as a result of different
linker sequence lengths at each domain junction and formation of a
predominantly polar interdomain interaction surface. The retrospective
structural analysis has provided an explanation for the basis of the
observed highly efficient energy transfer through chromophore arrangement
in the directly evolved protein scaffold and provides an insight into
the molecular principles by which to design new proteins with coupled
functions