computational folding
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Trojrozměrné struktury proteinů je možné předpovídat tak, že vezmeme denaturovaný protein a na počítači simulujeme proces jeho sbalení. Tento článek shrnuje úspěchy i úskalí tohoto postupu, zejména využití vysoce výkonných počítačů, projektů distribuovaných výpočtů, grafických karet a specializovaných počítačů.
The three-dimensional structure of a protein can be predicted by a simulation of its folding from fully denaturated state. This article review success stories as well as pitfalls of this approach, namely applications of high performance computers, distributed computing projects, graphical processing units and specialised hardware.
The structure of proteins as well as their folding/unfolding equilibrium are commonly attributed to H-bonding and hydrophobic interactions. We have used the molecular dynamic simulations in an explicit water environment based on the standard empirical potential as well as more accurately (and thus also more reliably) on the QM/MM potential. The simulations where the dispersion term was suppressed have led to a substantial change of the tryptophan-cage protein structure (unfolded structure). This structure cannot fold without the dispersion energy term, whereas, if it is covered fully, the system finds its native structure relatively quickly. This implies that after such physical factors as temperature and pH, the dispersion energy is an important factor in protein structure determination as well as in the protein folding/unfolding equilibrium. The loss of dispersion also affected the R-helical structure. On the other hand, weakening the electrostatic interactions (and thus H-bonding) affected the R-helical structure only to a minor extent.
To be biologically active, proteins must adopt specific folded three-dimensional tertiary structures. Yet the genetic information for the proteins specifies only the primary structure, the linear sequence of amino acids in the polypeptide backbone. Many purified proteins can spontaneously refold in vitro after being completely unfolded, so the three-dimensional structure must be determined by the primary structure. How this occurs has become known as the protein-folding problem. It was primarily of academic interest, but the advent of protein engineering and the ability to produce any protein, often in an insoluble, unfolded, inactive and useless form, has made it also of great practical importance. The problem can be divided into two main questions. The first is by what kinetic process or pathway does protein adopt its native and biologically active folded conformation and the other, what is the physical basis of the stability of folded conformations. The present review summarizes the present state of knowledge of the problem and attempts to put it into perspective for what could follows.
- MeSH
- biologické modely MeSH
- Creutzfeldtova-Jakobova nemoc diagnóza MeSH
- encefalopatie bovinní spongioformní diagnóza MeSH
- konformace proteinů MeSH
- lidé MeSH
- molekulární biologie MeSH
- molekulární konformace MeSH
- proteiny diagnostické užití ultrastruktura MeSH
- sekvence aminokyselin MeSH
- techniky in vitro MeSH
- termodynamika MeSH
- výpočetní biologie MeSH
- zobrazování trojrozměrné využití MeSH
- Check Tag
- lidé MeSH
We study the folding of the designed hairpin chignolin, using simulations with four different force fields. Interestingly, we find a misfolded, out-of-register, structure comprising 20-50% of the ordered structures with three force fields, but not with a fourth. A defining feature of the misfold is that Gly-7 adopts a β(PR) conformation rather than α(L). By reweighting, we show that differences between the force fields can mostly be attributed to differences in glycine properties. Benchmarking against NMR data suggests that the preference for β(PR) is not a force-field artifact. For chignolin, we show that including the misfold in the ensemble results in back-recalculated NMR observables in slightly better agreement with experiment than parameters calculated from a folded ensemble only. For comparison, we show by NMR and circular dichroism spectroscopy that the G7K mutant of chignolin, in which formation of this misfold is impossible, is well folded with stability similar to the wild-type and does not populate the misfolded state in simulation. Our results highlight the complexity of interpreting NMR data for small, weakly structured, peptides in solution, as well as the importance of accurate glycine parameters in force fields, for a correct description of turn structures.
The pyranose 2-oxidases from Trametes ochracea and Trametes pubescens share markedly similar amino acid sequences with identity of 93.4%. When expressed from the recombinant plasmids based on the same vector in the Escherichia coli host strain BL21(DE3) at higher growth temperatures, they differ strikingly in the formation of the inclusion bodies. Upon overexpression in the cultures performed at 28 degrees C, the specific activity of pyranose 2-oxidase from T. pubescens was eight times higher than that from T. ochracea: 93% of pyranose 2-oxidase from T. ochracea and only 15% of that from T. pubescens was present in the form of inclusion bodies. To ascertain the cause of this difference, both cloned genes were shuffled. Site-directed recombination of p2o cDNAs revealed that DNA constructs ending with 3' end of p2o cDNA from T. pubescens code for proteins that are folded into an active form to the greater extent, regardless of the gene expression level. "In silicio" analysis of physico-chemical properties of the protein sequences of pyranose 2-oxidases revealed that the sequence of amino acid residues 368-430, constituting the small, head domain of pyranose 2-oxidase from T. pubescens, affects positively the enzyme folding at higher cultivation temperatures. The domain differs in six amino acid residues from that of T. ochracea.
- MeSH
- Basidiomycota enzymologie MeSH
- buněčná inkluze metabolismus MeSH
- elektroforéza v polyakrylamidovém gelu MeSH
- enzymová indukce MeSH
- Escherichia coli MeSH
- financování organizované MeSH
- karbohydrátdehydrogenasy biosyntéza chemie metabolismus MeSH
- mutageneze cílená MeSH
- rekombinace genetická genetika MeSH
- sbalování proteinů MeSH
- sekvence aminokyselin MeSH
- subcelulární frakce metabolismus MeSH
- výpočetní biologie MeSH
- vztahy mezi strukturou a aktivitou MeSH
The aeroacoustic mechanisms in human voice production are complex coupled processes that are still not fully understood. In this article, a hybrid numerical approach to analyzing sound generation in human voice production is presented. First, the fluid flow problem is solved using a parallel finite-volume computational fluid dynamics (CFD) solver on a fine computational mesh covering the larynx. The CFD simulations are run for four geometrical configurations: both with and without false vocal folds, and with fixed convergent or convergent-divergent motion of the medial vocal fold surface. Then the aeroacoustic sources and propagation of sound waves are calculated using Lighthill's analogy or acoustic perturbation equations on a coarse mesh covering the larynx, vocal tract, and radiation region near the mouth. Aeroacoustic sound sources are investigated in the time and frequency domains to determine their precise origin and correlation with the flow field. The problem of acoustic wave propagation from the larynx and vocal tract into the free field is solved using the finite-element method. Two different vocal-tract shapes are considered and modeled according to MRI vocal-tract data of the vowels /i/ and /u/. The spectra of the radiated sound evaluated from acoustic simulations show good agreement with formant frequencies known from human subjects.
- MeSH
- akustika * MeSH
- hlas * MeSH
- hlasové řasy fyziologie MeSH
- larynx fyziologie MeSH
- lidé MeSH
- vzduch * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.
- MeSH
- DNA chemie MeSH
- G-kvadruplexy * MeSH
- jednovláknová DNA chemie MeSH
- lidé MeSH
- simulace molekulární dynamiky * MeSH
- telomery chemie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.
In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson⁻Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB.
