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.
Frontiers in molecular biology
2nd ed. xxvi, 433 s. : il.
- MeSH
- sbalování proteinů MeSH
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- biologie
- biochemie
- MeSH
- chaperoniny chemie MeSH
- hydrofobní a hydrofilní interakce MeSH
- metabolické sítě a dráhy MeSH
- oxygenasy chemie MeSH
- proteindisulfidisomerasy chemie MeSH
- sbalování proteinů * MeSH
- sekundární struktura proteinů MeSH
- stabilita proteinů MeSH
- statická elektřina MeSH
- vodíková vazba MeSH
- Publikační typ
- přehledy MeSH
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
[1st ed.] 5 sv. : il.
- MeSH
- membránové proteiny MeSH
- molekulární chaperony MeSH
- prionové nemoci patofyziologie MeSH
- proteiny MeSH
- referenční knihy MeSH
- sbalování proteinů MeSH
- Publikační typ
- příručky MeSH
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- biochemie
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.
Life on Earth depends on photosynthesis, the conversion of light energy into chemical energy. Plants collect photons by light harvesting complexes (LHC)-abundant membrane proteins containing chlorophyll and xanthophyll molecules. LHC-like proteins are similar in their amino acid sequence to true LHC antennae, however, they rather serve a photoprotective function. Whether the LHC-like proteins bind pigments has remained unclear. Here, we characterize plant LHC-like proteins (LIL3 and ELIP2) produced in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). Both proteins were associated with chlorophyll a (Chl) and zeaxanthin and LIL3 was shown to be capable of quenching Chl fluorescence via direct energy transfer from the Chl Qy state to zeaxanthin S1 state. Interestingly, the ability of the ELIP2 protein to quench can be acquired by modifying its N-terminal sequence. By employing Synechocystis carotenoid mutants and site-directed mutagenesis we demonstrate that, although LIL3 does not need pigments for folding, pigments stabilize the LIL3 dimer.
- MeSH
- chlorofyl metabolismus MeSH
- karotenoidy metabolismus MeSH
- multimerizace proteinu MeSH
- mutace MeSH
- přenos energie MeSH
- proteiny chloroplastové chemie genetika metabolismus MeSH
- proteiny huseníčku chemie genetika metabolismus MeSH
- sbalování proteinů MeSH
- Synechocystis genetika metabolismus MeSH
- vazba proteinů MeSH
- xanthofyly metabolismus MeSH
- zeaxanthiny genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
