SciCombinator

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Concept: Folding

28

Novel enantiopure pseudopeptide models containing a central -(beta-lactam)-(Aa)- scaffold characterized by the combined presence of an alpha-alkyl-alpha-amino-beta-lactam (i+1) residue and a alpha-substituted (i+2) amino acid have been readily synthesized from alpha-alkyl serines. The conformational analysis of such beta-lactam pseudopeptides conducted in CDCl3 and DMSOd6 solutions using 1D and 2D-NMR techniques revealed an equilibrium between beta-II turn and gamma-turn conformers, which was ultimately modulated by the relative configuration of the -(beta-lactam)-(Aa)- residues. Long range chiral effects on the alpha-lactam pseudopeptide conformers were also found when two (i) and (i+3) chiral residues were attached to the termini of a central -(beta-lactam)-(Aib)- segment. In such mimetics, heterochiral (i) and (i+3) residues reinforced a beta-II turn conformer, whereas homochiral corner residues stabilized an overlapped beta-II/ beta-I double turn motif. No beta-hairpin nucleation was observed in any instance. In good agreement with the conformers found in solution, beta-turned and open structures were also characterized by X-ray crystallography. Relative stabilities of the different conformers were estimated computationally at a B3LYP/6-31++G** calculation level and, finally, a conformation equilibrium model based on steric inter-residual interactions around the -(beta-lactam)-(i+2)- segment was proposed to account for the observed chiral effects.

Concepts: Amino acid, Stereochemistry, Steric effects, Conformational isomerism, Isomer, Folding, Cyclohexane conformation

6

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) provides information on RNA structure at single-nucleotide resolution. It is most often used in conjunction with RNA secondary structure prediction algorithms as a probabilistic or thermodynamic restraint. With the recent advent of ultra-high-throughput approaches for collecting SHAPE data, the applications of this technology are extending beyond structure prediction. In this review, we discuss recent applications of SHAPE data in the transcriptomic context and how this new experimental paradigm is changing our understanding of these experiments and RNA folding in general. SHAPE experiments probe both the secondary and tertiary structure of an RNA, suggesting that model-free approaches for within and comparative RNA structure analysis can provide significant structural insight without the need for a full structural model. New methods incorporating SHAPE at different nucleotide resolutions are required to parse these transcriptomic data sets to transcend secondary structure modeling with global structural metrics. These ‘multiscale’ approaches provide deeper insights into RNA global structure, evolution, and function in the cell. For further resources related to this article, please visit the WIREs website.

Concepts: DNA, Protein, Bioinformatics, Molecular biology, RNA, Secondary structure, Non-coding RNA, Folding

2

A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop-receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding.

Concepts: Protein, RNA, Secondary structure, Molecular dynamics, Tertiary structure, Protein folding, Sociology, Folding

1

Late Embryogenesis Abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the questions of whether water deficit modulate their conformation and, if these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and, that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water-limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics.

Concepts: Enzyme, Plant, Structure, Tertiary structure, In vitro, Necessary and sufficient condition, Conformational isomerism, Folding

1

Protein domains can fold into stable tertiary structures while they are synthesized on the ribosome. We used a high-performance, reconstituted in vitro translation system to investigate the folding of a small five-helix protein domain-the N-terminal domain of Escherichia coli N5-glutamine methyltransferase HemK-in real time. Our observations show that cotranslational folding of the protein, which folds autonomously and rapidly in solution, proceeds through a compact, non-native conformation that forms within the peptide tunnel of the ribosome. The compact state rearranges into a native-like structure immediately after the full domain sequence has emerged from the ribosome. Both folding transitions are rate-limited by translation, allowing for quasi-equilibrium sampling of the conformational space restricted by the ribosome. Cotranslational folding may be typical of small, intrinsically rapidly folding protein domains.

Concepts: Protein, Protein structure, Amino acid, Enzyme, Tertiary structure, Protein folding, Escherichia coli, Folding

0

RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method.

Concepts: DNA, Protein, Amino acid, RNA, Secondary structure, Primary structure, Chemistry, Folding

0

Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly concerted rearrangement in P5abc RNA, a paradigm of RNA folding studies. With mutations that systematically disrupt or restore putative structural elements, we found that this transition reflects local folding of structural modules, with modest and incremental cooperativity that results in concerted behavior. First, two distant secondary structure changes are coupled through a bridging three-way junction and Mg2+-dependent tertiary structure. Second, long-range contacts are formed between modules, resulting in additional cooperativity. Given the sparseness of RNA tertiary contacts after secondary structure formation, we expect that modular folding and incremental cooperativity are generally important for specifying functional structures while also providing productive kinetic paths to these structures. Additionally, we expect our approach to be useful for uncovering modularity in other complex RNAs.

Concepts: DNA, Protein, Amino acid, Molecular biology, RNA, Secondary structure, Structure, Folding

0

Ion mobility experiments coupled with electrospray ionization (ESI) were conducted to evaluate the folding states of bovine carbonic anhydrase 2 (CA2) under three different pH conditions. Collision cross-section (CCS) of the CA2 ions generated by ESI revealed the presence of six discrete conformers in the gas phase under the conditions employed in this study. The CCS of the most extended conformer was three times larger than that of the most compact one. The charge state distribution of the CA2 ions was indicative of three conformers being present. Although there was consistency in conformer assignment conducted by CCS and charge state distribution, the CCS measurement was shown to be more effective because the information obtained provided more detailed knowledge of the conformation of the protein.

Concepts: Carbon dioxide, Hydrogen, Atom, Chemical bond, Ion source, Ions, Conformational isomerism, Folding

0

Interaction of cisplatin in activated diaqua-form with His-Met dipeptide is explored using DFT approach with PCM model. First the conformation space of the dipeptide is explored to find the most stable structure (labeled 0683). Several functionals with double-zeta basis set are used for optimization and obtained order of conformers is confirmed by the CCSD(T) single-point calculations. Supermolecular model is used to determine reaction coordinate for the replacement of aqua ligands consequently by N-site of histidine and S-site of methionine and reversely. Despite the monoadduct of Pt-S(Met) is thermodynamically less stable this reaction passes substantially faster (by several orders of magnitude) than coordination of cisplatin to histidine. The consequent chelate formation occurs relatively fast with energy release up to 12 kcal mol-1.

Concepts: Mathematics, Stereochemistry, Computational chemistry, Ligand, Quantum chemistry, Basis set, Confirmation, Folding

0

The newly synthesized unfolded polypeptide attains its functional and unique three-dimensional conformation through the process of protein folding for which several models have been proposed. The protein misfolding diseases include Alzheimer’s, Parkinson’s and Cataract which are result of formation of amyloid or amorphous aggregates, respectively. The distinction in morphology shows relation with the melting temperature ™. The temperatures near or slightly higher than Tm induces amyloids while much higher or low temperature mediate amorphous aggregation. The aggregation is not always deleterious rather it also performs several important cellular functions essential for survival wide range of organisms called as functional amyloids. Protein gets modulated by several modulators which mediate the aggregation, acceleration, delay, transformations, inhibition and disaggregation of protein aggregates. The exclusive properties of inhibition and disaggregation displayed by various molecules can be employed to treat the life threatening disorders.

Concepts: Alzheimer's disease, Protein, Protein structure, Protein folding, Peptide, Prion, Solid, Folding