Evolution Of Secondary Structures Research Articles

Concurrent neutral evolution of mRNA secondary structures and encoded proteins.

Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins. We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure. We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient search for new variants on the protein level.

Pressure-induced unfolding/refolding of ribonuclease A: static and kinetic Fourier transform infrared spectroscopy study.

In this paper, we illustrate the use of high-pressure Fourier transform infrared (FT-IR) spectroscopy to study the reversible presssure-induced unfolding and refolding of ribonuclease A (RNase A) and compare it with the results obtained for the temperature-induced transition. FT-IR spectroscopy monitors changes in the secondary structural properties (amide I' band) or tertiary contacts (tyrosine band) of the protein upon pressurization or depressurization. Analysis of the amide I' spectral components reveals that the pressure-induced denaturation process sets in at 5. 5 kbar at 20 degrees C and pH 2.5. It is accompanied by an increase in disordered structures while the content of beta-sheets and alpha-helices drastically decreases. The denatured state above 7 kbar retains nonetheless some degree of beta-like secondary structure and the molecule cannot be described as an extended random coil. Increase of pH from 2.5 to 5.5 has no influence on the structure of the pressure-denatured state; it slightly changes the stability of the protein only. All experimental evidence indicates that the pressure-denatured states of monomeric proteins have more secondary structure than the temperature-denatured states. Different modes of denaturation, including pressure, may correlate differently with the roughness of the energy scale and slope of the folding funnel. For these reasons we have also carried out pressure-jump kinetic studies of the secondary structural evolution in the unfolding/refolding reaction of RNase A. In agreement with the theoretical model presented by Hummer et al. [(1998) Proc. Natl. Acad. Sci. U.S.A. 95, 1552-1555], the experimental data show that pressure slows down folding and unfolding kinetics (here 1-2 orders of magnitude), corresponding to an increasingly rough landscape. The kinetics remains non-two-state under pressure. Assuming a two-step folding scenario, the calculated relaxation times for unfolding of RNase A at 20 degrees C and pH 2.5 can be estimated to be tau(1) approximately 0.7 min and tau(2) approximately 17 min. The refolding process is considerably faster (tau(1) approximately 0.3 min, tau(2) approximately 4 min). Our data show that the pressure stability and pressure-induced unfolding/refolding kinetics of monomeric proteins, such as wild-type staphylococcal nuclease (WT SNase) and RNase A, may be significantly different. The differences are largely due to the four disulfide bonds in RNase A, which stabilize adjacent structures. They probably lead to the much higher denaturation pressure compared to SNase, and this might also explain why the volume change of WT SNase upon unfolding is about twice as large.

Nanosecond UV Resonance Raman Examination of Initial Steps in α-Helix Secondary Structure Evolution

Nanosecond UV Resonance Raman Examination of Initial Steps in α-Helix Secondary Structure Evolution

The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein Secondary Structure and Photosynthetic Oxygen Evolution

Cholesterol induces large perturbations in the physical properties of membranes, especially in the structural organization of the phospholipid bilayers and the aggregation and solubility of proteins at physiological temperatures. This study was designed to examine the interaction of cholesterol with lipid and proteins of chloroplasts photosystem II (PSII) submembrane fractions in air dried film at pH 6–7 with cholesterol concentrations of 0.01 to 20 mM.Fourier transform infrared difference spectroscopy with its self-deconvolution and second derivative methods as well as curve-fitting procedures are used, in order to determine the cholesterol binding mode, the protein conformational changes, and the structural properties of cholesterol–protein complexes. Correlations between the effect of cholesterol on the protein secondary structure and the rate of oxygen evolution in PSII are also established. Spectroscopic evidence showed that at low cholesterol concentration (0.01 and 0.1 mM), minor chol–protein and chol–lipid interactions (through hydrogen bonding) occur with no major perturbations of the protein secondary structure. As cholesterol concentration increases (5 and 10 and 20 mM), major alterations of the protein secondary structure are observed from that of the α-helix 47% (uncomplexed protein) to 43–39% (complexes) and the β-sheet structure 18% (uncomplexed protein) to 22–26% (complexes). Those changes coincide with a partial decrease in the rate of the oxygen evolution (8–33%) is observed in the presence of cholesterol at high concentration.

RNA secondary structure and compensatory evolution.

The classic concept of epistatic fitness interactions between genes has been extended to study interactions within gene regions, especially between nucleotides that are important in maintaining pre-mRNA/mRNA secondary structures. It is shown that the majority of linkage disequilibria found within the Drosophila Adh gene are likely to be caused by epistatic selection operating on RNA secondary structures. A recently proposed method of RNA secondary structure prediction based on DNA sequence comparisons is reviewed and applied to several types of RNAs, including tRNA, rRNA, and mRNA. The patterns of covariation in these RNAs are analyzed based on Kimura's compensatory evolution model. The results suggest that this model describes the substitution process in the pairing regions (helices) of RNA secondary structures well when the helices are evolutionarily conserved and thermodynamically stable, but fails in some other cases. Epistatic selection maintaining pre-mRNA/mRNA secondary structures is compared to weak selective forces that determine features such as base composition and synonymous codon usage. The relationships among these forces and their relative strengths are addressed. Finally, our mutagenesis experiments using the Drosophila Adh locus are reviewed. These experiments analyze long-range compensatory interactions between the 5' and 3' ends of Adh mRNA, the different constraints on secondary structures in introns and exons, and the possible role of secondary structures in RNA splicing.

Prion proteins: evolution and preservation of secondary structure

Prions cause a variety of neurodegenerative disorders that seem to result from a conformational change in the prion protein (PrP). Thirty-two PrP sequences have been subjected to phylogenetic analysis followed by reconstruction of the most probable evolutionary spectrum of amino acid replacements. The replacement rates suggest that the protein does not seem to be very conservative, but in the course of evolution amino acids have only been substituted within the elements of the secondary structure by those with very similar physico-chemical properties. Analysis of the full spectrum of single-step amino acid substitutions in human PrP using secondary structure prediction algorithms shows an over-representation of substitutions that tend to destabilize α-helices.

Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes.

Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their "ruggedness." Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively "flat" peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of "neighboring" RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences increases. The patterns that are generated in the RNA sequences and the RNA secondary structures are not directly selected for and can be regarded as a side effect of the evolutionary dynamics of the system.

Interaction and "apparent" reconnection of 3D vortex tubes via direct numerical simulations

We present evidence of: "binding" of anti-parallel vortex tube segments; strong noncircular core development; evolution of new secondary finger-like vortex structures: and finally "apparent" vortex reconnections due to entanglement. The latter three processes are not present in Biot-Savart filament simulations.

The corrected nucleotide sequences of 5 S RNAs from six angiosperms: With some notes on 5 S RNA secondary structure and molecular evolution

The corrected nucleotide sequences of the cytoplasmic 5 S ribosomal RNAs of 6 angiosperms are reported. The previously reported sequences, reconstructed from oligonucleotide catalogs, had been suspected for some time to contain errors. The corrected sequences fit in a universal 5-helix model for 5 S RNA secondary structure. The model involves the existence of a dynamic equilibrium between slightly different base-pairing schemes in two areas of the structure. Reconstruction of a phylogenetic tree from over 200 known 5 S RNA sequences yields a general picture of biological evolution. It confirms the tripartite descent of living species — eubacteria, archaebacteria, eukaryotes — and the endosymbiotic origin of plant mitochondria and chloroplasts.

Formation of secondary structure in bulk polymer from heterophase polymerization of vinyl chloride

The theory was developed for the formation and evolution of secondary polymer bulk structures by heterophase polymerization of vinylchloride. Conversion for polymerizate volume fixation and for the completion of the period of forming secondary structures were determined. Formulae were derived for calculating main characteristics of the porous structure of a polymer in bulk, according to conversion. Results were compared with experimental data in the literature.