Fold usage on genomes and protein fold evolution

We review fold usage on completed genomes to explore protein structure evolution. The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds, the age of different folds and how we have arrived at the set of folds we see today. We examine the relationships between different measures which describe protein fold usage, such as the number of copies of a fold per genome, the number of families per fold, and the number of genomes a fold occurs on. We obtained these measures of fold usage by searching for the structural domains on 157 completed genome sequences from all three kingdoms of life. In our comparisons of these measures we found that bacteria have relatively more distinct folds on their genomes than archaea. Eukaryotes were found to have many more copies of a fold on their genomes. If we separate out the different fold classes, the alpha/beta class has relatively fewer distinct folds on large genomes, more copies of a fold on bacteria and more folds occurring in all three kingdoms simultaneously. These results possibly indicate that most alpha/beta folds originated earlier than other folds. The expected power law distribution is observed for copies of a fold per genome and we found a similar distribution for the number of families per fold. However, a more complicated distribution appears for fold occurrence across genomes, which strongly depends on fold class and kingdom. We also show that there is not a clear relationship between the three measures of fold usage. A fold which occurs on many genomes does not necessarily have many copies on each genome. Similarly, folds with many copies do not necessarily have many families or vice versa.     

Fold or hold: experimental evolution in vitro

We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative polymerase chain reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form structures that self‐prime under defined conditions. Selection acts on the phenotype of self‐priming, after which differences in fitness are amplified and quantified using qPCR. We outline the methodological and bioinformatics tools for the Oli system here and demonstrate that it can be used as a conventional experimental evolution model system by test‐driving it in an experiment investigating adaptive evolution under different rates of environmental change.     

Tracing protein evolution through ancestral structures of fish galectin

Ancestral structures of fish galectins (congerins) were determined. The extant isoforms I and II of congerin are the components of a fish biological defense system and have rapidly differentiated under natural selection pressure, by which congerin I has experienced a protein-fold evolution. The dimer structure of the ancestral congerin demonstrated intermediate features of the extant isoforms. The protein-fold evolution was not observed in the ancestral structure, indicating it specifically occurred in congerin I lineage. Details of hydrogen bonding pattern at the dimer interface and the carbohydrate-binding site of the ancestor were different from the current proteins. The differences implied these proteins were under selection pressure for stabilizing dimer structure and differentiation in carbohydrate specificity. The ancestor had rather low cytotoxic activity than offspring, indicating selection was made to enhance this activity of congerins. Combined with functional analyses, the structure revealed atomic details of the differentiation process of the proteins.     

An evolution based classifier for prediction of protein interfaces without using protein structures

MOTIVATION: The number of available protein structures still lags far behind the number of known protein sequences. This makes it important to predict which residues participate in protein-protein interactions using only sequence information. Few studies have tackled this problem until now. RESULTS: We applied support vector machines to sequences in order to generate a classification of all protein residues into those that are part of a protein interface and those that are not. For the first time evolutionary information was used as one of the attributes and this inclusion of evolutionary importance rankings improves the classification. Leave-one-out cross-validation experiments show that prediction accuracy reaches 64%.     

Glucosinolate structures in evolution

By 2000, around 106 natural glucosinolates (GSLs) were probably documented. In the past decade, 26 additional natural GSL structures have been elucidated and documented. Hence, the total number of documented GSLs from nature by 2011 can be estimated to around 132. A considerable number of additional suggested structures are concluded not to be sufficiently documented. In many cases, NMR spectroscopy would have provided the missing structural information. Of the GSLs documented in the past decade, several are of previously unexpected structures and occur at considerable levels. Most originate from just four species: Barbarea vulgaris, Arabidopsis thaliana, Eruca sativa and Isatis tinctoria. Acyl derivatives of known GSLs comprised 15 of the 26 newly documented structures, while the remaining exhibited new substitution patterns or chain length, or contained a mercapto group or related thio-functionality.GSL identification methods are reviewed, and the importance of using authentic references and structure-sensitive detection methods such as MS and NMR is stressed, especially when species with relatively unknown chemistry are analyzed. An example of qualitative GSL analysis is presented with experimental details (group separation and HPLC of both intact and desulfated GSLs, detection and structure determination by UV, MS, NMR and susceptibility to myrosinase) with emphasis on the use of NMR for structure elucidation of even minor GSLs and GSL hydrolysis products. The example includes identification of a novel GSL, (R)-2-hydroxy-2-(3-hydroxyphenyl)ethylglucosinolate.Recent investigations of GSL evolution, based on investigations of species with well established phylogeny, are reviewed. From the relatively few such investigations, it is already clear that GSL profiles are regularly subject to evolution. This result is compatible with natural selection for specific GSL side chains. The probable existence of structure-specific GSL catabolism in intact plants suggests that biochemical evolution of GSLs has more complex implications than the mere liberation of a different hydrolysis product upon tissue disruption.     

Analysis of ribosomal protein gene structures: implications for intron evolution

Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be “conserved,” i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.     

Linear repetitions of amino acids and convergent evolution inside protein subregions of ordered secondary structures

51 polypeptides of known 3-dimensional structures have been submitted to a search for internal similarities. It is shown that the frequency of proteins displaying significant amounts of internal similarities is higher than predicted by chance. A non-negligible part of those similarities probably occurs in connection with the existence of ordered secondary structures. Indeed, similarity occurs at a much more important rate when analyses are restricted to protein subsequences corresponding to alpha helices or beta pleated sheets. Furthermore, the correlation existing between the rates at which linear and inverted repeats occur inside protein subregions of ordered secondary structures suggests that a significant part of short similarities are analogies rather than homologies. An hypothesis is put forward suggesting that the regular alternations of hydrophobicity which characterize most of alpha helices and beta strands could provoke the occurrence of significant amounts of similarities inside protein sequences.     

Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures.

The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three interlocking subunits, each with two eight-stranded viral jelly rolls normal to the viral capsid, and putative membrane-interacting regions. Surprisingly, the P3 molecule closely resembles hexon, the equivalent protein in human adenovirus. Both viruses also have similar overall architecture, with identical capsid lattices and attachment proteins at their vertices. Although these two dsDNA viruses infect hosts from very different kingdoms, their striking similarities, from major coat protein through capsid architecture, strongly suggest their evolutionary relationship.     

The structure of protein evolution and the evolution of protein structure

The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models explaining the observed distribution of structures have focused on the inherent functional capabilities and structural properties of different folds and on the evolutionary dynamics. Increasingly, these elements are being combined.     

Chiral interaction in protein structures

A new mode of interaction, to be termed chiral interaction, is proposed between chiral molecules such as proteins and polar solvents (H₂O). Such a mode of interaction is well-recognized for macroscopic chiral devices, such as windmills or electric cells, and various media, such as wind or electrolyte. This mode of interaction requires several structural ingredients, all possessed by proteins, and its source is in ionic motion in the solvent. Such an interaction exists only for chiral objects or molecules and therefore possesses several peculiar and uncommon features, which may be of special biological significance. From a thermodynamical viewpoint this phenomenon is non-ergodic and time-irreversible, and therefore does not obey the principle of detailed balance. The energy content of this interaction is rather small and therefore it is to be regarded as a subthermal organization. Chiral interaction appears in the form of an intrinsic flow of perturbation or currents throughout the molecule and hence it is not easily observable. Two experiments are proposed for its observation. One is direct and the other is based on an assumption that couples chiral interaction with enzymatic activity. A model is proposed that links this interaction with the natural selection of the L-enantiomer of amino acids via the magnetic field of the earth. Several structural and other properties may obtain biological significance via the concept of chiral interaction. It is conjectured that chiral interaction may play a significant role in the control of protein activity.