Prokaryotic and eukaryotic pyridoxal-dependent decarboxylases are homologous

Summary A database search has revealed significant and extensive sequence similarities among prokaryotic and eukaryotic pyridoxal phosphate (PLP)-dependent decarboxylases, includingDrosophila glutamic acid decarboxylase (GAD) and bacterial histidine decarboxylase (HDC). Based on these findings, the sequences of seven PLP-dependent decarboxylases from five different organisms have been aligned to derive a consensus sequence for this family of enzymes. In addition, quantitative methods have been employed to calculate the relative evolutionary distances between pairs of the decarboxylases comprising this family. The multiple sequence analysis together with the quantitative results strongly suggest an ancient and common origin for all PLP-dependent decarboxylases. This analysis also indicates that prokaryotic and eukaryotic HDC activities evolved independently. Finally, a sensitive search algorithm (PROFILE) was unable to detect additional members of this decarboxylase family in protein sequence databases.     

152 Order from disorder: defining structure in disordered proteins

Intrinsically disordered proteins are involved in a range of functional roles in the cell, as well as being associated with a number of diverse diseases, including cancers, neurodegenerative disorders, and cardiac myopathies. We use single-molecule fluorescence approaches to characterize disordered proteins implicated in the progression of Parkinson’s and Alzheimer’s diseases. Our goal is to understand, how disease-associated modifications to these proteins alter their conformational and dynamic properties and to relate these changes to disease pathology.     

Comparison of folding rates of homologous prokaryotic and eukaryotic proteins

The rate of polypeptide chain elongation is up to one order of magnitude faster in prokaryotic cells than in eukaryotes. Here we report that the rates of in vitro refolding of orthologous prokaryotic and eukaryotic proteins correlate with their differential rates of biosynthesis. The mitochondrial and cytosolic aspartate aminotransferases of chicken and aspartate aminotransferase of Escherichia coli show pairwise sequence identities of 41-48% and nearly identical three-dimensional structures. Nevertheless, the prokaryotic enzyme refolded 6 times faster (at 25 degrees C) than the eukaryotic isoenzymes after denaturation in 6 m guanidine hydrochloride. Prokaryotic malate dehydrogenase and lactate dehydrogenase also renatured faster than their orthologous eukaryotic counterparts, suggesting that evolutionary pressure has adapted the rate of folding to the rate of elongation of polypeptide chains.     

A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.

Computer analysis using profiles generated by the PSI-BLAST program identified a superfamily of proteins homologous to eukaryotic transglutaminases. The members of the new protein superfamily are found in all archaea, show a sporadic distribution among bacteria, and were detected also in eukaryotes, such as two yeast species and the nematode Caenorhabditis elegans. Sequence conservation in this superfamily primarily involves three motifs that center around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.     

Chlamydiae-specific proteins and indels: novel tools for studies

Chlamydiae species are important human and animal pathogens. Their obligate intracellular mode of replication has precluded the use of genetic and molecular biological approaches for understanding their biology. Comparative genomics have identified many rare genetic changes consisting of whole proteins and conserved indels (i.e. inserts or deletions) in widely distributed proteins that are distinctive characteristics of either all, or various subgroups within, chlamydiae. Additionally, several interesting cases of the lateral transfer of genes from free-living bacteria to a common ancestor of chlamydiae, and from chlamydiae to Trypanosoma/Leishmania, have been identified. These novel signatures have possible applications for advancing our understanding of the chlamydiae.     

Mutual effects of disorder and order in fusion proteins between intrinsically disordered domains and fluorescent proteins

Intrinsically disordered proteins are being paid an increasing amount of interest due to the understanding of the crucial role that flexible regions play in molecular recognition and in signaling. Accordingly, reports focusing on the structural and functional characterization of intrinsically disordered proteins or regions are growing exponentially. Relatively few studies have however been reported on the mutual effects of ordered and disordered moieties in artificial fusion proteins. In this review, we focus on the few available experimental data based on the use of chimeras in which fluorescent proteins were fused to disordered domains of different lengths, compactness and propensity to form secondary structures. The impact of the artificial fusion on the conformational and functional properties of the resulting proteins is discussed.     

The acidic proteins of eukaryotic ribosomes. A comparative study

The acidic proteins extracted by 0.4 M NH4Cl and 50% ethanol from ribosomes from Saccharomyces cerevisiae, wheat germ, Artemia salina, Drosophila melanogaster, rat liver and rabbit reticulocytes have been studied comparatively in several structural and functional aspects. All the species studied have in the ribosome two strongly acidic proteins with pI values not greater than pH 4.5., which appear to be monophosphorylated in the case of S. cerevisiae, A.Salina, D. melanogaster and wheat germ. Rat liver proteins are multiphosphorylated, as possibly are those from reticulocytes. The molecular weight of these acidic proteins as determined by SDS electrophoresis ranges from around 13,500 to 17,000 and, except in the case of yeast, of which both proteins have the same molecular weight, the size of the two proteins in the other species differs by approx. 1,000-2,000. In general, the size of the proteins increases with the evolutionary position of the organism, as seems to be the case with the degree of phosphorylation. From an immunological point of view the ribosomal acid proteins of eukaryotic cells are partically related, since antisera against yeast protein cross-react with proteins from wheat germ, rat liver and reticulocytes. Bacterial proteins L7 and L12 are very weakly recognized by the anti-yeast sera. Anti-bacterial acidic proteins do not cross-react with any of the protein from the species studied. The proteins from all the species studied are functional equivalents and can reconstitute the activity of particles of S. cerevisiae deprived of their acidic proteins.     

Large-scale survey for potentially targetable indels in bacterial and protozoan proteins

Our previous results demonstrated that some essential, housekeeping proteins from pathogenic microorganisms may contain sizable insertions-deletions in their sequences (compared to close human homologs) that can be responsible for unexpected virulence properties. For example, we found that indel-bearing elongation factor-1alpha from several pathogenic protozoa can activate a human tyrosine phosphatase SHP-1 leading to deactivation of macrophages. On the one hand, these findings allowed development of a strategy for targeting some indel-containing pathogen proteins that have similar human counterparts. On the other hand, the results raised numerous questions regarding the nature and implications of sequence indels in pathogen proteins. In the present study, we conducted a large-scale survey of indels in proteins from 136 bacterial and protozoan genomes. It has been established that sizable insertions and deletions occur in approximately 5-10% of bacterial proteins with close human homologs, while proteins from the protozoan pathogens such as Trypanosoma cruzi, Plasmodium falciparum, and Leishmania donovani exhibit elevated indel content that can reach up to 25%. The finding suggested that the occurrence of sequence indels may be involved in the evolution of pathogenic mechanisms in these protozoa.     

Intrinsically disordered proteins: regulation and disease

Intrinsically disordered proteins (IDPs) are enriched in signaling and regulatory functions because disordered segments permit interaction with several proteins and hence the re-use of the same protein in multiple pathways. Understanding IDP regulation is important because altered expression of IDPs is associated with many diseases. Recent studies show that IDPs are tightly regulated and that dosage-sensitive genes encode proteins with disordered segments. The tight regulation of IDPs may contribute to signaling fidelity by ensuring that IDPs are available in appropriate amounts and not present longer than needed. The altered availability of IDPs may result in sequestration of proteins through non-functional interactions involving disordered segments (i.e., molecular titration), thereby causing an imbalance in signaling pathways. We discuss the regulation of IDPs, address implications for signaling, disease and drug development, and outline directions for future research.     

Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

Background  

The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.     

Bidirectional Long Short-Term Memory Networks for predicting the subcellular localization of eukaryotic proteins

An algorithm called bidirectional long short-term memory networks (BLSTM) for processing sequential data is introduced. This supervised learning method trains a special recurrent neural network to use very long-range symmetric sequence context using a combination of nonlinear processing elements and linear feedback loops for storing long-range context. The algorithm is applied to the sequence-based prediction of protein localization and predicts 93.3 percent novel nonplant proteins and 88.4 percent novel plant proteins correctly, which is an improvement over feedforward and standard recurrent networks solving the same problem. The BLSTM system is available as a Web service at http://stepc.stepc.gr/-synaptic/blstm.html.     

Phylogenetic utility and evolution of indels: a study in neognathous birds

Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the retrieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.     

Dynamics of well-folded and natively disordered proteins in solution: a time-of-flight neutron scattering study

Casein proteins belong to the class of natively disordered proteins. The existence of disordered biologically active proteins questions the assumption that a well-folded structure is required for function. A hypothesis generally put forward is that the unstructured nature of these proteins results from the functional need of a higher flexibility. This interplay between structure and dynamics was investigated in a series of time-of-flight neutron scattering experiments, performed on casein proteins, as well as on three well-folded proteins with distinct secondary structures, namely, myoglobin (alpha), lysozyme (alpha/beta) and concanavalin A (beta). To illustrate the subtraction of the solvent contribution from the scattering spectra, we used the dynamic susceptibility spectra emphasizing the high frequency part of the spectrum, where the solvent dominates. The quality of the procedure is checked by comparing the corrected spectra to those of the dry and hydrated protein with negligible solvent contamination. Results of spectra analysis reveal differences in motional amplitudes of well-folded proteins, where beta-sheet structures appear to be more rigid than a cluster of alpha-helices. The disordered caseins display the largest conformational displacements. Moreover their global diffusion rates deviate from the expected dependence, suggesting further large-scale conformational motions.     

Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes

Combining the motif discovery and disorder protein segment identification in PDB allows us to create the first and largest library of disordered patterns. At present the library includes 109 disordered patterns. Here we offer a comprehensive analysis of the occurrence of selected disordered patterns and 20 homorepeats of 6 residues long in 123 proteomes. 27 disordered patterns occur sparsely in all considered proteomes, but the patterns of low-complexity-homorepeats-appear more often in eukaryotic than in bacterial proteomes. A comparative analysis of the number of proteins containing homorepeats of 6 residues long and the disordered selected patterns in these proteomes has been performed. The matrices of correlation coefficients between numbers of proteins where at least once a homorepeat of six residues long for each of 20 types of amino acid residues and 109 disordered patterns from the library appears in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside the considered kingdom than between them. The largest fraction of homorepeats of 6 residues belongs to Amoebozoa proteomes (D. discoideum), 46%. Moreover, the longest uninterrupted repeats belong to S306 from D. discoideum (Amoebozoa). Homorepeats of some amino acids occur more frequently than others and the type of homorepeats varies across different proteomes, . For example, E6 appears most frequent for all considered proteomes for Chordata, Q6 for Arthropoda, S6 for Nematoda. The averaged occurrence of multiple long runs of 6 amino acids in a decreasing order for 97 eukaryotic proteomes is as follows: Q6, S6, A6, G6, N6, E6, P6, T6, D6, K6, L6, H6, R6, F6, V6, I6, Y6, C6, M6, W6, and for 26 bacterial proteomes it is A6, G6, P6, and the others occur seldom. This suggests that such short similar motifs are responsible for common functions for nonhomologous, unrelated proteins from different organisms.     

Comparison of force fields for Alzheimer's A : A case study for intrinsically disordered proteins

Intrinsically disordered proteins are essential for biological processes such as cell signalling, but are also associated to devastating diseases including Alzheimer's disease, Parkinson's disease or type II diabetes. Because of their lack of a stable three‐dimensional structure, molecular dynamics simulations are often used to obtain atomistic details that cannot be observed experimentally. The applicability of molecular dynamics simulations depends on the accuracy of the force field chosen to represent the underlying free energy surface of the system. Here, we use replica exchange molecular dynamics simulations to test five modern force fields, OPLS, AMBER99SB, AMBER99SB*ILDN, AMBER99SBILDN‐NMR and CHARMM22*, in their ability to model Aβ₄₂, an intrinsically disordered peptide associated with Alzheimer's disease, and compare our results to nuclear magnetic resonance (NMR) experimental data. We observe that all force fields except AMBER99SBILDN‐NMR successfully reproduce local NMR observables, with CHARMM22* being slightly better than the other force fields.     

A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins

A growing number of proteins are being identified that are biologically active though intrinsically disordered, in sharp contrast with the classic notion that proteins require a well-defined globular structure in order to be functional. At the same time recent work showed that aggregation and amyloidosis are initiated in amino acid sequences that have specific physico-chemical properties in terms of secondary structure propensities, hydrophobicity and charge. In intrinsically disordered proteins (IDPs) such sequences would be almost exclusively solvent-exposed and therefore cause serious solubility problems. Further, some IDPs such as the human prion protein, synuclein and Tau protein are related to major protein conformational diseases. However, this scenario contrasts with the large number of unstructured proteins identified, especially in higher eukaryotes, and the fact that the solubility of these proteins is often particularly good. We have used the algorithm TANGO to compare the beta aggregation tendency of a set of globular proteins derived from SCOP and a set of 296 experimentally verified, non-redundant IDPs but also with a set of IDPs predicted by the algorithms DisEMBL and GlobPlot. Our analysis shows that the beta-aggregation propensity of all-alpha, all-beta and mixed alpha/beta globular proteins as well as membrane-associated proteins is fairly similar. This illustrates firstly that globular structures possess an appreciable amount of structural frustration and secondly that beta-aggregation is not determined by hydrophobicity and beta-sheet propensity alone. We also show that globular proteins contain almost three times as much aggregation nucleating regions as IDPs and that the formation of highly structured globular proteins comes at the cost of a higher beta-aggregation propensity because both structure and aggregation obey very similar physico-chemical constraints. Finally, we discuss the fact that although IDPs have a much lower aggregation propensity than globular proteins, this does not necessarily mean that they have a lower potential for amyloidosis.