Number Of Homologous Proteins Research Articles

PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.

The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.

Signatures of conserved and unique molecular features in Afrotheria

Afrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.

Structural and functional insights into the basic globulin 7S of soybean seeds by using trypsin as a molecular probe

The basic 7S globulin (Bg7S) is one of the major globulins of soybean seeds. Despite its dual subunit composition and oligomeric assembly, Bg7S has a compact 3D structure (PDB: 3AUP) which is stabilized by a network of inter- and intra-chain disulphide bridges. Bg7S shares several structural elements with a number of homologous proteins from other seeds, whose function is still uncertain.In this work, Bg7S native conformation was probed by using the proteolytic enzyme trypsin. In spite of the presence of many arginine and lysine residues, the protein resulted extremely recalcitrant to in vitro enzymatic cleavage. Indeed, only two scissile bonds located near the C- and N-termini of the large and small subunits, respectively, were cleaved. The partially cleaved products were stable even at prolonged incubation times. Although the generated small peptide fragments were not covalently bound to the remnant of the main chains, they were held in place, as assessed by denaturing and non-denaturing chromatographic approaches. Moreover, both the already observed pH-dependent association/dissociation behaviour of the protein and its insulin binding capacity were preserved both at neutral and acidic pH values.These results are in line with the growing view that the degradation of seed proteins, either storage and non-storage, may be a controlled process related to specific functionalities.

3-Oxo-hexahydro-1H-isoindole-4-carboxylic Acid as a Drug Chiral Bicyclic Scaffold: Structure-Based Design and Preparation of Conformationally Constrained Covalent and Noncovalent Prolyl Oligopeptidase Inhibitors.

Bicyclic chiral scaffolds are privileged motifs in medicinal chemistry. Over the years, we have reported covalent bicyclic prolyl oligopeptidase inhibitors that were highly selective for POP over a number of homologous proteins. Herein, we wish to report the structure-based design and synthesis of a novel class of POP inhibitors based on hexahydroisoindoles. A docking study guided the selection of structures for synthesis. The stereochemistry, decoration, and position within the molecule of the bicyclic scaffolds were assessed virtually. Following the synthesis of the best candidates, in vitro assays revealed that one member of this chemical series was more active than any of our previous inhibitors with a Ki of 1.0 nM. Additional assays also showed that the scaffold of this potent inhibitor, in contrast to one of our previously reported chemical series, is highly metabolically stable, despite the foreseen potential sites of metabolism. Interestingly, computer docking calculations accurately predicted the optimal features of the inhibitors.

Amino acid substitutions at protein–protein interfaces that modulate the oligomeric state

Despite similarities in their sequence and structure, there are a number of homologous proteins that adopt various oligomeric states. Comparisons of these homologous protein pairs, in terms of residue substitutions at the protein-protein interfaces, have provided fundamental characteristics that describe how proteins interact with each other. We have prepared a dataset composed of pairs of related proteins with different homo-oligomeric states. Using the protein complexes, the interface residues were identified, and using structural alignments, the shadow-interface residues have been defined as the surface residues that align with the interface residues. Subsequently, we investigated residue substitutions between the interfaces and the shadow interfaces. Based on the degree of the contributions to the interactions, the aligned sites of the interfaces and shadow interfaces were divided into primary and secondary sites; the primary sites are the focus of this work. The primary sites were further classified into two groups (i.e. exposed and buried) based on the degree to which the residue is buried within the shadow interfaces. Using these classifications, two simple mechanisms that mediate the oligomeric states were identified. In the primary-exposed sites, the residues on the shadow interfaces are replaced by more hydrophobic or aromatic residues, which are physicochemically favored at protein-protein interfaces. In the primary-buried sites, the residues on the shadow interfaces are replaced by larger residues that protrude into other proteins. These simple rules are satisfied in 23 out of 25 Structural Classification of Proteins (SCOP) families with a different-oligomeric-state pair, and thus represent a basic strategy for modulating protein associations and dissociations.

The fold recognition of CP2 transcription factors gives new insights into the function and evolution of tumor suppressor protein p53

The CP2 transcription factor (TFCP2) is a critical regulator of erythroid gene expression. Apart from the involvement in the transcriptional switch of globin gene promoters it activates an array of cellular and viral gene promoters. A number of homologous proteins was identified in genomes of Metazoa, with additional five homologues encoded by the human genome (TFCP2L1, UBP1, GRHL1, GRHL2, GRHL3). Although several experimental studies have already been published, the knowledge on the molecular mechanism of activity of this transcription factors remains very limited. Here we present the application of fold recognition and protein structure prediction in drafting the structure-to-function relationship of the CP2 family. The employed procedure clearly shows that the family adopts a DNA binding immunoglobulin fold homologous to the p53 (TP53) core domain, and a novel type of ubiquitin-like domain and a sterile alpha motif (SAM) form oligomerization modules. With a traceable evolution of CP2 family throughout the Metazoa group this protein family is highly likely to represent an ancestor of the critical cell cycle regulator p53. Based on this observation several functional hypotheses on structure-to-function relationship of p53 were drawn. The DNA motif recognized by p53 is a result of further specialization of the CP2 DNA-binding module. The analysis also shows the critical role of protein oligomerization for the function of this protein superfamily. Finally, the identification of distant homologs of TP53 allowed performing a phylogenetic footprinting analysis explaining the role of the specific amino acids important for both - the protein folding and the binding of DNA.

Towards Alignment Independent Quantitative Assessment of Homology Detection

Identification of homologous proteins provides a basis for protein annotation. Sequence alignment tools reliably identify homologs sharing high sequence similarity. However, identification of homologs that share low sequence similarity remains a challenge. Lowering the cutoff value could enable the identification of diverged homologs, but also introduces numerous false hits. Methods are being continuously developed to minimize this problem. Estimation of the fraction of homologs in a set of protein alignments can help in the assessment and development of such methods, and provides the users with intuitive quantitative assessment of protein alignment results. Herein, we present a computational approach that estimates the amount of homologs in a set of protein pairs. The method requires a prevalent and detectable protein feature that is conserved between homologs. By analyzing the feature prevalence in a set of pairwise protein alignments, the method can estimate the number of homolog pairs in the set independently of the alignments' quality. Using the HomoloGene database as a standard of truth, we implemented this approach in a proteome-wide analysis. The results revealed that this approach, which is independent of the alignments themselves, works well for estimating the number of homologous proteins in a wide range of homology values. In summary, the presented method can accompany homology searches and method development, provides validation to search results, and allows tuning of tools and methods.

Probabilistic reconstruction of ancestral protein sequences.

Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales linearly with the number of homologous proteins used to reconstruct the ancestral sequence.

Characterization of Spiroplasmas by one- and two-dimensional protein analysis on polyacrylamide slab gels

Differences betweenSpiroplasma citri isolates were detected by one-dimensional electrophoresis of proteins on gradient polyacrylamide slab gels. Two-dimensional protein maps (electrofocusing followed by electrophoresis) showed a highly characteristic pattern for allS. citri isolates examined. Coanalysis of mixed protein samples from pairs ofS. citri strains revealed more than 150 comigrating proteins common to allS. citri isolates, but also a number of noncomigrating proteins. Some noncomigrating proteins were present in one isolate but not in another, while other proteins whose migrational properties were only slightly different from one isolate to the other (homologous proteins), were present in more than one isolate.S. citri isolates had many common and only a few homologous proteins. Comparisons ofS. citri with the corn stunt spiroplasma revealed few common proteins and a large number of homologous proteins. When comparingS. citri and the suckling mouse cataract spiroplasma, few common and homologous proteins were apparent. However, several of these common proteins were also shared by the corn stunt spiroplasma, suggesting that they may well represent genus-specific proteins. The data also offer additional evidence that the suckling mouse cataract spiroplasma differs significantly fromS. citri and corn stunt spiroplasmas and probably deserves a separate species designation.

Electrophoretic Studies of Soluble Proteins from Aspergillus spp.

A. flavus Link, A. leporis States & Christensen, A. oryzae (Ahlb.) Cohn, A. parasiticus Speare, and A. tainarii Kita), A. fumigatus Fresenius, and A. ochraceus Wilhelm were fractionated by polyacrylamide gel electrophoresis. Preparations from A. fumigatus exhibited 48 protein fractions, those from A. flavus and A. oryzae each exhibited 47, there were 43 from 4. parasiticus, and A. ochraceus, A. tamarii, and A. leporis showed 32. 31, and 29 fractions, respectively. Comparison of each of these 7 Aspergillus spp. with one another for homologous protein fractions seemed to indicate that more protein components are shared among A. flavus, A. oryzae, and A. parasiticus than between A. flavus and A. fumigatus. However, comparison between A. fumigatus and A. parasiticus revealed the same number of homologous proteins exhibited by A. oryzae and A. parasiticus. Our results did not support the contention that A. flavus and A. parasiticus may be more closely related to each other than to other members of the A. flavus group. It appeared however that A. flavus and A. oryzae may be more closely related. Protein preparations from all 7 taxa contained 2 common protein fractions. Preparations from the 5 species of the A. flavus group had 2 other common protein fractions not found in A. fumigatus or A. ochraceus. The 3 strains of each of the 7 Aspergillus spp. used in this investigation did not contain the same protein complements. These strains differed only in minor morphological characteristics but may have differed significantly in some of their biochemical processes. Raper and Fennell (1965) recognized 132 species of the genus Aspergillus and separated them into 18 groups. This separation was based primarily on conidial color and morphology of the conidial head. Of all these groups, the A. flavus group may be the most important to man. Its members play a very important role in the deterioration of foods, feeds, grains, and seeds and in the production of aflatoxins. Our interest in the A. flavus group centers around its role in seed deterioration. In our laboratory, we often isolate A. flavus from stored