Denatured bactericidal proteins: Active per se,or reservoirs of active peptides?

According to the structure-to-function paradigm proteins fold into a 3D structure for exerting their functions. Intrinsically destructured proteins with important biological functions have been identified and studied, but they assume a structure when interacting in the cell with their partners. There are instead bactericidal proteins, endowed also with other diverse activities (glycoside hydrolases, RNases, a defensin), which are lost when the proteins are denatured or inactivated, whereas the bactericidal activity is surprisingly conserved.The hypothesis is advanced that these proteins are not bactericidal per se, but because they store in their amino acid sequences peptide segments that display bactericidal activity when cut out as free peptides from the proteins. These bactericidal proteins would thus be merely containers of bactericidal peptides.     

On the origin of eukaryotic cytoskeleton.

The origin of eukaryote-specific cytoskeletal proteins is an issue which is closely related to the origin of the domain Eukarya. As nearly all of these proteins are not found in prokaryotes, the prokaryotic origin of eukaryotic cytoskeletal network suggested by most models is questionable. Eukaryotic cytoskeletal proteins might descend from subpopulations of pre-cells co-existing with Bacteria and Archaea prior to the origin of eukaryotes. The pre-karyote (the host for a-proteobacterial ancestors of mitochondria) might have already possessed eukaryotic-like cytoskeleton. A possible role for viruses in the origin of eukaryotic cytoskeletal proteins is discussed. Viruses parasitizing on pre-cells and/or on the pre-karyote might have themselves used several eukaryotic-like cytoskeletal proteins for segregation and packing of their genomes.     

高迁移率族蛋白与真核基因表达调控

高迁移率族蛋白 (high mobility group protein , HMG) 是一系列的染色质相关蛋白,广泛存在于真核生物细胞中,含量丰富,因其在聚丙烯酰胺凝胶电泳中的高迁移率而得名 . HMG 蛋白家族可分为 HMGB 、 HMGA 和 HMGN 三类亚家族,各亚家族有其特征的结构域,这些结构域介导了 HMG 和 DNA 或染色质相关区域的相互作用 . 现已发现这些蛋白质具有多种重要生物学功能,其中几乎所有 HMG 都可以通过修饰、弯曲或改变染色质 /DNA 的结构,促进各种蛋白质因子形成大分子复合物来调节基因转录 .     

The CCN family of proteins: structure-function relationships

The CCN proteins are key signalling and regulatory molecules involved in many vital biological functions, including cell proliferation, angiogenesis, tumourigenesis and wound healing. How these proteins influence such a range of functions remains incompletely understood but is probably related to their discrete modular nature and a complex array of intra- and inter-molecular interactions with a variety of regulatory proteins and ligands. Although certain aspects of their biology can be attributed to the four individual modules that constitute the CCN proteins, recent results suggest that some of their biological functions require cooperation between modules. Indeed, the modular structure of CCN proteins provides important insight into their structure-function relationships.     

Insights into the functional expansion of the astacin peptidase family in parasitic helminths

Helminths secrete a plethora of proteins involved in parasitism-related processes such as tissue penetration, migration, feeding and immunoregulation. Astacins, a family of zinc metalloproteases belonging to the peptidase family M12, are one of the most abundantly represented protein families in the secretomes of helminths. Despite their involvement in virulence, very few studies have addressed the role of this loosely defined protein group in parasitic helminths. Herein, we have analysed the predicted proteomes from 154 helminth species and confirmed the expansion of the astacin family in several nematode taxa. The astacin domain associated with up to 110 other domains into 145 unique domain architectures, where CUB and ShK constitute the principal and nearly independent bi-domain frameworks. The presence of co-existing domains suggests promiscuous adaptable functions to several roles. These activities could be related either to substrate specificity or to higher-order functions, such as anti-angiogenesis and immunomodulation, where the astacin domain would play an accessory role. Furthermore, some phylogenetically restricted mutations in the astacin domain affected residues located at the active cleft and binding sub-pockets, suggesting adaptation to different substrate specificities. Altogether, these findings suggest the astacin domain is a highly adaptable module that fulfils multiple proteolytic needs of the parasitic lifestyle. This study contributes to the understanding of helminth-secreted astacins and, ultimately, provides the foundation to guide future investigations about the role of this diverse family of proteins in host–parasite interactions.     

Proteomic analysis of heat-stable proteins in Escherichia coli

Some proteins of E. coli are stable at temperatures significantly higher than 49 degrees C, the maximum temperature at which the organism can grow. The heat stability of such proteins would be a property which is inherent to their structures, or it might be acquired by evolution for their specialized functions. In this study, we describe the identification of 17 heat-stable proteins from E. coli. Approximately one-third of these proteins were recognized as having functions in the protection of other proteins against denaturation. These included chaperonin (GroEL and GroES), molecular chaperones (DnaK and FkpA) and peptidyl prolyl isomerases (trigger factor and FkpA). Another common feature was that five of these proteins (GroEL, GroES, Ahpc, RibH and ferritin) have been shown to form a macromolecular structure. These results indicated that the heat stability of certain proteins may have evolved for their specialized functions, allowing them to cope with harsh environments, including high temperatures.     

Structural and functional properties of ras proteins

The ras proteins belong to a family of related polypeptides that are present in all eukaryotic organisms from yeast to human. Their extraordinary evolutionary conservation suggests that they have essential cellular functions, although their exact role remains unknown. Mutations in specific amino acids and overexpression of normal proteins have been linked to altered proliferation and/or differentiation and, particularly, to neoplastic processes. Mature ras proteins are located on the inner side of the plasma membrane, and their biochemical properties include binding and exchange of guanine nucleotides and GTPase activity. The favored hypothesis for ras function is that these proteins exist in an equilibrium between an inactive conformation (p21.GDP) and an active conformation (p21. GTP) in which they are able to interact with their as yet unknown cellular target or targets. Similarities in cellular location, structure, and biochemistry with other known regulatory (G) proteins suggest that they play a role in transduction of signals from the cell surface. The elucidation of the crystal structure of normal and transforming ras proteins and the identification of cellular proteins that interact directly with them (GAP, CDC25) or suppress some of their biological effects (Krev-1) have opened new avenues in the search for their elusive cellular targets and in the elucidation of the functional role of ras gene products.     

Prediction of protein function from protein sequence and structure

The sequence of a genome contains the plans of the possible life of an organism, but implementation of genetic information depends on the functions of the proteins and nucleic acids that it encodes. Many individual proteins of known sequence and structure present challenges to the understanding of their function. In particular, a number of genes responsible for diseases have been identified but their specific functions are unknown. Whole-genome sequencing projects are a major source of proteins of unknown function. Annotation of a genome involves assignment of functions to gene products, in most cases on the basis of amino-acid sequence alone. 3D structure can aid the assignment of function, motivating the challenge of structural genomics projects to make structural information available for novel uncharacterized proteins. Structure-based identification of homologues often succeeds where sequence-alone-based methods fail, because in many cases evolution retains the folding pattern long after sequence similarity becomes undetectable. Nevertheless, prediction of protein function from sequence and structure is a difficult problem, because homologous proteins often have different functions. Many methods of function prediction rely on identifying similarity in sequence and/or structure between a protein of unknown function and one or more well-understood proteins. Alternative methods include inferring conservation patterns in members of a functionally uncharacterized family for which many sequences and structures are known. However, these inferences are tenuous. Such methods provide reasonable guesses at function, but are far from foolproof. It is therefore fortunate that the development of whole-organism approaches and comparative genomics permits other approaches to function prediction when the data are available. These include the use of protein-protein interaction patterns, and correlations between occurrences of related proteins in different organisms, as indicators of functional properties. Even if it is possible to ascribe a particular function to a gene product, the protein may have multiple functions. A fundamental problem is that function is in many cases an ill-defined concept. In this article we review the state of the art in function prediction and describe some of the underlying difficulties and successes.     

Chemical mapping of co-existing RNA structures.

In many cases RNA can assume co-existing or meta-stable structures preventing structure determination by chemical mapping. A novel method is described, by which RNA is modified with dimethyl sulphate without shifting the distribution of different structures. The different structures are then separated in native gel electrophoresis, and structure determination by primer extension can be carried out separately for each structure.     

VDAC proteomics: Post-translation modifications

Voltage-dependent anion channels are abundant mitochondrial outer membrane proteins expressed in three isoforms, VDAC1-3, and are considered as "mitochondrial gatekeepers". Most tissues express all three isoforms. The functions of VDACs are several-fold, ranging from metabolite and energy exchange to apoptosis. Some of these functions depend on or are affected by interaction with other proteins in the cytosol and intermembrane space. Furthermore, the function of VDACs, as well as their interaction with other proteins, is affected by posttranslational modification, mainly phosphorylation. This review summarizes recent findings on posttranslational modification of VDACs and discusses the physiological outcome of these modifications. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.     

Invertebrate intracellular fatty acid binding proteins

Fatty acid binding proteins are multigenic cytosolic proteins largely distributed along the zoological scale. Their overall identity at primary and tertiary structure is conserved. They are involved in the uptake and transport of hydrophobic ligands to different cellular fates. The precise functions of each FABP type remain imperfectly understood, since sub-specialization of functions is suggested. Evolutionary studies have distinguished major subfamilies that could have been derived from a common ancestor close to vertebrate/invertebrate split. Since the isolation of the first invertebrate FABP from Schistocerca gregaria in 1990, the number of FABPs isolated from invertebrates has been increasing. Differences at the sequence level are appreciable and relationships with vertebrate FABPs are not clear, and lesser among invertebrate proteins, introducing some uncertainty to infer functional relatedness and phylogenetic relationships. The objective of this review is to summarize the information available on invertebrate FABPs to elucidate their mutual relationships, the relationship with their vertebrate counterparts and putative functions. Structure, gene structure, putative functions, expression studies and phylogenetic relationships with vertebrate counterparts are analyzed. Previous suggestions of the ancestral position concerning the heart-type of FABPs are reinforced by evidence from invertebrate models.     

Novel aquatic silk genes from Simulium (Psilozia) vittatum (Zett) Diptera: Simuliidae

The silks of arthropods have an elementary role in the natural history of the organisms that spin them, yet they are coded by rapidly evolving genes leading some authors to speculate that silk proteins are non-homologous proteins co-opted multiple times independently for similar functions. However, some general structural patterns are emerging. In this work we identified three major silk gland proteins using a combined biochemical, proteomic, next-generation sequencing and bioinformatic approach. Biochemical characterization determined that they were phosphorylated with multiple isoforms and potentially differential phosphorylation. Structural characterization showed that their structure was more similar to silk proteins from distantly related aquatic Trichopteran species than more closely related terrestrial or aquatic Diptera. Overall, our approach is easily transferable to any non-model species and if used across a larger number of aquatic species, we will be able to better understand the processes involved in linking the secondary structure of silk proteins with their function between in an organisms and its habitat.     

New insights into the mycobacterial PE and PPE proteins provide a framework for future research

The PE and PPE proteins of Mycobacterium tuberculosis have been studied with great interest since their discovery. Named after the conserved proline (P) and glutamic acid (E) residues in their N-terminal domains, these proteins are postulated to perform wide-ranging roles in virulence and immune modulation. However, technical challenges in studying these proteins and their encoding genes have hampered the elucidation of molecular mechanisms and leave many open questions regarding the biological functions mediated by these proteins. Here, I review the shared and unique characteristics of PE and PPE proteins from a molecular perspective linking this information to their functions in mycobacterial virulence. I discuss how the different subgroups (PE_PGRS, PPE-PPW, PPE-SVP and PPE-MPTR) are defined and why this classification of paramount importance to understand the PE and PPE proteins as individuals and or groups. The goal of this MicroReview is to summarize and structure the existing information on this gene family into a simplified framework of thinking about PE and PPE proteins and genes. Thereby, I hope to provide helpful starting points in studying these genes and proteins for researchers with different backgrounds. This has particular implications for the design and monitoring of novel vaccine candidates and in understanding the evolution of the M. tuberculosis complex.