Extra domains in secondary transport carriers and channel proteins

“Extra” domains in members of the families of secondary transport carrier and channel proteins provide secondary functions that expand, amplify or restrict the functional nature of these proteins. Domains in secondary carriers include TrkA and SPX domains in DASS family members, DedA domains in TRAP-T family members (both of the IT superfamily), Kazal-2 and PDZ domains in OAT family members (of the MF superfamily), USP, IIA^Fru and TrkA domains in ABT family members (of the APC superfamily), ricin domains in OST family members, and TrkA domains in AAE family members. Some transporters contain highly hydrophilic domains consisting of multiple repeat units that can also be found in proteins of dissimilar function. Similarly, transmembrane α-helical channel-forming proteins contain unique, conserved, hydrophilic domains, most of which are not found in carriers. In some cases the functions of these domains are known. They may be ligand binding domains, phosphorylation domains, signal transduction domains, protein/protein interaction domains or complex carbohydrate-binding domains. These domains mediate regulation, subunit interactions, or subcellular targeting. Phylogenetic analyses show that while some of these domains are restricted to closely related proteins derived from specific organismal types, others are nearly ubiquitous within a particular family of transporters and occur in a tremendous diversity of organisms. The former probably became associated with the transporters late in the evolutionary process; the latter probably became associated with the carriers much earlier. These domains can be located at either end of the transporter or in a central region, depending on the domain and transporter family. These studies provide useful information about the evolution of extra domains in channels and secondary carriers and provide novel clues concerning function.     

Extra domains in secondary transport carriers and channel proteins

"Extra" domains in members of the families of secondary transport carrier and channel proteins provide secondary functions that expand, amplify or restrict the functional nature of these proteins. Domains in secondary carriers include TrkA and SPX domains in DASS family members, DedA domains in TRAP-T family members (both of the IT superfamily), Kazal-2 and PDZ domains in OAT family members (of the MF superfamily), USP, IIA(Fru) and TrkA domains in ABT family members (of the APC superfamily), ricin domains in OST family members, and TrkA domains in AAE family members. Some transporters contain highly hydrophilic domains consisting of multiple repeat units that can also be found in proteins of dissimilar function. Similarly, transmembrane alpha-helical channel-forming proteins contain unique, conserved, hydrophilic domains, most of which are not found in carriers. In some cases the functions of these domains are known. They may be ligand binding domains, phosphorylation domains, signal transduction domains, protein/protein interaction domains or complex carbohydrate-binding domains. These domains mediate regulation, subunit interactions, or subcellular targeting. Phylogenetic analyses show that while some of these domains are restricted to closely related proteins derived from specific organismal types, others are nearly ubiquitous within a particular family of transporters and occur in a tremendous diversity of organisms. The former probably became associated with the transporters late in the evolutionary process; the latter probably became associated with the carriers much earlier. These domains can be located at either end of the transporter or in a central region, depending on the domain and transporter family. These studies provide useful information about the evolution of extra domains in channels and secondary carriers and provide novel clues concerning function.     

New types of conserved sequence domains in DNA-binding regions of homing endonucleases

We have identified four new types of short conserved sequence domains in homing endonucleases and related proteins. These domains are modular, appearing in various combinations. One domain includes a motif known by structure as a novel sequence-specific DNA-binding helix. Sequence similarity shows two other domains to be new types of helix-turn-helix DNA-binding domains. We term the new domains nuclease-associated modular DNA-binding domains (NUMODs).     

Hierarchic organization of domains in globular proteins

An automatic procedure is developed for the identification of domains in globular proteins from X-ray elucidated co-ordinates. Using this tool, domains are shown to be iteratively decomposable into subdomains, leading to a hierarchic molecular architecture.There is no convenient geometry that will fully characterize the atom by atom interdigitation at an interface between domains, and the strategy adopted here was devised to reduce this unwieldy three-dimensional problem to a closely approximating companion analysis in a plane. These analytically derived domain choices can be used subsequently to construct computer-generated, space-filling, color-coded views of the domains; and when this is done, the derived domains are seen to be completely resolved.The number of domains in a protein is a mathematically well-behaved function of the chain length, lending support to the supposition that the domains are an implicit structural consequence of the folding process. A spectrum of domains ranging in size from whole protein monomers to the individual units of secondary structure is apparent in each of the 22 proteins analyzed here.The hierarchic organization of structural domains is evidence in favor of an underlying protein folding process that proceeds by hierarchic condensation. In this highly constrained model, every pathway leading to the native state can be described by a tree of local folding interactions.     

Domains in the fibrinogen molecule

Intramolecular melting of fibrinogen and its degradation products has been studied by a scanning microcalorimetric method in various solution environments (especially variations in pH), and inferences are made about the features that seemed to be independently folding segments (“domains”), as evidenced by their independent resistance to thermal denaturation. It was shown that there are 12 more or less independent co-operative regions of ordered compact structure in fibrinogen, which can be considered as structural domains of this macromolecule. Of these 12 domains, two are in the central part of the molecule, corresponding to the E fragment, four are in each terminal part, corresponding to the D fragments, and two are formed by the carboxy-terminal portions of the α-chains. All fibrinogen domains can be divided into two groups according to their thermodynamic properties: (1) thermolabile domains, to which belong three domains from each terminal part of the molecule and the domains formed by the carboxy-terminal portions of the α-chains; (2) thermostable domains, to which belong both domains from the central part and one domain from each terminal part of the molecule. This division seems to reflect the structural differences between the domains.     

Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families.

Several types of domain occur in beta-1, 4-glycanases. The best characterized of these are the catalytic domains and the cellulose-binding domains. The domains may be joined by linker sequences rich in proline or hydroxyamino acids or both. Some of the enzymes contain repeated sequences up to 150 amino acids in length. The enzymes can be grouped into families on the basis of sequence similarities between the catalytic domains. There are sequence similarities between the cellulose-binding domains, of which two types have been identified, and also between some domains of unknown function. The beta-1, 4-glycanases appear to have arisen by the shuffling of a relatively small number of progenitor sequences.     

Mutagenesis and selection of PDZ domains that bind new protein targets

PDZ domains are a recently characterized protein-recognition module. In most cases, PDZ domains bind to the C-terminal end of target proteins and are thought thereby to link these target proteins into functional signaling networks. We report the isolation of artificial PDZ domains selected via a mutagenesis screen in vivo, each recognizing a different C-terminal peptide. We demonstrate that the PDZ domains isolated can bind selectively to their target peptides in vitro and in vivo. Two of the target peptides chosen are the C-terminal ends of two cellular transmembrane proteins with which no known PDZ domains have been reported to interact. By targeting these artificial PDZ domains to the nucleus, interacting target peptides were efficiently transported to the same subcellular localization. One of the isolated PDZ domains was tested and shown to be efficiently directed to the plasma membrane when cotransfected with the full-length transmembrane protein in mammalian cells. Thus, artificial PDZ domains can be engineered and used to target intracellular proteins to different subcellular compartments.     

Morphology and Phase Behavior of Two-Component Lipid Membranes

The stability and shapes of domains with different bending rigidities in lipid membranes are investigated. These domains can be formed from the inclusion of an impurity in a lipid membrane or from the phase separation within the membrane. We show that, for weak line tensions, surface tensions and finite spontaneous curvatures, an equilibrium phase of protruding circular domains or striped domains may be obtained. We also predict a possible phase transition between the investigated morphologies.     

Reduced polymorphism in domains involved in protein-protein interactions

Genome sequencing of various individuals or isolates of the same species allows studying the polymorphism level of specific proteins and protein domains. Here we ask whether domains that are known to be involved in mediating protein-protein interactions show lower polymorphism than other domains. To this end we take advantage of a recent genome sequence dataset of 39 Saccahromyces cerevisiae strains and the experimentally determined protein interaction network of the laboratory strain. We analyze the polymorphism in domain residues involved in interactions at various levels of resolution, depending on their likelihood to be interaction mediators. We find that domains involved in interactions are less polymorphic than other domains. Furthermore, as the likelihood of a residue to be involved in interaction increases, its polymorphism decreases. Our results suggest that purifying selection operates on domains capable of mediating protein interactions to maintain their function.     

Domains of laminin

Extracellular matrix molecules are often very large and made up of several independent domains, frequently with autonomous activities. Laminin is no exception. A number of globular and rod-like domains can be identified in laminin and its isoforms by sequence analysis as well as by electron microscopy. Here we present the structure-function relations in laminins by examination of their individual domains. This approach to viewing laminin is based on recent results from several laboratories. First, some mutations in laminin genes that cause disease have affected single laminin domains, and some laminin isoforms lack particular domains. These mutants and isoforms are informative with regard to the activities of the mutated and missing domains. Second, laminin-like domains have now been found in a number of other proteins, and data on these proteins may be informative in terms of structure-function relationships in laminin. Finally, a large body of data has accumulated on the structure and activities of proteolytic fragments, recombinant fragments, and synthetic peptides from laminin. The proposed activities of these domains can now be confirmed and extended by in vivo experiments. © 1996 Wiley-Liss, Inc.     

Immunoglobulin-like domains on bacteriophage: weapons of modest damage?

Recent work has shown that Immunoglobulin-like (Ig-like) domains occur frequently on the surface of tailed dsDNA bacteriophages. Several of these Ig-like domains are added to bacteriophage structural proteins via programmed ribosomal frameshifts, and their evolutionary patterns suggest that they can be exchanged by horizontal transfer, independently of the protein to which they are attached. We propose that Ig-like domains on phages interact with carbohydrates on the cell surface and facilitate phage adsorption. Furthermore, Ig-like domains appear to be one of a number of conserved domains displayed on phage surfaces that serve to increase infectivity by binding to or degrading polysaccharides.     

Regulatory systems of genome domains with vague boundaries

The specific features of genome domains lacking distinct boundaries are considered. These domains cannot be mapped by testing extended genome regions for nuclease sensitivity and thereby differ from structural domains determined at the level of DNA folding in chromatin. Yet they possess the properties of typical functional domains, containing a gene or several coordinated genes along with a complex of cis-regulatory elements, which control these genes. Domains with vague boundaries may be mapped with certain structural tests, e.g., by assessing histone acetylation or the distribution of tissue-specific DNase I-hypersensitive sites through extended genome regions. The mechanisms are described in detail that regulate the function of genes in domains with vague boundaries, including overlapping domains with genes differing in tissue specificity of expression.     

Regulatory Systems of Genome Domains with Vague Boundaries

The specific features of genome domains lacking distinct boundaries are considered. These domains cannot be mapped by testing extended genome regions for nuclease sensitivity and thereby differ from structural domains determined at the level of DNA folding in chromatin. Yet they possess the properties of typical functional domains, containing a gene or several coordinated genes along with a complex of cis-regulatory elements, which control these genes. Domains with vague boundaries may be mapped with certain structural tests, e.g., by assessing histone acetylation or the distribution of tissue-specific DNase I-hypersensitive sites through extended genome regions. The mechanisms are described in detail that regulate the function of genes in domains with vague boundaries, including overlapping domains with genes differing in tissue specificity of expression.     

Modules, multidomain proteins and organismic complexity

Originally the term 'protein module' was coined to distinguish mobile domains that frequently occur as building blocks of diverse multidomain proteins from 'static' domains that usually exist only as stand-alone units of single-domain proteins. Despite the widespread use of the term 'mobile domain', the distinction between static and mobile domains is rather vague as it is not easy to quantify the mobility of domains. In the present work we show that the most appropriate measure of the mobility of domains is the number of types of local environments in which a given domain is present. Ranking of domains with respect to this parameter in different evolutionary lineages highlighted marked differences in the propensity of domains to form multidomain proteins. Our analyses have also shown that there is a correlation between domain size and domain mobility: smaller domains are more likely to be used in the construction of multidomain proteins, whereas larger domains are more likely to be static, stand-alone domains. It is also shown that shuffling of a limited set of modules was facilitated by intronic recombination in the metazoan lineage and this has contributed significantly to the emergence of novel complex multidomain proteins, novel functions and increased organismic complexity of metazoa.     

Most partial domains in proteins are alignment and annotation artifacts

BackgroundProtein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally compact, units from which larger functional proteins are assembled; however, almost 4% of Pfam27 PfamA domains are shorter than 50% of their family model length, suggesting that more than half of the domain is missing at those locations. To better understand the structural nature of partial domains in proteins, we examined 30,961 partial domain regions from 136 domain families contained in a representative subset of PfamA domains (RefProtDom2 or RPD2).ResultsWe characterized three types of apparent partial domains: split domains, bounded partials, and unbounded partials. We find that bounded partial domains are over-represented in eukaryotes and in lower quality protein predictions, suggesting that they often result from inaccurate genome assemblies or gene models. We also find that a large percentage of unbounded partial domains produce long alignments, which suggests that their annotation as a partial is an alignment artifact; yet some can be found as partials in other sequence contexts.ConclusionsPartial domains are largely the result of alignment and annotation artifacts and should be viewed with caution. The presence of partial domain annotations in proteins should raise the concern that the prediction of the protein’s gene may be incomplete. In general, protein domains can be considered the structural building blocks of proteins.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0656-7) contains supplementary material, which is available to authorized users.     

Transmembrane domain analysis of polycystin-1, the product of the polycystic kidney disease-1 (PKD1) gene: evidence for 11 membrane-spanning domains

Polycystin-1, the protein product of the polycystic kidney disease-1 (PKD1) gene, was originally predicted to be an integral membrane glycoprotein with 11 transmembrane (TM) domains (TM 1-11). Subsequent comparative sequence analyses led to a revision of the original model, which retained the overall topology and 11 TM segments (TM I-XI) but dropped 3 of the original domains and introduced 3 new TM domains. The membrane-spanning potential and the orientation of each of the proposed TM domains following the extracellular REJ domain (TM I-XI and TM 11) have now been tested. Using a series of N-terminal polycystin TM-glycosylation reporter gene fusions expressed in vivo, we assayed N-linked glycosylation of the C-terminal glycosylation reporter as an indicator of TM domain presence and orientation. This approach has clearly demonstrated that 7 of the 12 TM domains tested function as membrane-spanning domains. In vitro analysis of the topogenic potential of the five remaining TM domains revealed that four of these also function as membrane-spanning domains, thus supporting an 11 TM structure for polycystin-1 comprised of TM domains I-XI. In addition, these studies suggest that the membrane insertion of TM domains I-IX occurs in a cotranslational and sequential manner, while multiple topogenic determinants appear to be required for the integration of the C-terminal-most TM segments of polycystin-1.     

The domains of death: evolution of the apoptosis machinery

Recent progress in research into programmed cell death has resulted in the identification of the principal protein domains involved in this process. The evolution of many of these domains can be traced back in evolution to unicellular eukaryotes or even bacteria, where the domains appear to be involved in other regulatory functions. Cell-death systems in animals and plants share several conserved domains, in particular the family of apoptotic ATPases; this allows us to suggest a plausible, even if still incomplete, scenario for the evolution of apoptosis.     

What are oligomerization domains good for?

Collagen triple helices, coiled coils and other oligomerization domains mediate the subunit assembly of a large number of proteins. Oligomerization leads to functional advantages of multivalency and high binding strength, increased structure stabilization and combined functions of different domains. These features seen in naturally occurring proteins can be engineered by protein design by combining oligomerization domains with functional domains.     

Spontaneous domain formation of phospholipase A2 at interfaces: fluorescence microscopy of the interaction of phospholipase A2 with mixed monolayers of lecithin, lysolecithin and fatty acid.

Fluorescence microscopy has recently been proven to be an ideal tool to investigate the specific interaction of phospholipase A2 with oriented substrate monolayers. Using a dual labeling technique, it could be shown that phospholipase A2 can specifically attack and hydrolyze solid analogous L-alpha-DPPC domains. After a critical extent of monolayer hydrolysis the enzyme itself starts to aggregate forming regular shaped protein domains (Grainger et al. (1990) Biochim. Biophys. Acta 1023, 365-379). In order to confirm that the existence of hydrolysis products in the monolayer is necessary for the observed aggregation of phospholipase A2, mixed monolayers of D- and L-alpha-DPPC, L-alpha-lysoPPC and palmitic acid in different ratios were examined. The phase behavior and the interaction of these films with phospholipase A2 were directly visualized with an epifluorescence microscope. Above a certain critical concentration of lysolecithin and palmitic acid in the monolayer, compression of these mixed films leads to phase separation and formation of mixed domains of unknown composition. Their high negative charge density is evidenced by preferential binding of a cationic dye to these phase-separated areas. Introduction of fluorescence-labeled phospholipase A2 underneath these mixed domains results in rapid binding of the protein to the domains without visible hydrolytic activity, regardless of whether the L-form or the D-form of the DPPC were used. In binary mixtures, only those with DPPC/palmitic acid show formation of phase-separated areas which can be specifically targeted by phospholipase A2 leading to a rapid formation (within 2 min) of protein domains. Experiments with pyrenedecanoic acid containing monolayers give the first direct evidence that acid is located above the enzyme domains. These results show that a locally high negative charge density of the phase-separated domains is one of the prerequisites for the binding of phospholipase A2. In addition, however, small amounts of D- or L-alpha-DPPC headgroups within the domains of the monolayer seem to be necessary for recognition followed by fast binding of the protein to the domains. This is confirmed by experiments with mixed monolayers of diacetylene carboxylic acid and D-alpha-DPPC. The acid--immiscible with lecithin--forms well defined pure acid domains in the monolayer. While the cationic dye can be docked rapidly to these phase separated areas, no preferential enzyme binding and thus no protein domain formation below these acid domains can be induced.     

Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins

Zona Pellucida (ZP) domains have been found in a wide variety of extracellular proteins, in which they play essential role for polymerization. They are shared by the ZP proteins, which constitute the extracellular coat of animal eggs. Except from ZP3, constituting the primary sperm receptor, the ZP proteins possess, in addition to their C-terminal ZP domains, N-terminal extensions, which are thought to play an important role in the species-specific gamete recognition. Here, we show that these extensions are made of single or multiple copies of a small globular domain, which can be significantly related to the N-terminal region of ZP domains (ZP-N domains). This finding brings new insights into the molecular evolution of ZP proteins, which may have evolved around a common ZP-N architecture, and more generally into the noticeable sequence diversity of ZP-N domains, which can be found as isolated subunits or tightly associated with ZP-C domains to form complete, canonical ZP domains.