What are three types of structural proteins?

Structural Proteins

The 191–amino acid segment at the amino terminus of the HCV polyprotein is cleaved from the nascent polypeptide by signal peptidase, forming the highly basic core protein, which has RNA-binding activity.47–50 A second cleavage occurs just upstream of the signal peptide sequence, directed by signal peptide peptidase within the membranes of the ER, producing a mature core protein of 173 amino acids that is trafficked to lipid droplets, where it associates with NS5A.51–53 The core protein is immunogenic; both core protein and antibody to it are typically present in the serum of infected individuals.

Many biologic activities have been associated with the core protein, including suppression of HBV replication, alterations in regulation of the cell cycle and transcription of cellular protooncogenes, either induction or suppression of apoptosis, and transformation of rat embryo fibroblasts.54–64 The core protein has also been suggested to interfere with anti-HCV immune responses through a variety of mechanisms, including NK cell inhibition via upregulation of major histocompatibility complex (MHC) class I expression, inhibition of T-cell proliferation via interaction with complement receptor gC1qR, and interaction with the cytoplasmic tail of several cellular receptors belonging to the tumor necrosis factor (TNF) receptor family.60,61,63,65,66 However, these data are derived largely from studies in which core has been overexpressed from recombinant cDNA. It is not clear whether core exerts any of these biologic effects when expressed by replicating virus within the liver, and in many cases there is contradictory evidence.

Yellow fever virus and other flaviviruses have a single major envelope protein and a glycosylated, cell-associated NS-1 protein that can elicit neutralizing antibodies. In contrast, hepaciviruses have two major envelope glycoproteins (E1 and E2) and no comparable NS-1 protein. Signal peptidases direct cleavage of the HCV polyprotein at amino-acid residues 383 and 746 (numbering based on the prototype strain H77), producing the E1 and E2 proteins, respectively (seeFig. 154.2).48 These are secreted into the ER as type 1 transmembrane proteins, fold cooperatively, and remain anchored to the membrane by a hydrophobic carboxyl-terminal anchor sequence (Fig. 154.3). The E1 and E2 proteins are heavily glycosylated, with sugar moieties representing about 50% of the mature mass of each. Although initially associated as a noncovalent heterodimeric complex because of oligomerization determinants in the transmembrane segments, covalently linked complexes have been identified in mature, infectious virions.67,68 In HCV cell culture, E1 and E2 are localized to the ER compartment, perhaps owing to ER-retention signals located in the transmembrane domain.52,69–71 This suggests that, like other members of the Flaviviridae, HCV particles assemble and exit the cell by budding into intracytoplasmic vesicles and then follow the secretory pathway for release.

The N-Genes are Shared Between IVSPERS and Viral Segments

The IVSPERs characterized in Hyposoter dydimator contain members of a gene family, the N-gene family, also present in the encapsidated genome. The N-genes were first described in CsIV segment N and they are reported in all sequenced IV packaged genomes (Tanaka et al., 2007; Webb et al., 2006). In HdIV, several viral segments encode N-genes (Volkoff, personal data) including the two segments located in the vicinity of IVSPER-1 and IVSPER-2 (Fig. 2). In both T. rostrale and C. sonorensis, an N-gene not present in the packaged genome sequenced was found among the ESTs. Those additional T. rostrale and C. sonorensis N-genes are most likely located within an IVSPER. This suggests that in the three Campopleginae species, N-genes are present in the packaged genome and expressed in the parasitized host while other N-genes are present in the IVSPERs and expressed in the wasp ovaries.

In H. didymator, viral segments located in the vicinity of an IVSPER contain an N-gene. Presence of N-genes in both IVSPERs and viral segments suggest genomic exchanges and/or common ancestral sequences between HdIV and the H. didymator IVSPERs. When a phylogenetic tree is drawn using an alignment of IVSPER and packaged N-gene sequences (Fig. 4), the IVSPER N-genes group together and are separated from those located on the viral segment. This suggests that IVSPER N-genes have diverged from the packaged ones.

Mouse Models for Structural and Desmosomal Proteins

The generation of mouse models has significantly increased our understanding of skin biology and the pathophysiology of genodermatoses. Animals harboring mutational “hot spots” that have been identified in humans are also useful for testing novel disease-targeted treatments38 (Table 56.5). In the case of dominant-negative mutations, the mutant allele can potentially be silenced using short interfering RNA (siRNA) technology. Promising results were obtained in a reporter mouse model where non-invasive, pain-free administration of siRNAs into the skin was achieved via topical administration39. Such investigation in mouse models can help to bring new technologies closer to clinical use.

Viral immunomodulators

Structural proteins of some plant viruses are elicitors of defense responses in the hosts (Chapter 7). For instance, the 17.5 kDa TMV CP induces HR in resistant tobacco species and cultivars. It possesses the elicitor only in the form of crystalline aggregates. A 17 kDa cytokine (cytokines are the protein molecules involved in transmission of the immune signal between the immune cells) the tumor necrosis factor (TNF) produced by T-lymphocytes and macrophages, causes development of the classical inflammation signs: swelling, redness, pain, and fever. It causes cell necrosis. The three-molecule aggregate is also active. The TNF protein is homologous to the structural protein of the TNV satellite virus.

Protein RepA of plant heminiviruses as well as proteins EA and E7 of animal viruses suppress the retinoblastoma gene, the role of which was described earlier.

Filaggrin and other structural proteins

Filaggrin is a keratinfilament-aggregating protein that serves as a major structural component of the stratum corneum. Loss-of-functionFLG mutations represent the strongest known genetic risk factor for AD and are also responsible for ichthyosis vulgaris19–22 (seeCh. 57), with carrier frequencies of up to 10% in European and ~3% in East Asian populations23–25. Approximately 20–50% of European and Asian children with moderate-to-severe AD have at least oneFLG mutation; the penetrance of AD is ~40% for one and ~90% for two mutant alleles20. This implicates epidermal barrier dysfunction in the initiation of AD, with subsequent development of Th2-biased immune responses24. Of note, filaggrin expression is also affected by intragenic copy number variation and reduced by increased local pH, protease activity, and Th2 cytokine levels22,26.

FLG mutations are associated with early-onset AD, greater disease severity, and persistence into adulthood as well as enhanced epicutan­eous sensitization and an increased risk of irritant contact dermatitis, hand eczema, herpes simplex virus (HSV) infections, and food allergy20,25,27.FLG mutations have also been linked to an increased risk for the development of asthma and greater asthma severity; however, these effects are only seen in patients with pre-existing AD28. Since filaggrin is not found in the gastrointestinal or bronchial mucosa, the association ofFLG mutations with food allergy and asthma strongly suggests that epicutaneous sensitization and/or cutaneous inflammation can contribute to the development of systemic atopic disease29.

Filaggrin breakdown products such as histidine contribute to epidermal hydration, acid mantle formation, lipid processing, and barrier function20,27. Gene expression profiling and immunohistochemical analysis of lesional and nonlesional skin from AD patients have shown broad defects in terminal differentiation, with down-regulation of other epidermal barrier proteins such as loricrin, corneodesmosin, involucrin, small prolene rich proteins 3/4 (SPRR3/4), claudin-1, and late cornified envelope protein 2B30–34.

50 Explain why autosomal dominant diseases usually affect structural proteins and receptors rather than enzymes

Structural proteins and receptors are associated with dominant inheritance because they typically interact to form multimeric complexes. The presence of defective protein in patients with one mutant allele may be sufficient to render the entire complex nonfunctional. For example, patients with osteogenesis imperfecta synthesize an abnormal collagen chain that blocks the assembly of trimeric collagen fibrils. In contrast, enzymes are commonly associated with recessive inheritance because a 50% reduction in enzyme activity in patients with one mutant allele is typically corrected by increasing substrate concentration. Complete (100%) reduction in enzyme activity in patients with two mutant alleles cannot be corrected and is associated with clinical evidence of disease.

Proteins

Structural proteins of most members of the family consist of a major CP and of a diverged copy of it denoted minor CP (CPm), with a size ranging from 22 to 46 kDa (CP) and 23 to 80 kDa (CPm), according to the individual species. A group of ampeloviruses with a small-sized genome (ca. 13,000 nt) apparently lacks a true CPm. With BYV, and presumably for most other members of the family, CPm is required for the assembly of the 5′-extremity of the virion, the protein of about 60 kDa is required for incorporation of both HSP70h and CPm to virions, which also incorporate a 20 kDa protein that may form the tip segment of the virion head.

Conclusions

Protein structural classifications categorise protein structures deposited in the PDB according to their 3D structural characteristics and evolutionary relationships. There are three major classifications publically available to use: SCOP, CATH, and ECOD. A range of algorithms have been developed to recognise domain boundaries within protein structures using sequence-, structure-, and ab-initio-based methods. Algorithms have also been developed to detect homologous relationships, which are used to assign these domains into homologous superfamily groups and thereby classifying them within a classification hierarchy.

Nearest-neighbour clustering methods are an alternative way of searching for structural homologues. Structural comparison methods (e.g., Dali and VAST+) are used to compare one or more query structures against each other or the whole PDB archive, for example. Only information on structural similarity is provided, offering a fast way to generate lists of potential structural relatives and analogues.

SCOP, CATH and ECOD have many similarities in their protein structural classification hierarchies, which are discussed in Section “Hierarchical Structural Classification”. Consensus SCOP and CATH superfamily data have been identified through the Genome3D project and are currently being integrated into the InterPro resource to increase the coverage of data for the SUPERFAMILY and Gene3D resources (see Section “Integration of the SCOP and CATH Resources”).

A look into the current status of the protein structural universe highlights the large amounts of structural data that has been analysed and made publically available. As seen over recent years, there is an uneven distribution of domains assigned to protein folds and superfamilies. For example, the 100 most-populated CATH superfamilies have consistently accounted for around half of all structural domain sequences.

Taking a look at the vast amounts of genomic sequence data available, Section “Structural Families in the Genomic Era” describes how structural family data is used to annotate these data, which do not have any known structures. HMM libraries are built from structural domain data in CATH, which are then used by the sister resource Gene3D to scan genome sequences against to find significant structural matches for domain and homology detection. These scanning methods and libraries provide a very powerful way to annotate genomic data.

CATH superfamilies and functional families can be used to examine the evolution of protein sequence, structure and function. The mechanisms behind these divergences are discussed in Section “Evolution of Protein Structure, Sequence and Function”. Superfamily superpositions illustrate any structural diversity within a superfamily, yet clearly show that even diverse superfamily have a highly conserved structural core. Functional family data are an important part in exploring functional diversity within a superfamily, determining functional relatives and in annotating protein function for unknown sequences.

5 Summary

Protein structural comparison, classification, and searching for structural similarity are problems that have received considerable attention in the past several decades (Hasegawa & Holm, 2009). It has been shown that such methodologies can be used for establishing evolutionary and functional relationships between proteins (Ouzounis, Coulson, Enright, Kunin, & Pereira-Leal, 2003). Here and in prior work (Grigoryan & Degrado, 2011; Grigoryan et al., 2011), we have demonstrated that structural similarity, when considered at a detailed local level, can also shed light on the designability of different structural motifs comprising proteins. It can provide a connection between structure and sequence, invaluable in de novo computational protein design, and potentially in structure prediction. MaDCaT is a tool particularly well suited for establishing such links, as its definition of similarity is focused on the precise local geometry, with particular emphasis on close contacts. By making MaDCaT freely available, we hope to stimulate its application in protein design and structure prediction, as well as its further development.

Proteins

Structural proteins common to all genera include: three polypeptides that form the viral RdRp (e.g., PA, PB1, PB2 in FLUAV); a nucleoprotein (NP), which is associated with each genome ssRNA segment to form the RNP; a hemagglutinin (HA, HE [HEF] or GP), which is an integral, type I membrane glycoprotein involved in virus attachment, envelope fusion and neutralization; and a non-glycosylated matrix protein (M1 or M). The HA of FLUAV is acylated at the membrane-spanning region and has N-linked glycans at a number of sites. In addition to its hemagglutinating and fusion properties, the HE (HEF) protein of FLUCV has esterase activity that functions as a receptor-destroying enzyme. In contrast, the GP of THOV is unrelated to influenzavirus proteins, but shows sequence homology to a baculovirus surface glycoprotein. Members of the genera Influenzavirus A and Influenzavirus B have an integral, type II envelope glycoprotein (neuraminidase, NA), which contains sialidase activity. Depending on the genus, viruses possess small integral membrane proteins (M2, NB, BM2, or CM2) that may be glycosylated. M2 and BM2 function as proton-selective ion channels in mammalian cells, acidifying the virion interior during uncoating and fusion and equilibrating the intralumenal pH of the trans-Golgi apparatus with that of the cytoplasm. The ion-channel activity of only the former is inhibited by the adamantane anti-influenza A drugs, amantadine and rimantadine. In addition to the structural proteins and depending on the genus, viruses may code for two nonstructural proteins (NS1, NS2 [NEP]) although NS2 is also found in the virus particle. Virion enzymes (variously represented and reported among genera) include a transcriptase (PB1 in influenzaviruses A, B, C and thogotoviruses), an endonuclease (PA in influenzaviruses A, B, C), and a receptor-destroying enzyme (neuraminidase (NA) for FLUAV and FLUBV, or 9-0-acetyl-neuraminyl esterase in the case of the FLUCV HE [HEF] protein).