The Mysterious Unfoldome: Structureless, Underappreciated, Yet Vital Part of Any Given Proteome

Contrarily to the general believe, many biologically active proteins lack stable tertiary and/or secondary structure under physiological conditions in vitro. These intrinsically disordered proteins (IDPs) are highly abundant in nature and many of them are associated with various human diseases. The functional repertoire of IDPs complements the functions of ordered proteins. Since IDPs constitute a significant portion of any given proteome, they can be combined in an unfoldome; which is a portion of the proteome including all IDPs (also known as natively unfolded proteins, therefore, unfoldome), and describing their functions, structures, interactions, evolution, and so forth. Amino acid sequence and compositions of IDPs are very different from those of ordered proteins, making possible reliable identification of IDPs at the proteome level by various computational means. Furthermore, IDPs possess a number of unique structural properties and are characterized by a peculiar conformational behavior, including their high stability against low pH and high temperature and their structural indifference toward the unfolding by strong denaturants. These peculiarities were shown to be useful for elaboration of the experimental techniques for the large-scale identification of IDPs in various organisms. Some of the computational and experimental tools for the unfoldome discovery are discussed in this review

Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics

Recognition of the natural abundance and functional importance of intrinsically disordered proteins (IDPs), and protein hybrids that contain both intrinsically disordered protein regions (IDPRs) and ordered regions, is changing protein science. IDPs and IDPRs, i.e., functional proteins and protein regions without unique structures, can often be found in all organisms, and typically play vital roles in various biological processes. Disorder-based functionality complements the functions of ordered proteins and domains. However, by virtue of their existence, IDPs/IDPRs, which are characterized by remarkable conformational flexibility and structural plasticity, break multiple rules established over the years to explain structure, folding, and functionality of well-folded proteins with unique structures. Despite the general belief that unique biological functions of proteins require unique 3D-structures (which dominated protein science for more than a century), structure-less IDPs/IDPRs are functional, being able to engage in biological activities and perform impossible tricks that are highly unlikely for ordered proteins. With their exceptional spatio-temporal heterogeneity and high conformational flexibility, IDPs/IDPRs represent complex systems that act at the edge of chaos and are specifically tunable by various means. In this article, some of the wonders of intrinsic disorder are discussed as illustrations of their “mysterious” (meta)physics

From multifunctionality to polypathogenicity with intrinsic disorder

Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structure under physiological conditions in vitro. IDPs are characterized by an astonishing multilevel spatiotemporal heterogeneity, with their mosaic structure representing a complex combination of foldons, inducible foldons, morphing inducible foldons, non-foldons, semifoldons, and unfoldons. IDPs are highly abundant in nature and have functional repertoire that is very broad and complements functions of ordered proteins. Often, IDPs are involved in regulation, signaling and control pathways, commonly acting as hubs in protein-protein interaction networks. Intrinsic disorder is an important constituent of the proteoform concept, representing one of the important means of functional diversification of the proteinaceous products of a gene. Functions of IDPs may arise from specific disordered forms, from inter-conversion of disordered forms, or from order ←→ disorder transitions. The choice between these conformations is determined by the peculiarities of the protein environment, and many IDPs possess an exceptional ability to differently fold in a template-dependent manner. As a result, many IDPs are capable of conducting multiple functions, with such multifunctionality being linked to their spatiotemporal heterogeneity. Therefore, a correlation between protein structure and function represents a “protein structure–function continuum”, where a given protein exists as a dynamic conformational ensemble containing multiple proteoforms characterized by diverse structural features and miscellaneous functions. IDPs are tightly controlled in the norm by various genetic and non-genetic mechanisms. Alteration in regulation of this disordered regulators are often detrimental to a cell, and many IDPs are associated with a variety of human diseases, such as cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, diabetes and others. Furthermore, many IDPs are multipathogenic, being associated with the origination and development of a number of different diseases. Therefore, there is a though-provoking interconnection between intrinsic disorder, cell signaling, and human diseases, with polypathogenicity of the involved proteins being linked to their structural plasticity and multifunctionality.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Nipah shell disorder, modes of infection, and virulence

The Nipah Virus (NiV) was first isolated during a 1998–9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (~71%, 2001–5, ~93%, 2008–12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r2 = 0.93, p < 0.01, ANOVA: p < 0.01). Distinct disorder and, therefore, genetic differences can be found in all three group of strains. The fact that the transmission modes of the Malaysia strain are different from those of the Bangladesh strains suggests that the correlations may also be linked to the modes of viral transmission. Analysis of the NiV and related viruses suggests links between modes of transmission and disorder of not just the N protein but, also, of M shell protein. The links among shell disorder, transmission modes, and virulence suggest mechanisms by which viruses are attenuated as they passed through different cell hosts from different animal species. These have implications for development of vaccines and epidemiological molecular analytical tools to contain outbreaks

Composition Profiler: a tool for discovery and visualization of amino acid composition differences

<p>Abstract</p> <p>Background</p> <p>Composition Profiler is a web-based tool for semi-automatic discovery of enrichment or depletion of amino acids, either individually or grouped by their physico-chemical or structural properties.</p> <p>Results</p> <p>The program takes two samples of amino acids as input: a query sample and a reference sample. The latter provides a suitable background amino acid distribution, and should be chosen according to the nature of the query sample, for example, a standard protein database (e.g. SwissProt, PDB), a representative sample of proteins from the organism under study, or a group of proteins with a contrasting functional annotation. The results of the analysis of amino acid composition differences are summarized in textual and graphical form.</p> <p>Conclusion</p> <p>As an exploratory data mining tool, our software can be used to guide feature selection for protein function or structure predictors. For classes of proteins with significant differences in frequencies of amino acids having particular physico-chemical (e.g. hydrophobicity or charge) or structural (e.g. α helix propensity) properties, Composition Profiler can be used as a rough, light-weight visual classifier.</p

A comparative analysis of viral matrix proteins using disorder predictors

Abstract Background A previous study (Goh G.K.-M., Dunker A.K., Uversky V.N. (2008) Protein intrinsic disorder toolbox for comparative analysis of viral proteins. BMC Genomics. 9 (Suppl. 2), S4) revealed that HIV matrix protein p17 possesses especially high levels of predicted intrinsic disorder (PID). In this study, we analyzed the PID patterns in matrix proteins of viruses related and unrelated to HIV-1. Results Both SIVmac and HIV-1 p17 proteins were predicted by PONDR VLXT to be highly disordered with subtle differences containing 50% and 60% disordered residues, respectively. SIVmac is very closely related to HIV-2. A specific region that is predicted to be disordered in HIV-1 is missing in SIVmac. The distributions of PID patterns seem to differ in SIVmac and HIV-1 p17 proteins. A high level of PID for the matrix does not seem to be mandatory for retroviruses, since Equine Infectious Anemia Virus (EIAV), an HIV cousin, has been predicted to have low PID level for the matrix; i.e. its matrix protein p15 contains only 21% PID residues. Surprisingly, the PID percentage and the pattern of predicted disorder distribution for p15 resemble those of the influenza matrix protein M1 (25%). Conclusion Our data might have important implications in the search for HIV vaccines since disorder in the matrix protein might provide a mechanism for immune evasion.</p

Granulins Modulate Liquid-Liquid Phase Separation and Aggregation of Prion-Like C-Terminal Domain of the Neurodegeneration-Associated Protein TDP-43

Tar DNA binding protein 43 (TDP-43) has emerged as a key player in many neurodegenerative pathologies including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Hallmarks of both FTLD and ALS are the toxic cytoplasmic inclusions of the prion-like C-terminal fragments of TDP-43 (TDP-43 CTD), formed upon proteolytic cleavage of full-length TDP-43 in the nucleus and subsequent transport to the cytoplasm. Both full-length TDP-43 and its CTD are also known to form stress granules (SGs) by coacervating with RNA in the cytoplasm during stress and may be involved in these pathologies. Furthermore, mutations in PGRN gene, leading to haploinsufficiency and diminished function of progranulin (PGRN) protein, are strongly linked to FTLD and ALS. Recent reports have indicated that proteolytic processing of PGRN to smaller protein modules called granulins (GRNs) contributes to FTLD and ALS progression, with specific GRNs exacerbating TDP-43–induced cytotoxicity. Here, we investigated the interactions between the proteolytic products of both TDP-43 and PGRN. Based on structural disorder and charge distributions, we hypothesized that GRNs -3 and -5 could interact with TDP-43 CTD. We also show that in both reducing and oxidizing conditions GRNs -3 and -5 interact with and differentially modulate TDP-43 CTD aggregation and/or liquid-liquid phase separation (LLPS) in vitro. While GRN-3 promoted insoluble aggregates of TDP-43 CTD, GRN-5 mediated LLPS. These results constitute the first observation of an interaction between GRNs and TDP-43, suggesting a mechanism by which attenuated PGRN function could lead to familial FTLD or ALS

Molecular Mechanisms of Persistence of Mutualistic Bacteria Photorhabdus in the Entomopathogenic Nematode Host

Symbioses between microbes and animals are ubiquitous, yet little is known about the intricate mechanisms maintaining such associations. In an emerging mutualistic model system, insect-pathogenic bacteria Photorhabdus and their insect-parasitic nematode partner Heterorhabditis, we found that the bacteria undergo major transcriptional reshaping in the nematode intestine. Besides general starvation mechanisms, the bacteria induce cellular acidification to slow down growth, switch to pentose phosphate pathway to overcome oxidative stress and nutrition limitation, and shed motility but develop biofilm to persist in the nematode intestine until being released into the insect hemolymph. These findings demonstrate how the symbiotic bacteria reduce their nutritional dependence on the enduring nematode partner to ensure successful transmission of the couple to the next insect host