Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo

Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of “inert” macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid–liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).     

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.     

Methods of probing the interactions between small molecules and disordered proteins

It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.     

Helix insertion into bilayers and the evolution of membrane proteins

Polytopic α-helical membrane proteins cannot spontaneously insert into lipid bilayers without assistance from polytopic α-helical membrane proteins that already reside in the membrane. This raises the question of how these proteins evolved. Our current knowledge of the insertion of α-helices into natural and model membranes is reviewed with the goal of gaining insight into the evolution of membrane proteins. Topics include: translocon-dependent membrane protein insertion, antibiotic peptides and proteins, in vitro insertion of membrane proteins, chaperone-mediated insertion of transmembrane helices, and C-terminal tail-anchored (TA) proteins. Analysis of the E. coli genome reveals several predicted C-terminal TA proteins that may be descendents of proteins involved in pre-cellular membrane protein insertion. Mechanisms of pre-translocon polytopic α-helical membrane protein insertion are discussed.     

Radioactive amino acid incorporation into the rat pancreatic juice proteins

Zusammenfassung Es wurde der zeitliche Verlauf des Einbaus radioaktiver Aminosäuren (Phenylalanin-3-C¹⁴, Alanin-1-C¹⁴, Histidin-2-C¹⁴ und Methionin-S³⁵) in die Proteine des Pankreassaftes der Ratte untersucht. Ein Maximum des Einbaus kommt zwischen der zweiten und vierten Stunde nach Injektion der Aminosäuren vor, während in der ersten Stunde praktisch keine radioaktiven Proteine nachgewiesen werden konnten. Die Ergebnisse werden verglichen mit denen früher beschriebener Versuche mit Glyzin-C¹⁴.

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Aided partially by grants from the Conselho Nacional de Pesquisas and Deutsche Forschungsgemeinschaft.     

G-protein signaling: back to the future

Heterotrimeric G-proteins are intracellular partners of G-protein-coupled receptors (GPCRs). GPCRs act on inactive G·GDP/G heterotrimers to promote GDP release and GTP binding, resulting in liberation of G from G. G·GTP and G target effectors including adenylyl cyclases, phospholipases and ion channels. Signaling is terminated by intrinsic GTPase activity of G and heterotrimer reformation – a cycle accelerated by regulators of G-protein signaling (RGS proteins). Recent studies have identified several unconventional G-protein signaling pathways that diverge from this standard model. Whereas phospholipase C (PLC) is activated by G_q and G, novel PLC isoforms are regulated by both heterotrimeric and Ras-superfamily G-proteins. An Arabidopsis protein has been discovered containing both GPCR and RGS domains within the same protein. Most surprisingly, a receptor-independent G nucleotide cycle that regulates cell division has been delineated in both Caenorhabditis elegans and Drosophila melanogaster. Here, we revisit classical heterotrimeric G-protein signaling and explore these new, non-canonical G-protein signaling pathways.Received 21 October 2004; received after revision 20 November 2004; accepted 30 November 2004     

Dps-like proteins: structural and functional insights into a versatile protein family

Dps-like proteins are key factors involved in the protection of prokaryotic cells from oxidative damage. They act by either oxidizing iron to prevent the formation of oxidative radicals or by forming Dps-DNA complexes to physically protect DNA. All Dps-like proteins are characterized by a common three-dimensional architecture and are found as spherical dodecamers with a hollow central cavity. Despite their structural similarities, recent biochemical and structural data have suggested different functions among members of the family that range from protection inside the cells in response to various stress signals to adhesion and virulence during bacterial infections. Moreover, the Dps-like proteins have lately attracted considerable interest in the field of nanotechnology owing to their ability to act as protein cages for iron and various other metals. A better understanding of their function and mechanism could therefore lead to novel applications in biotechnology and nanotechnology.     

Autoradiographic study of the penetration of non-histone chromatin proteins into differentiating cells

Summary Attention has previously been drawn to a specific effect of NHCP on embryonicPleurodeles cell differentiation. With a modified NHCP labelling technique, autoradiography has revealed a cytoplasmic concentration of labelled NHCP and has not revealed any difference between homospecific and heterospecific NHCP penetration.This work has been supported financially by research grants from the C.N.R.S. (ERA No. 327 and ATP No. 4310 on the cellular differentiation), and INSERM (No. 711019).The authors wish to extend their thands to Dr.Mazarguil who kindly initiated us in the techniques of enzyme binding. Many thanks are also due to Mr.Hawks for most valuable help in correcting the English.     

Autoradiographic study of the penetration of non-histone chromatin proteins into differentiating cells.

Attention has previously been drawn to a specific effect of NHCP on embryonic Pleurodeles cell differentiation. With a modified NHCP labelling technique, autoradiography has revealed a cytoplasmic concentration of labelled NHCP and has not revealed any difference between homospecific and heterospecific NHCP penetration.     

Looking forward,not back: Supporting structuralism in the present

The view that the fundamental kind properties are intrinsic properties enjoys reflexive endorsement by most metaphysicians of science. But ontic structural realists deny that there are any fundamental intrinsic properties at all. Given that structuralists distrust intuition as a guide to truth, and given that we currently lack a fundamental physical theory that we could consult instead to order settle the issue, it might seem as if there is simply nowhere for this debate to go at present. However, I will argue that there exists an as-yet untapped resource for arguing for ontic structuralism – namely, the way that fundamentality is conceptualized in our most fundamental physical frameworks. By arguing that physical objects must be subject to the ‘Goldilock's principle’ if they are to count as fundamental at all, I argue that we can no longer view the majority of properties defining them as intrinsic. As such, ontic structural realism can be regarded as the most promising metaphysics for fundamental physics, and that this is so even though we do not yet claim to know precisely what that fundamental physics is.     

Investigations into the effects of ACTH on the half-life of mitochondrial proteins in the rat adrenal cortex

Summary ACTH elongates the half-life of the mitochondrial proteins from the rat adrenal cortex, and chloramphenicol inhibits this effect of ACTH. The hypothesis is advanced that the ACTH-provoked stabilization of the adrenocortical mitochondrial proteins requires continuous mitochondrial DNA-dependent protein synthesis.     

Immunophilins: for the love of proteins

Immunophilins are chaperones that may also exhibit peptidylprolyl isomerase (PPIase) activity. This review summarizes our knowledge of the two largest families of immunophilins, namely cyclophilin and FK506-binding protein, and a novel chimeric dual-family immunophilin, named FK506- and cyclosporin-binding protein (FCBP). The larger members of each family are modular in nature, consisting of multiple PPIase and/or protein-protein interaction domains. Despite the apparent difference in their sequence and three-dimensional structure, the three families encode similar enzymatic and biological functions. Recent studies have revealed that many immunophilins possess a chaperone function independent of PPIase activity. Knockout animal studies have confirmed multiple essential roles of immunophilins in physiology and development. An immunophilin is indeed a natural ‘protein-philin’ (Greek ‘philin’ = friend) that interacts with proteins to guide their proper folding and assembly. Received: 7 May 2006; received after revision 3 July 2006; accepted 24 August 2006     

Expansion of amino acid homo-sequences in proteins: Insights into the role of amino acid homo-polymers and of the protein context in aggregation

Expansion of amino acid homo-sequences, such as polyglutamines or polyalanines, in proteins has been directly implicated in various degenerative diseases through a mechanism of protein misfolding and aggregation. However, it is still unclear how the nature of the expansion and the protein context influence the tendency of a protein to aggregate. Here, we have addressed these questions using spinocerebellar ataxia type-3 (ATX3) protein, the best characterised of the polyglutamine proteins, chosen as a model system. Using a transfected mammalian cell line, we demonstrate that ATX3 aggregation is noticeably reduced by deletion or replacement of regions other than the polyglutamine tract. The nature of the amino acid homo-sequences also has a strong influence on aggregation. From our studies, we draw general conclusions on the effect of the protein architecture and of the amino acid homo-sequence on pathology. Received 3 March 2006; received after revision 19 April 2006; accepted 22 May 2006     

Investigations into the effects of ACTH on the half-life of mitochondrial proteins in the rat adrenal cortex.

ACTH elongates the half-life of the mitochondrial proteins from the rat adrenal cortex, and chloramphenicol inhibits this effect of ACTH. The hypothesis is advanced that the ACTH-provoked stabilization of the adrenocortical mitochondrial proteins requires continuous mitochondrial DNA-dependent protein synthesis.     

Stimulation of the incorporation of3H-leucine into proteins by oestradiol in the foetal uterus of the guinea-pig

Summary Oestradiol treatment increases the incorporation of³H-leucine into acid insoluble proteins in the foetal guineapig uterus (50–65 days of gestation) 10 times above control values by 8 h and 20 times by 24 h after administration of oestradiol to the mother.