Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners

Annexins and S100 proteins form two large families of Ca2+-binding proteins. They are quite different both structurally and functionally, with S100 proteins being small (10–12 kDa) acidic regulatory proteins from the EF-hand superfamily of Ca2+-binding proteins, and with annexins being at least three-fold larger (329 ± 12 versus 98 ± 7 residues) and using non-EF-hand-based mechanism for calcium binding. Members of both families have multiple biological roles, being able to bind to a large cohort of partners and possessing a multitude of functions. Furthermore, annexins and S100 proteins can interact with each other in either a Ca2+-dependent or Ca2+-independent manner, forming functional annexin-S100 complexes. Such functional polymorphism and binding indiscrimination are rather unexpected, since structural information is available for many annexins and S100 proteins, which therefore are considered as ordered proteins that should follow the classical “one protein–one structure–one function” model. On the other hand, the ability to be engaged in a wide range of interactions with multiple, often unrelated, binding partners and possess multiple functions represent characteristic features of intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs); i.e., functional proteins or protein regions lacking unique tertiary structures. The aim of this paper is to provide an overview of the functional roles of human annexins and S100 proteins, and to use the protein intrinsic disorder perspective to explain their exceptional multifunctionality and binding promiscuity.

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Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1

Nucleic Acids Research ◽

10.1093/nar/gkaa285 ◽

2020 ◽

Vol 48 (10) ◽

pp. 5318-5331 ◽

Cited By ~ 4

Author(s):

Akshay Sridhar ◽

Modesto Orozco ◽

Rosana Collepardo-Guevara

Keyword(s):

Binding Affinity ◽

Binding Proteins ◽

Intrinsically Disordered Proteins ◽

Order Transition ◽

Disordered Proteins ◽

Chromatin Binding ◽

Intrinsically Disordered ◽

Terminal Domain ◽

Wide Range ◽

Nucleosome Binding

Abstract Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.

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Insight into Calcium-Binding Motifs of Intrinsically Disordered Proteins

Biomolecules ◽

10.3390/biom11081173 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1173

Author(s):

Estella A. Newcombe ◽

Catarina B. Fernandes ◽

Jeppe E. Lundsgaard ◽

Inna Brakti ◽

Kresten Lindorff-Larsen ◽

...

Keyword(s):

Calcium Binding ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Binding Motif ◽

Binding Motifs ◽

Functional Roles ◽

Intrinsically Disordered ◽

Ef Hand ◽

Folded Proteins ◽

Affinity Quantification

Motifs within proteins help us categorize their functions. Intrinsically disordered proteins (IDPs) are rich in short linear motifs, conferring them many different roles. IDPs are also frequently highly charged and, therefore, likely to interact with ions. Canonical calcium-binding motifs, such as the EF-hand, often rely on the formation of stabilizing flanking helices, which are a key characteristic of folded proteins, but are absent in IDPs. In this study, we probe the existence of a calcium-binding motif relevant to IDPs. Upon screening several carefully selected IDPs using NMR spectroscopy supplemented with affinity quantification by colorimetric assays, we found calcium-binding motifs in IDPs which could be categorized into at least two groups—an Excalibur-like motif, sequentially similar to the EF-hand loop, and a condensed-charge motif carrying repetitive negative charges. The motifs show an affinity for calcium typically in the ~100 μM range relevant to regulatory functions and, while calcium binding to the condensed-charge motif had little effect on the overall compaction of the IDP chain, calcium binding to Excalibur-like motifs resulted in changes in compaction. Thus, calcium binding to IDPs may serve various structural and functional roles that have previously been underreported.

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Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures

Biomolecules ◽

10.3390/biom11121788 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1788

Author(s):

Vy T. Duong ◽

Elizabeth M. Diessner ◽

Gianmarc Grazioli ◽

Rachel W. Martin ◽

Carter T. Butts

Keyword(s):

Protein Structure ◽

Intrinsically Disordered Proteins ◽

Dynamic Models ◽

Structural Information ◽

Coarse Graining ◽

Molecular Structures ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Scalable Network ◽

Atomic Coordinates

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs.

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Supramolecular Fuzziness of Intracellular Liquid Droplets: Liquid–Liquid Phase Transitions, Membrane-Less Organelles, and Intrinsic Disorder

Molecules ◽

10.3390/molecules24183265 ◽

2019 ◽

Vol 24 (18) ◽

pp. 3265 ◽

Cited By ~ 12

Author(s):

Vladimir N. Uversky

Keyword(s):

Phase Transitions ◽

Liquid Phase ◽

Intrinsically Disordered Proteins ◽

Intrinsically Disordered Protein ◽

Disordered Proteins ◽

Bacterial Cells ◽

Liquid Droplets ◽

Intrinsically Disordered ◽

Wide Range ◽

Characteristic Features

Cells are inhomogeneously crowded, possessing a wide range of intracellular liquid droplets abundantly present in the cytoplasm of eukaryotic and bacterial cells, in the mitochondrial matrix and nucleoplasm of eukaryotes, and in the chloroplast’s stroma of plant cells. These proteinaceous membrane-less organelles (PMLOs) not only represent a natural method of intracellular compartmentalization, which is crucial for successful execution of various biological functions, but also serve as important means for the processing of local information and rapid response to the fluctuations in environmental conditions. Since PMLOs, being complex macromolecular assemblages, possess many characteristic features of liquids, they represent highly dynamic (or fuzzy) protein–protein and/or protein–nucleic acid complexes. The biogenesis of PMLOs is controlled by specific intrinsically disordered proteins (IDPs) and hybrid proteins with ordered domains and intrinsically disordered protein regions (IDPRs), which, due to their highly dynamic structures and ability to facilitate multivalent interactions, serve as indispensable drivers of the biological liquid–liquid phase transitions (LLPTs) giving rise to PMLOs. In this article, the importance of the disorder-based supramolecular fuzziness for LLPTs and PMLO biogenesis is discussed.

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Chasing coevolutionary signals in intrinsically disordered proteins complexes

Scientific Reports ◽

10.1038/s41598-020-74791-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Javier A. Iserte ◽

Tamas Lazar ◽

Silvio C. E. Tosatto ◽

Peter Tompa ◽

Cristina Marino-Buslje

Keyword(s):

Protein Interactions ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Protein Protein Interactions ◽

Contact Prediction ◽

Intrinsically Disordered ◽

Regulatory Processes ◽

Wide Range ◽

Predict Protein Structure ◽

Biological Interpretation

Abstract Intrinsically disordered proteins/regions (IDPs/IDRs) are crucial components of the cell, they are highly abundant and participate ubiquitously in a wide range of biological functions, such as regulatory processes and cell signaling. Many of their important functions rely on protein interactions, by which they trigger or modulate different pathways. Sequence covariation, a powerful tool for protein contact prediction, has been applied successfully to predict protein structure and to identify protein–protein interactions mostly of globular proteins. IDPs/IDRs also mediate a plethora of protein–protein interactions, highlighting the importance of addressing sequence covariation-based inter-protein contact prediction of this class of proteins. Despite their importance, a systematic approach to analyze the covariation phenomena of intrinsically disordered proteins and their complexes is still missing. Here we carry out a comprehensive critical assessment of coevolution-based contact prediction in IDP/IDR complexes and detail the challenges and possible limitations that emerge from their analysis. We found that the coevolutionary signal is faint in most of the complexes of disordered proteins but positively correlates with the interface size and binding affinity between partners. In addition, we discuss the state-of-art methodology by biological interpretation of the results, formulate evaluation guidelines and suggest future directions of development to the field.

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A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility inSalmonella enterica

Journal of Bacteriology ◽

10.1128/jb.00415-18 ◽

2018 ◽

Vol 201 (2) ◽

Cited By ~ 2

Author(s):

Tamiko Oguri ◽

Youjeong Kwon ◽

Jerry K. K. Woo ◽

Gerd Prehna ◽

Hyun Lee ◽

...

Keyword(s):

Intrinsically Disordered Proteins ◽

Expression Profiles ◽

Functional Characterization ◽

Disordered Proteins ◽

Wild Type ◽

Content Type ◽

Cellular Pathway ◽

Intrinsically Disordered ◽

Small Proteins ◽

Wide Range

ABSTRACTBy screening a collection ofSalmonellamutants deleted for genes encoding small proteins of ≤60 amino acids, we identified three paralogous small genes (ymdF,STM14_1829, andyciG) required for wild-type flagellum-dependent swimming and swarming motility. TheymdF,STM14_1829, andyciGgenes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829mutant due to the downregulation of theflhDCoperon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829mutant, suggesting the indirect repression of theflhDCoperon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, includingEscherichia coliandPseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs inE. coliandP. aeruginosaalso alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility.IMPORTANCEThis study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility inSalmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.

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Small-angle scattering and the protein crystallographer: A relationship of ever-increasing interest

The Biochemist ◽

10.1042/bio03601044 ◽

2014 ◽

Vol 36 (1) ◽

pp. 44-48 ◽

Cited By ~ 1

Author(s):

David J. Scott

Keyword(s):

High Resolution ◽

Small Angle ◽

Intrinsically Disordered Proteins ◽

Structural Information ◽

Crystallographic Analysis ◽

Small Angle Scattering ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Angle Scattering ◽

Relationship Of

Protein crystallography is one of the great intellectual achievements of the 20th Century, and it continues to open up new vistas of research as scientists are able to visualize in exquisite detail the molecules of Life. It has become increasingly apparent, however, that not all proteins are amenable to crystallographic analysis. These include (but are not confined to) proteins with functional flexible segments, glycoproteins and intrinsically disordered proteins. There are also proteins that, although rigid and folded, refuse to crystallize as an entire full-length construct, and hence high-resolution information has to be pieced together domain by domain. It is into this space that small-angle scattering is increasingly being used as the technique of choice with regard to attainable structural information.

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Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell

10.1101/646901 ◽

2019 ◽

Cited By ~ 2

Author(s):

Antonio Deiana ◽

Sergio Forcelloni ◽

Alessandro Porrello ◽

Andrea Giansanti

Keyword(s):

Binding Proteins ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

General Category ◽

Large Set ◽

Functional Roles ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Structured Proteins ◽

Disordered Regions

AbstractMany studies about classification and the functional annotation of intrinsically disordered proteins (IDPs) are based on either the occurrence of long disordered regions or the fraction of disordered residues in the sequence. Taking into account both criteria we separate the human proteome, taken as a case study, into three variants of proteins: i) ordered proteins (ORDPs), ii) structured proteins with intrinsically disordered regions (IDPRs), and iii) intrinsically disordered proteins (IDPs). The focus of this work is on the different functional roles of IDPs and IDPRs, which up until now have been generally considered as a whole. Previous studies assigned a large set of functional roles to the general category of IDPs. We show here that IDPs and IDPRs have non-overlapping functional spectra, play different roles in human diseases, and deserve to be treated as distinct categories of proteins. IDPs enrich only a few classes, functions, and processes: nucleic acid binding proteins, chromatin binding proteins, transcription factors, and developmental processes. In contrast, IDPRs are spread over several functional protein classes and GO annotations which they partly share with ORDPs. As regards to diseases, we observe that IDPs enrich only cancer-related proteins, at variance with previous results reporting that IDPs are widespread also in cardiovascular and neurodegenerative pathologies. Overall, the operational separation of IDPRs from IDPs is relevant towards correct estimates of the occurrence of intrinsically disordered proteins in genome-wide studies and in the understanding of the functional spectra associated to different flavors of protein disorder.

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Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins

Biomolecules ◽

10.3390/biom9040146 ◽

2019 ◽

Vol 9 (4) ◽

pp. 146 ◽

Cited By ~ 9

Author(s):

Supriyo Bhattacharya ◽

Xingcheng Lin

Keyword(s):

Single Molecule ◽

Degrees Of Freedom ◽

Intrinsically Disordered Proteins ◽

Structural Information ◽

Conformational Dynamics ◽

Resonance Energy ◽

Structural Data ◽

Disordered Proteins ◽

Conformational Ensemble ◽

Intrinsically Disordered

Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and exist as an ensemble of conformations. This enables the IDPs to signal through multiple signaling pathways and serve as scaffolds for multi-protein complexes. The challenge in studying IDPs experimentally stems from their disordered nature. Nuclear magnetic resonance (NMR), circular dichroism, small angle X-ray scattering, and single molecule Förster resonance energy transfer (FRET) can give the local structural information and overall dimension of IDPs, but seldom provide a unified picture of the whole protein. To understand the conformational dynamics of IDPs and how their structural ensembles recognize multiple binding partners and small molecule inhibitors, knowledge-based and physics-based sampling techniques are utilized in-silico, guided by experimental structural data. However, efficient sampling of the IDP conformational ensemble requires traversing the numerous degrees of freedom in the IDP energy landscape, as well as force-fields that accurately model the protein and solvent interactions. In this review, we have provided an overview of the current state of computational methods for studying IDP structure and dynamics and discussed the major challenges faced in this field.

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Structure of the 5′ Untranslated Region of Enteroviral Genomic RNA

Journal of Virology ◽

10.1128/jvi.01288-19 ◽

2019 ◽

Vol 93 (23) ◽

Cited By ~ 2

Author(s):

Bejan Mahmud ◽

Christopher M. Horn ◽

William E. Tapprich

Keyword(s):

Untranslated Region ◽

Intrinsically Disordered Proteins ◽

Structural Information ◽

Disordered Proteins ◽

Type I ◽

Genomic Rna ◽

Entry Site ◽

Specific Chemical ◽

Intrinsically Disordered ◽

Viral Virulence

ABSTRACT Enteroviral RNA genomes share a long, highly structured 5′ untranslated region (5′ UTR) containing a type I internal ribosome entry site (IRES). The 5′ UTR is composed of stably folded RNA domains connected by unstructured RNA regions. Proper folding and functioning of the 5′ UTR underlies the efficiency of viral replication and also determines viral virulence. We have characterized the structure of 5′ UTR genomic RNA from coxsackievirus B3 using selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) and base-specific chemical probes in solution. Our results revealed novel structural features, including realignment of major domains, newly identified long-range interactions, and an intrinsically disordered connecting region. Together, these newly identified features contribute to a model for enteroviral 5′ UTRs with type I IRES elements that links structure to function during the hierarchical processes directed by genomic RNA during viral infection. IMPORTANCE Enterovirus infections are responsible for human diseases, including myocarditis, pancreatitis, acute flaccid paralysis, and poliomyelitis. The virulence of these viruses depends on efficient recognition of the RNA genome by a large family of host proteins and protein synthesis factors, which in turn relies on the three-dimensional folding of the first 750 nucleotides of the molecule. Structural information about this region of the genome, called the 5′ untranslated region (5′ UTR), is needed to assist in the process of vaccine and antiviral development. This work presents a model for the structure of the enteroviral 5′ UTR. The model includes an RNA element called an intrinsically disordered RNA region (IDRR). Intrinsically disordered proteins (IDPs) are well known, but correlates in RNA have not been proposed. The proposed IDRR is a 20-nucleotide region, long known for its functional importance, where structural flexibility helps explain recognition by factors controlling multiple functional states.

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