Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions

No structure, no problem: Protein stabilization by Hero proteins and other chaperone-like IDPs

In order for a protein to function, it must fold into its proper three-dimensional structure. Otherwise, improperly folded proteins are typically prone to aggregate through a process that is detrimental to cellular health. It is widely known that a diverse group of proteins, called molecular chaperones, function to promote proper folding of other proteins and prevent aggregation. In contrast, intrinsically disordered proteins (IDPs) lack substantial tertiary structures, but nonetheless serve important functional roles. In some cases, IDPs have been observed to display remarkably chaperone-like activities, where they stabilize the activities of client proteins and prevent their aggregation. While it was previously thought that chaperone-like IDPs were mainly utilized by extremophilic organisms in their survival of extreme stress, we recently showed that a group of chaperone-like IDPs, we named heat-resistant obscure (Hero) proteins, are also widespread in non-extremophile animals, including humans and flies. Thus, we should consider the possibility that IDPs serve significant chaperone-like functions in protein stabilization relevant to physiological conditions. However, as most of our understanding of how chaperones function is based on insights from their structured domains, it is unclear how chaperone-like IDPs elicit chaperone-like effects without these structures. Here we summarize our understanding of Hero proteins to date and, based on experimental evidence, outline the features that are likely important for their protein stabilizing activities. We draw on concepts from the studies of chaperones and chaperone-like IDPs, in order to draft potential models of how chaperone-like IDPs achieve chaperone-like effects in the absence of well-defined structures.

Intrinsic disorder in protein interaction networks linking cancer with metabolic diseases

Complex diseases are usually driven by numerous proteins that operate as intricate network systems. Deciphering of their signals is required for more advanced level understanding of the cellular processes driven by protein interactions. Therefore, placing diseases into a framework, where they can be viewed together, represents an important and fruitful approach. The goal of this study was to assess the intrinsic disorder present in the proteins forming PPI networks linking cancer with different human diseases. To this end, we used a set of bioinformatics tools to explore intrinsic disorder and liquid-liquid phase separation predispositions of 340 proteins reported earlier by Hirsch et al. (Cancer Cell (2010) 17(4), 348-361; doi: 10.1016/j.ccr.2010.01.022) as differently expressed in common chronic diseases, such as cancer, obesity, diabetes, and cardiovascular diseases. We further examined selected proteins from this set for their interactability and intrinsic disorder-based functionality. Our analyses demonstrated that intrinsically disordered proteins and proteins with intrinsically disordered regions may act as active network promoters and operate as highly connected hubs, which further enables them to play key roles in the disease pathways. The study also indicated that differently expressed proteins involved in disease progression could be characterized by diverse degrees of intrinsic disorder and LLPS propensity. We hope that our findings in combination with the outputs of the proteomic and functional genomic analyses contain essential clues that can be used in further medical research leading to the design of better therapies.

Q-rich activation domains: flexible 'rulers' for transcription start site selection?

Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term 'ruler' TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.

SHARK-capture identifies functional motifs in intrinsically disordered protein regions

Increasing insights into how sequence motifs in intrinsically disordered regions (IDRs) provide functions underscore the need for systematic motif detection. Contrary to structured regions where motifs can be readily identified from sequence alignments, the rapid evolution of IDRs limits the usage of alignment-based tools in reliably detecting motifs within. Here, we developed SHARK-capture, an alignment-free motif detection tool designed for difficult-to-align regions. SHARK-capture innovates on word-based methods by flexibly incorporating amino acid physicochemistry to assess motif similarity without requiring rigid definitions of equivalency groups. SHARK-capture offers consistently strong performance in a systematic benchmark, with superior residue-level performance. SHARK-capture identified known functional motifs across orthologs of the microtubule-associated zinc finger protein BuGZ. We also identified a short motif in the IDR of S. cerevisiae RNA helicase Ded1p, which we experimentally verified to be capable of promoting ATPase activity. Our improved performance allows us to systematically calculate 10,889 motifs for 2695 yeast IDRs and provide it as a resource. SHARK-capture offers the most precise tool yet for the systematic identification of conserved regions in IDRs and is freely available as a Python package (https://pypi.org/project/bio-shark/) and on https://git.mpi-cbg.de/tothpetroczylab/shark.

Evolutionary Pro-To-Thr Mutation in the Intrinsically Disordered Domain of ANP32 Family Members Modulates Their Target Binding Modes

Gene duplication has allowed protein evolution toward novel functions and mechanisms. The differences between paralogous genes frequently rely on the sequence of disordered regions. For instance, in mammals, the chaperones ANP32A and ANP32B share a common evolutionary line and have some exchangeable functions based on their similar N-terminal domains. Nevertheless, their C-terminal low-complexity-acidic-regions (LCARs) display substantial sequence differences, unveiling some degree of variability between them, in agreement with their different tissue-specific expression patterns. These structural and computational results indicate that a substitution in the vicinity of the nuclear localization signal (NLS), of Pro in ANP32A for Thr in ANP32B, determines the overall compactness of the C-terminal LCAR. The different structural properties of the disordered region affect the binding mode of ANP32 members to their targets. This type of divergent binding mode is exemplified with the extra-mitochondrial cytochrome c (Cc), a well-known ANP32B partner and which now determine also binds to ANP32A; and with the RNA binding protein HuR, whose export to the cytoplasm is mediated by ANP32 proteins under stress. Therefore, differential expression patterns of ANP32A or ANP32B may affect the regulation of Cc and HuR and can help to explain the distinct roles of these proteins in diseases.

Boosting transcriptional activities by employing repeated activation domains in transcription factors

Enhancing the transcriptional activation activity of transcription factors (TFs) has multiple applications in organism improvement, metabolic engineering, and other aspects of plant science, but the approaches remain unclear. Here, we used gene activation assays and genetic transformation to investigate the transcriptional activities of two MYB TFs, PRODUCTION OF ANTHOCYANIN PIGMENT 1 (AtPAP1) from Arabidopsis (Arabidopsis thaliana) and EsMYBA1 from Epimedium (Epimedium sagittatum), and their synthetic variants in a range of plant species from several families. Using anthocyanin biosynthesis as a convenient readout, we discovered that homologous naturally occurring TFs showed differences in the transcriptional activation ability and that similar TFs induced large changes in the genetic program when heterologously expressed in different species. In some cases, shuffling the DNA-binding domains and transcriptional activation domains (ADs) between homologous TFs led to synthetic TFs that had stronger activation potency than the original TFs. More importantly, synthetic TFs derived from MYB, NAC, bHLH, and ethylene-insensitive3-like (EIL) family members containing tandemly repeated ADs had greatly enhanced activity compared to their natural counterparts. These findings enhance our understanding of TF activity and demonstrate that employing tandemly repeated ADs from natural TFs is a simple and widely applicable strategy to enhance the activation potency of synthetic TFs.

Binding mechanisms of intrinsically disordered proteins: Insights from experimental studies and structural predictions

Advances in the characterization of intrinsically disordered proteins (IDPs) have unveiled a remarkably complex and diverse interaction landscape, including coupled folding and binding, highly dynamic complexes, multivalent interactions, and even interactions between entirely disordered proteins. Here we review recent examples of IDP binding mechanisms elucidated by experimental techniques such as nuclear magnetic resonance spectroscopy, single-molecule Förster resonance energy transfer, and stopped-flow fluorescence. These techniques provide insights into the structural details of transition pathways and complex intermediates, and they capture the dynamics of IDPs within complexes. Furthermore, we discuss the growing role of artificial intelligence, exemplified by AlphaFold, in identifying interaction sites within IDPs and predicting their bound-state structures. Our review highlights the powerful complementarity between experimental methods and artificial intelligence-based approaches in advancing our understanding of the intricate interaction landscape of IDPs.

Versatile roles of disordered transcription factor effector domains in transcriptional regulation

Transcription, a crucial step in the regulation of gene expression, is tightly controlled and involves several essential processes, such as chromatin organization, recognition of the specific genomic sequences, DNA binding, and ultimately recruiting the transcriptional machinery to facilitate transcript synthesis. At the center of this regulation are transcription factors (TFs), which comprise at least one DNA-binding domain (DBD) and an effector domain (ED). Although the structure and function of DBDs have been well studied, our knowledge of the structure and function of effector domains is limited. EDs are of particular importance in generating distinct transcriptional responses between protein members of the same TF family that have similar DBDs and specificities. The study of transcriptional activity conferred by effector domains has traditionally been conducted through examining protein-protein interactions. However, recent research has uncovered alternative mechanisms by which EDs regulate gene expression, such as the formation of condensates that increase the local concentration of transcription factors, cofactors, and coregulated genes, as well as DNA binding. Here, we provide a comprehensive overview of the known roles of transcription factor EDs, with a specific focus on disordered regions. Additionally, we emphasize the significance of intrinsically disordered regions (IDRs) during transcriptional regulation. We examine the mechanisms underlying the establishment and maintenance of transcriptional specificity through the structural properties of predominantly disordered EDs. We then provide a comprehensive overview of the current understanding of these domains, including their physical and chemical characteristics, as well as their functional roles.

PERspectives on circadian cell biology

Daily rhythms in the activities of PERIOD proteins are critical to the temporal regulation of mammalian physiology. While the molecular partners and genetic circuits that allow PERIOD to effect auto-repression and regulate transcriptional programmes are increasingly well understood, comprehension of the time-resolved mechanisms that allow PERIOD to conduct this daily dance is incomplete. Here, we consider the character and controversies of this central mammalian clock protein with a focus on its intrinsically disordered nature.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Molecular determinants of condensate composition

Cells use membraneless compartments to organize their interiors, and recent research has begun to uncover the molecular principles underlying their assembly. Here, we explore how site-specific and chemically specific interactions shape the properties and functions of condensates. Site-specific recruitment involves precise interactions at specific sites driven by partially or fully structured interfaces. In contrast, chemically specific recruitment is driven by complementary chemical interactions without the requirement for a persistent bound-state structure. We propose that site-specific and chemically specific interactions work together to determine the composition of condensates, facilitate biochemical reactions, and regulate enzymatic activities linked to metabolism, signaling, and gene expression. Characterizing the composition of condensates requires novel experimental and computational tools to identify and manipulate the molecular determinants guiding condensate recruitment. Advancing this research will deepen our understanding of how condensates regulate cellular functions, providing valuable insights into cellular physiology and organization.

A metric and its derived protein network for evaluation of ortholog database inconsistency

BACKGROUND

Ortholog prediction, essential for various genomic research areas, faces growing inconsistencies amidst the expanding array of ortholog databases. The common strategy of computing consensus orthologs introduces additional arbitrariness, emphasizing the need to examine the causes of such inconsistencies and identify proteins susceptible to prediction errors.

RESULTS

We introduce the Signal Jaccard Index (SJI), a novel metric rooted in unsupervised genome context clustering, designed to assess protein similarity. Leveraging SJI, we construct a protein network and reveal that peripheral proteins within the network are the primary contributors to inconsistencies in orthology predictions. Furthermore, we show that a protein's degree centrality in the network serves as a strong predictor of its reliability in consensus sets.

CONCLUSIONS

We present an objective, unsupervised SJI-based network encompassing all proteins, in which its topological features elucidate ortholog prediction inconsistencies. The degree centrality (DC) effectively identifies error-prone orthology assignments without relying on arbitrary parameters. Notably, DC is stable, unaffected by species selection, and well-suited for ortholog benchmarking. This approach transcends the limitations of universal thresholds, offering a robust and quantitative framework to explore protein evolution and functional relationships.

Nucleic Acids and Electrical Signals

Nucleic acids are highly charged, and electrical forces are involved heavily in how our DNA is compacted and packaged into such a small space, how chromosomes are formed, and how DNA damage is repaired. In addition, electrical forces are crucial to the formation of non-canonical DNA structures called G-Quadruplexes which play multiple biological roles.

The conformation of FOXM1 homodimers in vivo is crucial for regulating transcriptional activities

Conformational changes in a transcription factor can significantly affect its transcriptional activity. The activated form of the FOXM1 transcription factor regulates the transcriptional network of genes essential for cell cycle progression and carcinogenesis. However, the mechanism and impact of FOXM1 conformational change on its transcriptional activity in vivo throughout the cell cycle progression remain unexplored. Here, we demonstrate that FOXM1 proteins form novel intermolecular homodimerizations in vivo, and these conformational changes in FOXM1 homodimers impact activity during the cell cycle. Specifically, during the G1 phase, FOXM1 undergoes autorepressive homodimerization, wherein the αβα motif in the C-terminal transcriptional activation domain interacts with the ββαβ motif in the N-terminal repression domain, as evidenced by FRET imaging. Phosphorylation of the αβα motif by PLK1 at S715/S724 disrupts ββαβ-αβα hydrophobic interactions, thereby facilitating a conserved αβα motif switch binding partner to the novel intrinsically disordered regions, leading to FOXM1 autostimulatory homodimerization persisting from the S phase to the G2/M phase in vivo. Furthermore, we identified a minimal ββαβ motif peptide that effectively inhibits cancer cell proliferation both in cell culture and in a mouse tumor model, suggesting a promising autorepression approach for targeting FOXM1 in cancer therapy.

Molecular insights into the interaction between a disordered protein and a folded RNA

Intrinsically disordered protein regions (IDRs) are well established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, Small ERDK-Rich Factor (SERF). At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 Trans-Activation Response (TAR) RNA with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.

Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective

When two proteins bind to each other, this process is often accompanied by a change in their structural states (from disordered to ordered or vice versa). As it turns out, there are 10 distinct possibilities for such binding-related order/disorder transitions. Out of this number, seven scenarios have been experimentally observed, while another three remain hitherto unreported. As an example, we discuss the so-called mutual synergistic folding, whereby two disordered proteins come together to form a fully structured complex. Our bioinformatics analysis of the Protein Databank found potential new examples of this remarkable binding mechanism.

HMGB1, an evolving pleiotropic protein critical for cellular and tissue homeostasis: Role in aging and age-related diseases

Aging is a universal biological process characterized by a progressive, cumulative decline in homeostatic capabilities and physiological functions, which inevitably increases vulnerability to diseases. A number of molecular pathomechanisms and hallmarks of aging have been recognized, yet we miss a thorough understanding of their complex interconnectedness. This review explores the molecular and cellular mechanisms underlying human aging, with a focus on the multiple roles of high mobility group Box 1 protein (HMGB1), the archetypal damage-associated molecular pattern (DAMP) molecule. In the nucleus, this non-histone chromatin-associated protein functions as a DNA chaperone and regulator of gene transcription, influencing DNA structure and gene expression. Moreover, this versatile protein can translocate to the cytoplasm to orchestrate other processes, such as autophagy, or be unconventionally secreted into the extracellular environment, where it acts as a DAMP, combining inflammatory and regenerative properties. Notably, lower expression of HMGB1 within the cell and its heightened extracellular release have been associated with diverse age-associated traits, making it a suitable candidate as a universal biomarker of aging. In this review, we outline the evidence implicating HMGB1 in aging, also in light of an evolutionary perspective on its functional pleiotropy, and propose critical issues that need to be addressed to gauge the value of HMGB1 as a potential biomarker across age-related diseases and therapeutic target to promote healthy longevity.

Fuzzy protein-DNA interactions and beyond: A common theme in transcription?

Gene expression regulation requires both diversity and specificity. How can these two contradictory conditions be reconciled? Dynamic DNA recognition mechanisms lead to heterogeneous bound conformations, which can be shifted by the cellular cues. Here we summarise recent experimental evidence on how fuzzy interactions contribute to chromatin remodelling, regulation of DNA replication and repair and transcription factor binding. We describe how the binding mode continuum between DNA and regulatory factors lead to variable, multisite contact patterns; polyelectrolyte competitions; on-the-fly shape readouts; autoinhibition controlled by posttranslational modifications or dynamic oligomerisation mechanisms. Increasing experimental evidence supports the rugged energy landscape of the bound protein-DNA assembly, modulation of which leads to distinct functional outcomes. Recent results suggest the evolutionary conservation of these combinatorial mechanisms with moderate sequence constraints in the malleable transcriptional machinery.

Structural and dynamic studies of chromatin by solid-state NMR spectroscopy

Chromatin is a complex of DNA with histone proteins organized into nucleosomes that regulates genome accessibility and controls transcription, replication and repair by dynamically switching between open and compact states as a function of different parameters including histone post-translational modifications and interactions with chromatin modulators. Continuing advances in structural biology techniques including X-ray crystallography, cryo-electron microscopy and nuclear magnetic resonance (NMR) spectroscopy have facilitated studies of chromatin systems, in spite of challenges posed by their large size and dynamic nature, yielding important functional and mechanistic insights. In this review we highlight recent applications of magic angle spinning solid-state NMR - an emerging technique that is uniquely-suited toward providing atomistic information for rigid and flexible regions within biomacromolecular assemblies - to detailed characterization of structure, conformational dynamics and interactions for histone core and tail domains in condensed nucleosomes and oligonucleosome arrays mimicking chromatin at high densities characteristic of the cellular environment.

Neuronal splicing regulator RBFOX3 (NeuN) distribution and organization are modified in response to monosodium glutamate in rat brain at postnatal day 14

Neuronal splicing regulator RNA binding protein, fox-1 homolog 3 (NeuN/RbFox3), is expressed in postmitotic neurons and distributed heterogeneously in the cell. During excitotoxicity events caused by the excess glutamate, several alterations that culminate in neuronal death have been described. However, NeuN/RbFox3 organization and distribution are still unknown. Therefore, our objective was to analyze the nucleocytoplasmic distribution and organization of NeuN/RbFox3 in hippocampal and cortical neurons using an excitotoxicity model with monosodium glutamate salt (MSG). We used neonatal Wistar rats administered subcutaneously with 4 MSG mg/kg during the postnatal day (PND) 1, 3, 5, and 7. The control group was rats without MSG administration. On 14 PND, the brain was removed, and coronal sections were used for immunodetection with the antibody NeuN, DAPI, and the propidium iodide staining for histological evaluation. The results indicate that in the control group, NeuN/RbFox3 was organized into macromolecular condensates inside and outside the nucleus, forming defined nuclear compartments. Additionally, NeuN/RbFox3 was distributed proximal to the nucleus in the cytoplasm. In contrast, in the group treated with MSG, the distribution was diffuse and dispersed in the nucleus and cytoplasm without the formation of compartments in the nucleus. Our findings, which highlight the significant impact of MSG administration in the neonatal period on the distribution and organization of NeuN/RbFox3 of neurons in the hippocampus and cerebral cortex, offer a new perspective to investigate MSG alterations in the developmental brain.

From molecular descriptions to cellular functions of intrinsically disordered protein regions

Molecular descriptions of intrinsically disordered protein regions (IDRs) are fundamental to understanding their cellular functions and regulation. NMR spectroscopy has been a leading tool in characterizing IDRs at the atomic level. In this review, we highlight recent conceptual breakthroughs in the study of IDRs facilitated by NMR and discuss emerging NMR techniques that bridge molecular descriptions to cellular functions. First, we review the assemblies formed by IDRs at various scales, from one-to-one complexes to non-stoichiometric clusters and condensates, discussing how NMR characterizes their structural dynamics and molecular interactions. Next, we explore several unique interaction modes of IDRs that enable regulatory mechanisms such as selective transport and switch-like inhibition. Finally, we highlight recent progress in solid-state NMR and in-cell NMR on IDRs, discussing how these methods allow for atomic characterization of full-length IDR complexes in various phases and cellular environments. This review emphasizes recent conceptual and methodological advancements in IDR studies by NMR and offers future perspectives on bridging the gap between in vitro molecular descriptions and the cellular functions of IDRs.

Revealing Missing Protein-Ligand Interactions Using AlphaFold Predictions

Protein-ligand interactions represent an essential step to understand the bases of molecular recognition, an intense field of research in many scientific areas. Structural biology has played a central role in unveiling protein-ligand interactions, but current techniques are still not able to reliably describe the interactions of ligands with highly flexible regions. In this work, we explored the capacity of AlphaFold2 (AF2) to estimate the presence of interactions between ligands and residues belonging to disordered regions. As these interactions are missing in the crystallographic-derived structures, we called them "ghost interactions". Using a set of protein structures experimentally obtained after AF2 was trained, we found that the obtained models are good predictors of regions associated with order-disorder transitions. Additionally, we found that AF2 predicts residues making ghost interactions with ligands, which are mostly buried and show differential evolutionary conservation with the rest of the residues located in the flexible region. Our findings could fuel current areas of research that consider, given their biological relevance and their involvement in diseases, intrinsically disordered proteins as potentially valuable targets for drug development.

Heterogeneous Slowdown of Dynamics in the Condensate of an Intrinsically Disordered Protein

The high concentration of proteins and other biological macromolecules inside biomolecular condensates leads to dense and confined environments, which can affect the dynamic ensembles and the time scales of the conformational transitions. Here, we use atomistic molecular dynamics (MD) simulations of the intrinsically disordered low complexity domain (LCD) of the human fused in sarcoma (FUS) RNA-binding protein to study how self-crowding inside a condensate affects the dynamic motions of the protein. We found a heterogeneous retardation of the protein dynamics in the condensate with respect to the dilute phase, with large-amplitude motions being strongly slowed by up to 2 orders of magnitude, whereas small-scale motions, such as local backbone fluctuations and side-chain rotations, are less affected. The results support the notion of a liquid-like character of the condensates and show that different protein motions respond differently to the environment.

Tau Protein and Tauopathies: Exploring Tau Protein-Protein and Microtubule Interactions, Cross-Interactions and Therapeutic Strategies

Tau, a microtubule-associated protein (MAP), is essential to maintaining neuronal stability and function in the healthy brain. However, aberrant modifications and pathological aggregations of Tau are implicated in various neurodegenerative disorders, collectively known as tauopathies. The most common Tauopathy is Alzheimer's Disease (AD) counting nowadays more than 60 million patients worldwide. This comprehensive review delves into the multifaceted realm of Tau protein, puzzling out its intricate involvement in both physiological and pathological roles. Emphasis is put on Tau Protein-Protein Interactions (PPIs), depicting its interaction with tubulin, microtubules and its cross-interaction with other proteins such as Aβ1-42, α-synuclein, and the chaperone machinery. In the realm of therapeutic strategies, an overview of diverse possibilities is presented with their relative clinical progresses. The focus is mostly addressed to Tau protein aggregation inhibitors including recent small molecules, short peptides and peptidomimetics with specific focus on compounds that showed a double anti aggregative activity on both Tau protein and Aβ amyloid peptide. This review amalgamates current knowledge on Tau protein and evolving therapeutic strategies, providing a comprehensive resource for researchers seeking to deepen their understanding of the Tau protein and for scientists involved in the development of new peptide-based anti-aggregative Tau compounds.

Self-association and multimer formation in AtLEA4-5, a desiccation-induced intrinsically disordered protein from plants

During seed maturation, plants may experience severe desiccation, leading to the accumulation of late embryogenesis abundant (LEA) proteins. These intrinsically disordered proteins also accumulate in plant tissues under water deficit. Functional roles of LEA proteins have been proposed based on in vitro studies, where monomers are considered as the functional units. However, the potential formation of homo-oligomers has been little explored. In this work, we investigated the potential self-association of Arabidopsis thaliana group 4 LEA proteins (AtLEA4) using in vitro and in vivo approaches. LEA4 proteins represent a compelling case of study due to their high conservation throughout the plant kingdom. This protein family is characterized by a conserved N-terminal region, with a high alpha-helix propensity and invitro protective activity, as compared to the highly disordered and low-conserved C-terminal region. Our findings revealed that full-length AtLEA4 proteins oligomerize and that both terminal regions are sufficient for self-association in vitro. However, the ability of both amino and carboxy regions of AtLEA4-5 to self-associate invivo is significantly lower than that of the entire protein. Using high-resolution and quantitative fluorescence microscopy, we were able to disclose the unreported ability of LEA proteins to form high-order oligomers in planta. Additionally, we found that high-order complexes require the simultaneous engagement of both terminal regions, indicating that the entire protein is needed to attain such structural organization. This research provides valuable insights into the self-association of LEA proteins in plants and emphasizes the role of protein oligomer formation.

AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions

Interactions mediated by intrinsically disordered protein regions (IDRs) pose formidable challenges in structural characterization. IDRs are highly versatile, capable of adopting diverse structures and engagement modes. Motivated by recent strides in protein structure prediction, we embarked on exploring the extent to which AlphaFold-Multimer can faithfully reproduce the intricacies of interactions involving IDRs. To this end, we gathered multiple datasets covering the versatile spectrum of IDR binding modes and used them to probe AlphaFold-Multimer's prediction of IDR interactions and their dynamics. Our analyses revealed that AlphaFold-Multimer is not only capable of predicting various types of bound IDR structures with high success rate, but that distinguishing true interactions from decoys, and unreliable predictions from accurate ones is achievable by appropriate use of AlphaFold-Multimer's intrinsic scores. We found that the quality of predictions drops for more heterogeneous, fuzzy interaction types, most likely due to lower interface hydrophobicity and higher coil content. Notably though, certain AlphaFold-Multimer scores, such as the Predicted Aligned Error and residue-ipTM, are highly correlated with structural heterogeneity of the bound IDR, enabling clear distinctions between predictions of fuzzy and more homogeneous binding modes. Finally, our benchmarking revealed that predictions of IDR interactions can also be successful when using full-length proteins, but not as accurate as with cognate IDRs. To facilitate identification of the cognate IDR of a given partner, we established "minD," which pinpoints potential interaction sites in a full-length protein. Our study demonstrates that AlphaFold-Multimer can correctly identify interacting IDRs and predict their mode of engagement with a given partner.

How to drug a cloud? Targeting intrinsically disordered proteins

Biologically active proteins/regions without stable structure (i.e., intrinsically disordered proteins and regions (IDPs and IDRs)) are commonly found in all proteomes. They have a unique functional repertoire that complements the functionalities of ordered proteins and domains. IDPs/IDRs are multifunctional promiscuous binders capable of folding at interaction with specific binding partners on a template- or context-dependent manner, many of which undergo liquid-liquid phase separation, leading to the formation of membrane-less organelles and biomolecular condensates. Many of them are frequently related to the pathogenesis of various human diseases. All this defines IDPs/IDRs as attractive targets for the development of novel drugs. However, their lack of unique structures, multifunctionality, binding promiscuity, and involvement in unusual modes of action preclude direct use of traditional structure-based drug design approaches for targeting IDPs/IDRs, and make disorder-based drug discovery for these "protein clouds" challenging. Despite all these complexities there is continuing progress in the design of small molecules affecting IDPs/IDRs. This article describes the major structural features of IDPs/IDRs and the peculiarities of the disorder-based functionality. It also discusses the roles of IDPs/IDRs in various pathologies, and shows why the approaches elaborated for finding drugs targeting ordered proteins cannot be directly used for the intrinsic disorder-based drug design, and introduces some novel methodologies suitable for these purposes. Finally, it emphasizes that regardless of their multifunctionality, binding promiscuity, lack of unique structures, and highly dynamic nature, "protein clouds" are principally druggable. Significance Statement Intrinsically disordered proteins and regions are highly abundant in nature, have multiple important biological functions, are commonly involved in the pathogenesis of a multitude of human diseases, and are therefore considered as very attractive drug targets. Although dealing with these unstructured multifunctional protein/regions is a challenging task, multiple innovative approaches have been designed to target them by small molecules.

Osmolytes as structure-function regulators of intrinsically disordered casein proteins

Intrinsically disordered proteins (IDPs), despite lacking a stable structure, play crucial role in majority of the cellular processes. Casein, a key milk protein, represents this category of proteins, due to its dynamic and flexible structure which contributes towards the nutritional and functional properties of milk. The present chapter summarizes the role of osmolytes (small molecular weight organic molecules generally accumulated by cells to protect against denaturing stresses) in regulating the structure-function integrity of intrinsically disordered casein proteins. Osmolyte - casein interplay is of particular interest as these osmolytes have been found to affect the conformational flexibility and functional properties of casein proteins and thus can affect their overall behavior in the cellular environment. The present chapter delves into this by discussing the unique structural and functional properties of casein IDPs and the influence of osmolytes on their structure, stability, and chaperone activity. Elucidation of the osmolyte effects on the structural-functional integrity of caseins should advance our understanding of the dynamics of protein structure and function in complex biological environments and also offer practical perceptions for their future applications.

On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution

Obviously, the discussion of different factors that could have contributed to the origin of life and evolution is clear speculation, since there is no way of checking the validity of most of the related hypotheses in practice, as the corresponding events not only already happened, but took place in a very distant past. However, there are a few undisputable facts that are present at the moment, such as the existence of a wide variety of living forms and the abundant presence of intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) in all living forms. Since it seems that the currently existing living forms originated from a common ancestor, their variety is a result of evolution. Therefore, one could ask a logical question of what role(s) the structureless and highly dynamic but vastly abundant and multifunctional IDPs/IDRs might have in evolution. This study represents an attempt to consider various ideas pertaining to the potential roles of protein intrinsic disorder in the origin of life and evolution.

Computational insights into intrinsically disordered regions in protein-nucleic acid complexes

We study transitions in intrinsically disordered regions (IDRs) upon complex formation, utilizing X-ray-solved structural dataset of protein-DNA and protein-RNA complexes, along with their available unbound protein forms. The identified IDRs are categorized into three classes: Disordered-to-Ordered (D-O), Disordered-to-Partial Ordered (D-PO) and Disordered-to-Disordered (D-D) after comparing them in unbound and complex forms. In the D-O class, IDRs form secondary structures like coils, helices, and strands upon binding to nucleic acids. Though a majority of these IDRs are present at the surface of the complexes, a significant number of IDRs are also observed at the interfaces and are involved in polar interactions. The hydrogen bonds made by the interface IDRs (B_IDRs) with phosphates and bases of nucleic acids are comparatively more than those formed with sugars. B_IDRs form more H-bonds with the ribose in protein-RNA than with the deoxyribose in protein-DNA. Among the B_IDRs, Arg and Lys prefer to interact with the major and minor grooves of DNA and RNA, respectively. Ser, however, prefers the minor groove in both the nucleic acids. Interestingly, we report 61 and 48 IDRs in 31 protein-DNA and 22 protein-RNA complexes, respectively, suggesting nucleic acid binding to proteins may also result in ordered-to-disordered transitions.

Ensembles of interconverting protein complexes with multiple interaction domains

Many critical biological processes depend on protein complexes that exist as ensembles of subcomplexes rather than a discrete complex. The subcomplexes dynamically interconvert with one another, and the ability to accurately resolve the composition of the diverse molecular species in the ensemble is crucial for understanding the contribution of each subcomplex to the overall function of the protein complex. Advances in computational programs have made it possible to predict the various molecular species in these ensembles, but experimental approaches to identify the pool of subcomplexes and associated stoichiometries are often challenging. This review highlights some experimental approaches that can be used to resolve the diverse molecular species in protein complexes that exist as ensembles of sub complexes.

The role of intrinsic protein disorder in regulation of cyclin-dependent kinases

While the structure/function paradigm for folded domains was established decades ago, our understanding of how intrinsically disordered regions (IDRs) contribute to biological function is still evolving. IDRs exist as conformational ensembles that can range from highly compact to highly extended depending on their sequence composition. IDR sequences are less conserved than those of folded domains, but often display short, conserved segments termed short linear motifs (SLiMs), that often mediate protein-protein interactions and are often regulated by posttranslational modifications, giving rise to complex functionality when multiple, differently regulated SLiMs are combined. This combinatorial functionality was associated with signaling and regulation soon after IDRs were first recognized as functional elements within proteins. Here, we discuss roles for disorder in proteins that regulate cyclin-dependent kinases, the master timekeepers of the eukaryotic cell cycle. We illustrate the importance of intrinsic flexibility in the transmission of regulatory signals by these entirely disordered proteins.

Predicting the Dynamic Interaction of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) participate in various biological processes. Interactions involving IDPs are usually dynamic and are affected by their inherent conformation fluctuations. Comprehensive characterization of these interactions based on current techniques is challenging. Here, we present GSALIDP, a GraphSAGE-embedded LSTM network, to capture the dynamic nature of IDP-involved interactions and predict their behaviors. This framework models multiple conformations of IDP as a dynamic graph, which can effectively describe the fluctuation of its flexible conformation. The dynamic interaction between IDPs is studied, and the data sets of IDP conformations and their interactions are obtained through atomistic molecular dynamic (MD) simulations. Residues of IDP are encoded through a series of features including their frustration. GSALIDP can effectively predict the interaction sites of IDP and the contact residue pairs between IDPs. Its performance in predicting IDP interactions is on par with or even better than the conventional models in predicting the interaction of structural proteins. To the best of our knowledge, this is the first model to extend the protein interaction prediction to IDP-involved interactions.

Design of intrinsically disordered protein variants with diverse structural properties

Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Computational design of IDPs with specific conformational properties has, however, been difficult because of their substantial dynamics and structural complexity. We describe a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs that differ in compaction, long-range contacts, and propensity to phase separate. We experimentally tested and validated our designs and analyzed the sequence features that determine conformations. We show how our results are captured by a machine learning model, enabling us to speed up the algorithm. Our work expands the toolbox for computational protein design and will facilitate the design of proteins whose functions exploit the many properties afforded by protein disorder.

nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat

Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.

The Disorderly Nature of Caliciviruses

An intrinsically disordered protein (IDP) or region (IDR) lacks or has little protein structure but still maintains function. This lack of structure creates flexibility and fluidity, allowing multiple protein conformations and potentially transient interactions with more than one partner. Caliciviruses are positive-sense ssRNA viruses, containing a relatively small genome of 7.6-8.6 kb and have a broad host range. Many viral proteins are known to contain IDRs, which benefit smaller viral genomes by expanding the functional proteome through the multifunctional nature of the IDR. The percentage of intrinsically disordered residues within the total proteome for each calicivirus type species can range between 8 and 23%, and IDRs have been experimentally identified in NS1-2, VPg and RdRP proteins. The IDRs within a protein are not well conserved across the genera, and whether this correlates to different activities or increased tolerance to mutations, driving virus adaptation to new selection pressures, is unknown. The function of norovirus NS1-2 has not yet been fully elucidated but includes involvement in host cell tropism, the promotion of viral spread and the suppression of host interferon-λ responses. These functions and the presence of host cell-like linear motifs that interact with host cell caspases and VAPA/B are all found or affected by the disordered region of norovirus NS1-2. The IDRs of calicivirus VPg are involved in viral transcription and translation, RNA binding, nucleotidylylation and cell cycle arrest, and the N-terminal IDR within the human norovirus RdRP could potentially drive liquid-liquid phase separation. This review identifies and summarises the IDRs of proteins within the Caliciviridae family and their importance during viral replication and subsequent host interactions.

Aqueous Ionic Liquid Mixtures as Minimal Models of Lipid Bilayer Membranes

We introduce aqueous ionic liquid (IL) mixtures, specifically mixtures of 1-butyl-3-imidazoliumtetrafluoroborate (BMImBF4), with water as a minimal model of lipid bilayer membranes. Imidazolium-based ILs are known to form clustered nanoscale structures in which local inhomogeneities, micellar or lamellar structures, are formed to shield hydrophobic parts of the cation from the polar cosolvent (water). To investigate these nanostructures, dynamic light scattering (DLS) on samples with different mixing ratios of water and BMImBF4 was performed. At mixing ratios of 50% and 45% (v/v), small and homogeneous nanostructures can indeed be detected. To test whether, in particular, these stable nanostructures in aqueous mixtures may mimic the effects of phospholipid bilayer membranes, we further investigated their interaction with myelin basic protein (MBP), a peripheral, intrinsically disordered membrane protein of the myelin sheath. Using dynamic light scattering (DLS), continuous wave (CW) and pulse electron paramagnetic resonance (EPR), and small-angle X-ray scattering (SAXS) on recombinantly produced, "healthy" charge variants rmC1WT and double cysteine variant C1S17CH85C, we find that the size and the shape of the determined nanostructures in an optimum mixture offer model membranes in which the protein exhibits native behavior. SAXS measurements illuminate the size and shape of the nanostructures and indicate IL-rich "beads" clipped together by functional MBP, one of the in vivo roles of the protein in the myelin sheath. All the gathered data combined indicate that the 50% and 45% aqueous IL mixtures can be described as offering minimal models of a lipid mono- or bilayer that allow native processing and potential study of at least peripheral membrane proteins like MBP.

Intramolecular CH⋯π attraction mediated conformational polymorphism of constrained helical peptides

In nature, biochemical processes depend on polymorphism, a phenomenon by which discrete biomolecules can adopt specific conformations based on their environment. However, it is often difficult to explore the generation mechanism and achieve polymorphic control in artificial supramolecular assembly systems. In this work, we propose a feasible thought for exploring the transformation mechanism of polymorphism in peptide assembly from the perspective of thermodynamic regulation, which enables polymorphic composition to be limited by switchable intramolecular CH⋯π attraction within a certain temperature range. Combined with the density functional theory calculations, we obtained thermodynamic theoretical data supporting the conformation transition and the underlying polymorphism formation principle. Afterward, we properly designed the peptide to alter the probability of CH⋯π attraction occurring. Then, we selectively obtained a homogeneous morphological form with corresponding molecular conformation, which further demonstrated the important role of molecular conformational manipulation in polymorphism selection. This unique template-based strategy developed in this study may provide scientists with an additional line of thought to guide assembly paths in other polymorphic systems.

Context-dependent, fuzzy protein interactions: Towards sequence-based insights

Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound configurations. A multiplicity of binding modes (MBM) enables transition between these states under different cellular conditions. This review focuses on how the cellular environment affects protein interactions, highlighting the molecular mechanisms, biophysical origin, and sequence-based principles of context-dependent, fuzzy interactions. It summarises experimental and computational approaches to address the challenge of interaction heterogeneity and its contribution to a wide range of biological functions. These insights will help in understanding complex cellular processes, involving conversions between protein assembly states, such as from liquid-like droplet state to the amyloid state.

Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end

The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.

The C-terminal disordered loop domain of Apc8 unlocks APC/C mitotic activation

The anaphase-promoting complex/cyclosome (APC/C) is a critical and tightly regulated E3 ligase that orchestrates the cellular life cycle by controlling the degradation of cell cycle regulators. An intriguing feature of this complex is an autoinhibition mechanism: an intrinsically disordered loop domain, Apc1-300L, blocks Cdc20 coactivator binding, yet phosphorylation of Apc1-300L counteracts this autoinhibition. Many such disordered loops within APC/C remain unexplored. Our systematic analysis of loop-deficient APC/C mutants uncovered a pivotal role for Apc8's C-terminal loop (Apc8-L) in mitotic activation. Apc8-L directly recruits the CDK adaptor protein, Xe-p9/Cks2, positioning the Xe-p9-CDK-CycB complex near Apc1-300L. This stimulates the phosphorylation and removal of Apc1-300L, prompting the formation of active APC/CCdc20. Strikingly, without both Apc8-L and Apc3-L, the APC/C is rendered inactive during mitosis, highlighting Apc8-L's synergistic role with other loops and kinases. This study broadens our understanding of the intricate dynamics in APC/C regulation and provides insights on the regulation of macromolecular complexes.

Intrinsic Disorder in the Host Proteins Entrapped in Rabies Virus Particles

A proteomics analysis of purified rabies virus (RABV) revealed 47 entrapped host proteins within the viral particles. Out of these, 11 proteins were highly disordered. Our study was particularly focused on five of the RABV-entrapped mouse proteins with the highest levels of disorder: Neuromodulin, Chmp4b, DnaJB6, Vps37B, and Wasl. We extensively utilized bioinformatics tools, such as FuzDrop, D2P2, UniProt, RIDAO, STRING, AlphaFold, and ELM, for a comprehensive analysis of the intrinsic disorder propensity of these proteins. Our analysis suggested that these disordered host proteins might play a significant role in facilitating the rabies virus pathogenicity, immune system evasion, and the development of antiviral drug resistance. Our study highlighted the complex interaction of the virus with its host, with a focus on how the intrinsic disorder can play a crucial role in virus pathogenic processes, and suggested that these intrinsically disordered proteins (IDPs) and disorder-related host interactions can also be a potential target for therapeutic strategies.

Direct prediction of intermolecular interactions driven by disordered regions

Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.

Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator

Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.

A complete map of specificity encoding for a partially fuzzy protein interaction

Thousands of human proteins function by binding short linear motifs embedded in intrinsically disordered regions. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of 'fuzzy' dynamic residues to affinity and specificity in protein-protein interactions. Here we report the first complete map of specificity encoding for a globular protein domain. Quantifying >200,000 energetic interactions between a PDZ domain and its ligand identifies 20 major energetically coupled pairs of sites that control specificity. These are organized into six modules, with most mutations in each module reprogramming specificity for a single position in the ligand. Nine of the major energetic couplings controlling specificity are between structural contacts and 11 have an allosteric mechanism of action. The dynamic tail of the ligand is more robust to mutation than the structured residues but contributes additively to binding affinity and communicates with structured residues to enable changes in specificity. Our results quantify the binding specificities of >1,800 globular proteins to reveal how specificity is encoded and provide a direct comparison of the encoding of affinity and specificity in structured and dynamic molecular recognition.

Investigating the Interactions of the Cucumber Mosaic Virus 2b Protein with the Viral 1a Replicase Component and the Cellular RNA Silencing Factor Argonaute 1

The cucumber mosaic virus (CMV) 2b protein is a suppressor of plant defenses and a pathogenicity determinant. Amongst the 2b protein's host targets is the RNA silencing factor Argonaute 1 (AGO1), which it binds to and inhibits. In Arabidopsis thaliana, if 2b-induced inhibition of AGO1 is too efficient, it induces reinforcement of antiviral silencing by AGO2 and triggers increased resistance against aphids, CMV's insect vectors. These effects would be deleterious to CMV replication and transmission, respectively, but are moderated by the CMV 1a protein, which sequesters sufficient 2b protein molecules into P-bodies to prevent excessive inhibition of AGO1. Mutant 2b protein variants were generated, and red and green fluorescent protein fusions were used to investigate subcellular colocalization with AGO1 and the 1a protein. The effects of mutations on complex formation with the 1a protein and AGO1 were investigated using bimolecular fluorescence complementation and co-immunoprecipitation assays. Although we found that residues 56-60 influenced the 2b protein's interactions with the 1a protein and AGO1, it appears unlikely that any single residue or sequence domain is solely responsible. In silico predictions of intrinsic disorder within the 2b protein secondary structure were supported by circular dichroism (CD) but not by nuclear magnetic resonance (NMR) spectroscopy. Intrinsic disorder provides a plausible model to explain the 2b protein's ability to interact with AGO1, the 1a protein, and other factors. However, the reasons for the conflicting conclusions provided by CD and NMR must first be resolved.

Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae

Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.

Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure

The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.

Inhibitory protein-protein interactions of the SIRT1 deacetylase are choreographed by post-translational modification

Regulation of SIRT1 activity is vital to energy homeostasis and plays important roles in many diseases. We previously showed that insulin triggers the epigenetic regulator DBC1 to prime SIRT1 for repression by the multifunctional trafficking protein PACS-2. Here, we show that liver DBC1/PACS-2 regulates the diurnal inhibition of SIRT1, which is critically important for insulin-dependent switch in fuel metabolism from fat to glucose oxidation. We present the x-ray structure of the DBC1 S1-like domain that binds SIRT1 and an NMR characterization of how the SIRT1 N-terminal region engages DBC1. This interaction is inhibited by acetylation of K112 of DBC1 and stimulated by the insulin-dependent phosphorylation of human SIRT1 at S162 and S172, catalyzed sequentially by CK2 and GSK3, resulting in the PACS-2-dependent inhibition of nuclear SIRT1 enzymatic activity and translocation of the deacetylase in the cytoplasm. Finally, we discuss how defects in the DBC1/PACS-2-controlled SIRT1 inhibitory pathway are associated with disease, including obesity and non-alcoholic fatty liver disease.

Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation

Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assemblies. Despite its significance, the physicochemical property and the molecular mechanism followed by TNP1 for histone replacement and DNA condensation are still poorly understood. This study reports the first-time in vitro expression and purification of human TNP1 and investigates the hierarchical dynamics of TNP1-DNA interaction using a combination of computational simulations, biochemical assays, fluorescence imaging, and atomic force microscopy. We explored three crucial facets of TNP1-DNA interactions. Initially, we delve into the molecular binding process that entails fuzzy interactions between TNP1 and DNA at the atomistic scale. Subsequently, we analyze how TNP1 binding affects the electrostatic and mechanical characteristics of DNA and influences its morphology. Finally, we study the biomolecular condensation of TNP1-DNA when subjected to high concentrations. The findings of our study set the foundation for comprehending the potential involvement of TNP1 in histone replacement and DNA condensation in spermatogenesis.

Uncovering the Association Mechanism between Two Intrinsically Flexible Proteins

The understanding of protein-protein interaction mechanisms is key to the atomistic description of cell signaling pathways and for the development of new drugs. In this context, the mechanism of intrinsically disordered proteins folding upon binding has attracted attention. The VirB9 C-terminal domain (VirB9Ct) and the VirB7 N-terminal motif (VirB7Nt) associate with VirB10 to form the outer membrane core complex of the Type IV Secretion System injectisome. Despite forming a stable and rigid complex, VirB7Nt behaves as a random coil, while VirB9Ct is intrinsically dynamic in the free state. Here we combined NMR, stopped-flow fluorescence, and computer simulations using structure-based models to characterize the VirB9Ct-VirB7Nt coupled folding and binding mechanism. Qualitative data analysis suggested that VirB9Ct preferentially binds to VirB7Nt by way of a conformational selection mechanism at lower temperatures. However, at higher temperatures, energy barriers between different VirB9Ct conformations are more easily surpassed. Under these conditions the formation of non-native initial encounter complexes may provide alternative pathways toward the native complex conformation. These observations highlight the intimate relationship between folding and binding, calling attention to the fact that the two molecular partners must search for the most favored intramolecular and intermolecular interactions on a rugged and funnelled conformational energy landscape, along which multiple intermediates may lead to the final native state.