Molecular principles of the interactions of disordered proteins

Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation

Many ATP-binding cassette (ABC) transporters are regulated by phosphorylation on long and disordered loops which present a challenge to visualize with structural methods. We have trapped an activated state of the regulatory domain (R-domain) of Yeast Cadmium Factor 1 (Ycf1) by enzymatically enriching the phosphorylated state. A 3.2 Å cryo-EM structure reveals an R-domain structure with four phosphorylated residues and a position for the entire R-domain. The structure reveals key R-domain interactions including a bridging interaction between NBD1 and NBD2 as well as an interaction with the R-insertion, another regulatory region. We systematically probe these interactions with a linker substitution strategy along the R-domain and find a close match with these interactions and survival under Ycf1-dependent growth conditions. We propose a model where four overlapping phosphorylation sites bridge several regions of Ycf1 to engage in a transport-competent state.

Uncovering the structural stability of Magnaporthe oryzae effectors: a secretome-wide in silico analysis

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is a deadly disease and a major threat to global food security. The pathogen secretes small proteinaceous effectors, virulence factors, inside the host to manipulate and perturb the host immune system, allowing the pathogen to colonize and establish a successful infection. While the molecular functions of several effectors are characterized, very little is known about the structural stability of these effectors. We analyzed a total of 554 small secretory proteins (SSPs) from the M. oryzae secretome to decipher key features of intrinsic disorder (ID) and the structural dynamics of the selected putative effectors through thorough and systematic in silico studies. Our results suggest that out of the total SSPs, 66% were predicted as effector proteins, released either into the apoplast or cytoplasm of the host cell. Of these, 68% were found to be intrinsically disordered effector proteins (IDEPs). Among the six distinct classes of disordered effectors, we observed peculiar relationships between the localization of several effectors in the apoplast or cytoplasm and the degree of disorder. We determined the degree of structural disorder and its impact on protein foldability across all the putative small secretory effector proteins from the blast pathogen, further validated by molecular dynamics simulation studies. This study provides definite clues toward unraveling the mystery behind the importance of structural distortions in effectors and their impact on plant-pathogen interactions. The study of these dynamical segments may help identify new effectors as well.Communicated by Ramaswamy H. Sarma.

Hierarchical Assembly of Intrinsically Disordered Short Peptides

The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.

Effects of pH and NaCl on the Spatial Structure and Conformation of Myofibrillar Proteins and the Emulsion Gel System—Insights from Computational Molecular Dynamics on Myosin of Golden Pompano

In this study, the effects of pH and NaCl concentrations on the structure of golden pompano myosin and emulsion gel were analyzed using SEM in combination with molecular dynamics simulations (MDS). The microscopic morphology and spatial structure of myosin were investigated at different pH (3.0, 7.0, and 11.0) and NaCl concentrations (0.0, 0.2, 0.6, and 1.0 M), and their effects on the stability of emulsion gels were discussed. Our results show that pH had a greater effect on the microscopic morphology of myosin than NaCl. The MDS results show that under the condition of pH 7.0 and 0.6 M NaCl, the myosin expanded and experienced significant fluctuations in its amino acid residues. However, NaCl showed a greater effect on the number of hydrogen bonds than pH. Although changes in pH and NaCl concentrations only slightly altered the secondary structures in myosin, they, nevertheless, significantly influenced the protein spatial conformation. The stability of the emulsion gel was affected by pH changes but not NaCl concentrations, which only affect the rheology. The best elastic modulus G″ of the emulsion gel was obtained at pH 7.0 and 0.6 M NaCl. Based on the results, we conclude that pH changes have a greater influence than NaCl concentrations on the spatial structure and conformation of myosin, contributing to the instability of its emulsion gel state. The data from this study would serve as a valuable reference for emulsion gel rheology modification in future research.

Intrinsic protein disorder uncouples affinity from binding specificity

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins often function by molecular recognition, in which they undergo induced folding. Based on prior generalizations, the idea prevails in the IDP field that due to the entropic penalty of induced folding, the major functional advantage associated with this binding mode is "uncoupling" specificity from binding strength. Nevertheless, both weaker binding and high specificity of IDPs/IDRs rest on limited experimental observations, making these assumptions more speculations than evidence-supported facts. The issue is also complicated by the rather vague concept of specificity that lacks an exact measure, such as the K_d for binding strength. We addressed these issues by creating and analyzing a comprehensive dataset of well-characterized ID/globular protein complexes, for which both the atomic structure of the complex and free energy (ΔG, K_d ) of interaction is known. Through this analysis, we provide evidence that the affinity distributions of IDP/globular and globular/globular complexes show different trends, whereas specificity does not connote to weaker binding strength of IDPs/IDRs. Furthermore, protein disorder extends the spectrum in the direction of very weak interactions, which may have important regulatory consequences and suggest that, in a biological sense, strict correlation of specificity and binding strength are uncoupled by structural disorder.

Nanomedicines Meet Disordered Proteins: A Shift from Traditional Materials and Concepts to Innovative Polymers

Water-soluble nanomedicines have been widely studied for the targeted delivery of drugs for a very long time. As a notable example, biomaterials based on N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers have been under investigation for nearly half a century. In particular, anticancer drug carriers have been developed under the assumption that the leading mechanism with a therapeutic impact on solid tumors is the enhanced permeability and retention (EPR) effect, which dates back more than three decades. Nevertheless, these (and other) materials and concepts have encountered several barriers in their successful translation into clinical practice, and future nanomedicines need improvements in both passive and active targeting to their site of action. Notions borrowed from recent studies on intrinsically disordered proteins (IDPs) seem promising for enhancing the self-assembly, stimuli-responsiveness, and recognition properties of protein/peptide-based copolymers. Accordingly, IDP-based nanomedicines are ready to give new impetus to more traditional research in this field.

Prediction of protein-protein interaction sites in intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) participate in many biological processes by interacting with other proteins, including the regulation of transcription, translation, and the cell cycle. With the increasing amount of disorder sequence data available, it is thus crucial to identify the IDP binding sites for functional annotation of these proteins. Over the decades, many computational approaches have been developed to predict protein-protein binding sites of IDP (IDP-PPIS) based on protein sequence information. Moreover, there are new IDP-PPIS predictors developed every year with the rapid development of artificial intelligence. It is thus necessary to provide an up-to-date overview of these methods in this field. In this paper, we collected 30 representative predictors published recently and summarized the databases, features and algorithms. We described the procedure how the features were generated based on public data and used for the prediction of IDP-PPIS, along with the methods to generate the feature representations. All the predictors were divided into three categories: scoring functions, machine learning-based prediction, and consensus approaches. For each category, we described the details of algorithms and their performances. Hopefully, our manuscript will not only provide a full picture of the status quo of IDP binding prediction, but also a guide for selecting different methods. More importantly, it will shed light on the inspirations for future development trends and principles.

Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered

There is increasing evidence that many intrinsically disordered regions (IDRs) in proteins play key functional roles through interactions with other proteins or nucleic acids. These interactions often exhibit a context-dependent structural behavior. We hypothesize that low complexity regions (LCRs), often found within IDRs, could have a role in inducing local structure in IDRs. To test this, we predicted IDRs in the human proteome and analyzed their structures or those of homologous sequences in the Protein Data Bank (PDB). We then identified two types of simple LCRs within IDRs: regions with only one (polyX or homorepeats) or with only two types of amino acids (polyXY). We were able to assign structural information from the PDB more often to these LCRs than to the surrounding IDRs (polyX 61.8% > polyXY 50.5% > IDRs 39.7%). The most frequently observed polyX and polyXY within IDRs contained E (Glu) or G (Gly). Structural analyses of these sequences and of homologs indicate that polyEK regions induce helical conformations, while the other most frequent LCRs induce coil structures. Our work proposes bioinformatics methods to help in the study of the structural behavior of IDRs and provides a solid basis suggesting a structuring role of LCRs within them.

Multi-level analysis of intrinsically disordered protein docking methods

Intrinsically Disordered Proteins (IDPs) are a class of proteins in which at least some region of the protein does not possess any stable structure in solution in the physiological condition but may adopt an ordered structure upon binding to a globular receptor. These IDP-receptor complexes are thus subject to protein complex modeling in which computational techniques are applied to accurately reproduce the IDP ligand-receptor interactions. This often exists in the form of protein docking, in which the 3D structures of both the subunits are known, but the position of the ligand relative to the receptor is not. Here, we evaluate the performance of three IDP-receptor modeling tools with metrics that characterize the IDP-receptor interface at various resolutions. We show that all three methods are able to properly identify the general binding site, as identified by lower resolution metrics, but begin to struggle with higher resolution metrics that capture biophysical interactions.

High internal phase emulsions stabilized solely by sonicated quinoa protein isolate at various pH values and concentrations

In this study, stable high internal phase emulsions (HIPEs) constructed solely by sonicated quinoa protein isolate (QPI) at various pH values and protein concentrations (c) were constructed, and differences of HIPE microstructures at these conditions were discussed. HIPEs stabilized by QPI at pH 7.0, 9.0 possessed smaller droplet size (14-24 μm), smoother appearance, and higher physical stability which were caused by polyhedral framework microstructure. However, at acidic conditions, QPI aggregates filled in the gaps between droplets (30-52 μm) instead of adsorbing to oil-water interface, which decreased the stability. The solid-like viscoelasticity of HIPEs were enhanced when the c increased while the increment of pH value had the significant opposite effect (decreased from about G' 1000 Pa, G″ 280 Pa to G' 350 Pa, G″ 50 Pa) due to the microstructure difference. This study broadens the commercial applications of quinoa protein in novel food products like fat substitutes.

DisEnrich: database of enriched regions in human dark proteome

MOTIVATION

Intrinsically disordered proteins (IDPs) are involved in numerous processes crucial for living organisms. Bias in amino acid composition of these proteins determines their unique biophysical and functional features. Distinct intrinsically disordered regions (IDRs) with compositional bias play different important roles in various biological processes. IDRs enriched in particular amino acids in human proteome have not been described consistently.

RESULTS

We developed DisEnrich-the database of human proteome IDRs that are significantly enriched in particular amino acids. Each human protein is described using Gene Ontology (GO) function terms, disorder prediction for the full-length sequence using three methods, enriched IDR composition and ranks of human proteins with similar enriched IDRs. Distribution analysis of enriched IDRs among broad functional categories revealed significant overrepresentation of R- and Y-enriched IDRs in metabolic and enzymatic activities and F-enriched IDRs in transport. About 75% of functional categories contain IDPs with IDRs significantly enriched in hydrophobic residues that are important for protein-protein interactions.

AVAILABILITY AND IMPLEMENTATION

The database is available at http://prodata.swmed.edu/DisEnrichDB/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics Advances online.

Predicting Protein Conformational Disorder and Disordered Binding Sites

In the last two decades it has become increasingly evident that a large number of proteins adopt either a fully or a partially disordered conformation. Intrinsically disordered proteins are ubiquitous proteins that fulfill essential biological functions while lacking a stable 3D structure. Their conformational heterogeneity is encoded by the amino acid sequence, thereby allowing intrinsically disordered proteins or regions to be recognized based on their sequence properties. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to crystallization. This chapter focuses on the methods currently employed for predicting protein disorder and identifying intrinsically disordered binding sites.

Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions

Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of polysaccharides and are today divided into eight families (AA9-11, AA13-17) within the Auxiliary Activity enzyme class of the CAZy database. LPMOs minimal architecture encompasses a catalytic domain, to which can be appended a carbohydrate-binding module. Intriguingly, we observed that some LPMO sequences also display a C-terminal extension of varying length not associated with any known function or fold. Here, we analyzed 27,060 sequences from different LPMO families and show that 60% have a C-terminal extension predicted to be intrinsically disordered. Our analysis shows that these disordered C-terminal regions (dCTRs) are widespread in all LPMO families (except AA13) and differ in terms of sequence length and amino-acid composition. Noteworthily, these dCTRs have so far only been observed in LPMOs. LPMO-dCTRs share a common polyampholytic nature and an enrichment in serine and threonine residues, suggesting that they undergo post-translational modifications. Interestingly, dCTRs from AA11 and AA15 are enriched in redox-sensitive, conditionally disordered regions. The widespread occurrence of dCTRs in LPMOs from evolutionarily very divergent organisms, hints at a possible functional role and opens new prospects in the field of LPMOs.

Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins

Structure, function, and evolution are interdependent properties of proteins. Diversity of protein functions arising from structural variations is a potential driving force behind protein evolvability. Intrinsically disordered proteins or regions (IDPs or IDRs) lack well-defined structure under normal physiological conditions, yet, they are highly functional. Increased occurrence of IDPs in eukaryotes compared to prokaryotes indicates strong correlation of protein evolution and disorderedness. IDPs generally have higher evolution rate compared to globular proteins. Structural pliability allows IDPs to accommodate multiple mutations without affecting their functional potential. Nevertheless, how evolutionary signals vary between different classes of disordered residues (DRs) in IDPs is poorly understood. This study addresses variation of evolutionary behavior in terms of residue conservation and intra-protein coevolution among structural and functional classes of DRs in IDPs. Analyses are performed on 579 human IDPs, which are classified based on length of IDRs, interacting partners and functional classes. We find short IDRs are less conserved than long IDRs or full IDPs. Functional classes which require flexibility and specificity to perform their activity comparatively evolve slower than others. Disorder promoting amino acids evolve faster than order promoting amino acids. Pro, Gly, Ile, and Phe have unique coevolving nature which further emphasizes on their roles in IDPs. This study sheds light on evolutionary footprints in different classes of DRs from human IDPs and enhances our understanding of the structural and functional potential of IDPs.

Enthalpy-Entropy Compensation in the Promiscuous Interaction of an Intrinsically Disordered Protein with Homologous Protein Partners

Intrinsically disordered proteins (IDPs) can engage in promiscuous interactions with their protein targets; however, it is not clear how this feature is encoded in the primary sequence of the IDPs and to what extent the surface properties and the shape of the binding cavity dictate the binding mode and the final bound conformation. Here we show, using a combination of nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), that the promiscuous interaction of the intrinsically disordered regulatory domain of the mitogen-activated protein kinase kinase MKK4 with p38α and JNK1 is facilitated by folding-upon-binding into two different conformations, despite the high sequence conservation and structural homology between p38α and JNK1. Our results support a model whereby the specific surface properties of JNK1 and p38α dictate the bound conformation of MKK4 and that enthalpy–entropy compensation plays a major role in maintaining comparable binding affinities for MKK4 towards the two kinases.

BRCA2 binding through a cryptic repeated motif to HSF2BP oligomers does not impact meiotic recombination

BRCA2 and its interactors are required for meiotic homologous recombination (HR) and fertility. Loss of HSF2BP, a BRCA2 interactor, disrupts HR during spermatogenesis. We test the model postulating that HSF2BP localizes BRCA2 to meiotic HR sites, by solving the crystal structure of the BRCA2 fragment in complex with dimeric armadillo domain (ARM) of HSF2BP and disrupting this interaction in a mouse model. This reveals a repeated 23 amino acid motif in BRCA2, each binding the same conserved surface of one ARM domain. In the complex, two BRCA2 fragments hold together two ARM dimers, through a large interface responsible for the nanomolar affinity - the strongest interaction involving BRCA2 measured so far. Deleting exon 12, encoding the first repeat, from mBrca2 disrupts BRCA2 binding to HSF2BP, but does not phenocopy HSF2BP loss. Thus, results herein suggest that the high-affinity oligomerization-inducing BRCA2-HSF2BP interaction is not required for RAD51 and DMC1 recombinase localization in meiotic HR.

Intrinsic Disorder and Phosphorylation in BRCA2 Facilitate Tight Regulation of Multiple Conserved Binding Events

The maintenance of genome integrity in the cell is an essential process for the accurate transmission of the genetic material. BRCA2 participates in this process at several levels, including DNA repair by homologous recombination, protection of stalled replication forks, and cell division. These activities are regulated and coordinated via cell-cycle dependent modifications. Pathogenic variants in BRCA2 cause genome instability and are associated with breast and/or ovarian cancers. BRCA2 is a very large protein of 3418 amino acids. Most well-characterized variants causing a strong predisposition to cancer are mutated in the C-terminal 700 residues DNA binding domain of BRCA2. The rest of the BRCA2 protein is predicted to be disordered. Interactions involving intrinsically disordered regions (IDRs) remain difficult to identify both using bioinformatics tools and performing experimental assays. However, the lack of well-structured binding sites provides unique functional opportunities for BRCA2 to bind to a large set of partners in a tightly regulated manner. We here summarize the predictive and experimental arguments that support the presence of disorder in BRCA2. We describe how BRCA2 IDRs mediate self-assembly and binding to partners during DNA double-strand break repair, mitosis, and meiosis. We highlight how phosphorylation by DNA repair and cell-cycle kinases regulate these interactions. We finally discuss the impact of cancer-associated variants on the function of BRCA2 IDRs and more generally on genome stability and cancer risk.

Structural and Functional Annotation of Napin-Like Protein from Momordica charantia to Explore its Medicinal Importance

Seed storage proteins not just provide essential nutritional ingredients for growth of seedlings but also have their potential role in defense mechanisms of plants. Napin is a seed storage protein and belongs to 2S albumin family. Napin and napin-like protein have many biological defensive activities including antifungal, antimicrobial, trypsin inhibitor, and also act as antagonist of calmodulin. Napin protein possesses various isoforms with different biological activities. In this study, the protein sequence of napin from Momordica charantia was retrieved from GenPept database for characterization. A complete annotation of napin including its physicochemical properties was done. Three dimensional (3D) modeling and interactions of napin-like protein with other proteins were also predicted using various bioinformatics tools. A phylogram of napin-like protein from M. charantia with its homologs was also reconstructed to reveal its evolutionary relationships with napins and other 2S albumin proteins from various plants. The study has revealed the structural characterization, biological interactions, and evolutionary background which will play crucial role in exploring the medicinal and biological potentials of napin-like protein from M. charantia as well as worth of napin and napin-like protein has been disclosed.

Introducing intrinsic disorder reduces electrostatic steering in protein-protein interactions

Protein-protein interactions underlie many critical biology functions, such as cellular signaling and gene expression, in which electrostatic interactions can play a critical role in mediating the specificity and stability of protein complexes. A substantial portion of proteins are intrinsically disordered, and the influences of structural disorder on binding kinetics and thermodynamics have been widely investigated. However, whether the effect of electrostatic steering depends on structural disorder remains unexplored. In this work, we addressed the consequence of introducing intrinsic disorder in the electrostatic steering of the E3/Im3 complex using molecular dynamics simulation. Our results recapitulated the experimental observations that the responses of stability and kinetics to salt concentration for the ordered E3/Im3 complex were larger than those for the disordered E3/Im3 complex. Mechanistic analysis revealed that the native contact interactions involved in the encounter state and the transition state were essentially identical for both ordered and disordered E3. Therefore, the observed difference in electrostatic steering between ordered E3 and disordered E3 may result from their difference in conformation rather than their difference in binding mechanism. Because charged residues are frequently involved in protein-protein interactions, our results suggest that increasing structural disorder is expected to generally modulate the effect of electrostatic steering.

Molecular recognition of structurally disordered Pro/Ala-rich sequences (PAS) by antibodies involves an Ala residue at the hot spot of the epitope

Pro/Ala-rich sequences (PAS) are polypeptides that were developed as a biological alternative to poly-ethylene glycol (PEG) to generate biopharmaceuticals with extended plasma half-life. Like PEG, PAS polypeptides are conformationally disordered and show high solubility in water. Devoid of any charged or prominent hydrophobic side chains, these biosynthetic polymers represent an extreme case of intrinsically disordered proteins. Despite lack of immunogenicity of PAS tags in numerous animal studies we now succeeded in generating monoclonal antibodies (MAbs) against three different PAS versions. To this end, mice were immunized with a PAS#1, P/A#1 or APSA 40mer peptide conjugated to keyhole limpet hemocyanin as highly immunogenic carrier protein. In each case, one MAb with high binding activity and specificity towards a particular PAS motif was obtained. The apparent affinity was strongly dependent on the avidity effect and most pronounced for the bivalent MAb when interacting with a long PAS repeat. X-ray structural analysis of four representative anti-PAS Fab fragments in complex with their cognate PAS epitope peptides revealed interactions dominated by hydrogen bond networks involving the peptide backbone as well as multiple Van der Waals contacts arising from intimate shape complementarity. Surprisingly, Ala, the L-amino acid with the smallest side chain, emerged as a crucial feature for epitope recognition, contributing specific contacts at the center of the paratope in several anti-PAS complexes. Apart from these insights into how antibodies can recognize feature-less peptides without secondary structure, the MAbs characterized in this study offer valuable reagents for the preclinical and clinical development of PASylated biologics.

Autophagy and organelle homeostasis in cancer

Beginning with the earliest studies of autophagy in cancer, there have been indications that autophagy can both promote and inhibit cancer growth and progression; autophagy regulation of organelle homeostasis is similarly complicated. In this review we discuss pro- and antitumor effects of organelle-targeted autophagy and how this contributes to several hallmarks of cancer, such as evading cell death, genomic instability, and altered metabolism. Typically, the removal of damaged or dysfunctional organelles prevents tumor development but can also aid in proliferation or drug resistance in established tumors. By better understanding how organelle-specific autophagy takes place and can be manipulated, it may be possible to go beyond the brute-force approach of trying to manipulate all autophagy in order to improve therapeutic targeting of this process in cancer.

The Interaction Mechanism of Intrinsically Disordered PP2A Inhibitor Proteins ARPP-16 and ARPP-19 With PP2A

Protein phosphatase 2A (PP2A) activity is critical for maintaining normal physiological cellular functions. PP2A is inhibited by endogenous inhibitor proteins in several pathological conditions including cancer. A PP2A inhibitor protein, ARPP-19, has recently been connected to several human cancer types. Accordingly, the knowledge about ARPP-19—PP2A inhibition mechanism is crucial for the understanding the disease development and the therapeutic targeting of ARPP-19—PP2A. Here, we show the first structural characterization of ARPP-19, and its splice variant ARPP-16 using NMR spectroscopy, and SAXS. The results reveal that both ARPP proteins are intrinsically disordered but contain transient secondary structure elements. The interaction mechanism of ARPP-16/19 with PP2A was investigated using microscale thermophoresis and NMR spectroscopy. Our results suggest that ARPP—PP2A A-subunit interaction is mediated by linear motif and has modest affinity whereas, the interaction of ARPPs with B56-subunit is weak and transient. Like many IDPs, ARPPs are promiscuous binders that transiently interact with PP2A A- and B56 subunits using multiple interaction motifs. In summary, our results provide a good starting point for future studies and development of therapeutics that block ARPP-PP2A interactions.

The intrinsically disordered N-terminus of the voltage-dependent anion channel

The voltage-dependent anion channel (VDAC) is a critical β-barrel membrane protein of the mitochondrial outer membrane, which regulates the transport of ions and ATP between mitochondria and the cytoplasm. In addition, VDAC plays a central role in the control of apoptosis and is therefore of great interest in both cancer and neurodegenerative diseases. Although not fully understood, it is presumed that the gating mechanism of VDAC is governed by its N-terminal region which, in the open state of the channel, exhibits an α-helical structure positioned midway inside the pore and strongly interacting with the β-barrel wall. In the present work, we performed molecular simulations with a recently developed force field for disordered systems to shed new light on known experimental results, showing that the N-terminus of VDAC is an intrinsically disordered region (IDR). First, simulation of the N-terminal segment as a free peptide highlighted its disordered nature and the importance of using an IDR-specific force field to properly sample its conformational landscape. Secondly, accelerated dynamics simulation of a double cysteine VDAC mutant under applied voltage revealed metastable low conducting states of the channel representative of closed states observed experimentally. Related structures were characterized by partial unfolding and rearrangement of the N-terminal tail, that led to steric hindrance of the pore. Our results indicate that the disordered properties of the N-terminus are crucial to properly account for the gating mechanism of VDAC.

The voltage-dependent anion channel (VDAC) is a membrane protein playing a pivotal role in the transport of ions or ATP across the mitochondrial outer membrane as well as in the induction of apoptosis. At high enough membrane potential, VDAC is known to transition from an open state to multiple closed states, reducing the flow of ions through the channel and blocking the passage of large metabolites. While the structure of the open state was resolved more than a decade ago, a molecular description of the gating mechanism of the channel is still missing. Here we show that the N-terminus of VDAC is an intrinsically disordered region and that such a property has a profound impact on its dynamics either as a free peptide or as part of the channel. By taking disordered properties of the N-terminus into account, we managed to generate long-lived closed conformations of the channel at experimental values of the membrane potential. Our results provide new insights into the molecular mechanism driving the gating of VDAC.

Hepatitis B protein HBx binds the DLEU2 lncRNA to sustain cccDNA and host cancer-related gene transcription

OBJECTIVE

The HBV HBx regulatory protein is required for transcription from the covalently closed circular DNA (cccDNA) minichromosome and affects the epigenetic control of both viral and host cellular chromatin.

DESIGN

We explored, in relevant cellular models of HBV replication, the functional consequences of HBx interaction with DLEU2, a long non-coding RNA (lncRNA) expressed in the liver and increased in human hepatocellular carcinoma (HCC), in the regulation of host target genes and the HBV cccDNA.

RESULTS

We show that HBx binds the promoter region, enhances the transcription and induces the accumulation of DLEU2 in infected hepatocytes. We found that nuclear DLEU2 directly binds HBx and the histone methyltransferase enhancer of zeste homolog 2 (EZH2), the catalytic active subunit of the polycomb repressor complex 2 (PRC2) complex. Computational modelling and biochemical evidence suggest that HBx and EZH2 share two preferential binding sites in DLEU2 intron 1. HBx and DLEU2 co-recruitment on the cccDNA displaces EZH2 from the viral chromatin to boost transcription and viral replication. DLEU2-HBx association with target host promoters relieves EZH2 repression and leads to the transcriptional activation of a subset of EZH2/PRC2 target genes in HBV-infected cells and HBV-related HCCs.

CONCLUSIONS

Our results highlight the ability of HBx to bind RNA to impact on the epigenetic control of both viral cccDNA and host genes and provide a new key to understand the role of DLEU2 and EZH2 overexpression in HBV-related HCCs and HBx contribution to hepatocytes transformation.

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt

DisProt is the major repository of manually curated data for intrinsically disordered proteins collected from the literature. Although lacking a stable tertiary structure under physiological conditions, intrinsically disordered proteins carry out a plethora of biological functions, some of them directly arising from their flexible nature. A growing number of scientific studies have been published during the last few decades in an effort to shed light on their unstructured state, their binding modes, and their functions. DisProt makes use of a team of expert biocurators to provide up-to-date annotations of intrinsically disordered proteins from the literature, making them available to the scientific community. Here we present a comprehensive description on how to use DisProt in different contexts and provide a detailed explanation of how to explore and interpret manually curated annotations of intrinsically disordered proteins. We describe how to search DisProt annotations, using both the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, p53, a widely studied protein characterized by the presence of unstructured N-terminal and C-terminal regions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt Support Protocol 1: Downloading options Support Protocol 2: Programmatic access with DisProt REST API Basic Protocol 2: Visualizing and interpreting DisProt entries: the p53 use case Basic Protocol 3: Providing feedback and submitting new intrinsic disorder-related data.

Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations

Because proteins are fundamental to most biological processes, many genetic diseases can be traced back to single nucleotide variants (SNVs) that cause changes in protein sequences. However, not all SNVs that result in amino acid substitutions cause disease as each residue is under different structural and functional constraints. Influential studies have shown that protein–protein interaction interfaces are enriched in disease-associated SNVs and depleted in SNVs that are common in the general population. These studies focus primarily on folded (globular) protein domains and overlook the prevalent class of protein interactions mediated by intrinsically disordered regions (IDRs). Therefore, we investigated the enrichment patterns of missense mutation-causing SNVs that are associated with disease and cancer, as well as those present in the healthy population, in structures of IDR-mediated interactions with comparisons to classical globular interactions. When comparing the different categories of interaction interfaces, division of the interface regions into solvent-exposed rim residues and buried core residues reveal distinctive enrichment patterns for the various types of missense mutations. Most notably, we demonstrate a strong enrichment at the interface core of interacting IDRs in disease mutations and its depletion in neutral ones, which supports the view that the disruption of IDR interactions is a mechanism underlying many diseases. Intriguingly, we also found an asymmetry across the IDR interaction interface in the enrichment of certain missense mutation types, which may hint at an increased variant tolerance and urges further investigations of IDR interactions.

Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach

Intrinsically disordered proteins (IDPs) play important roles in biology, but little is known about the energetics of their inter-residue interactions. Methods that have been successfully applied to analyze the energetics of globular proteins are not applicable to the fluctuating partially ordered ensembles populated by IDPs. A combined computational experimental strategy is introduced for analyzing the energetic role of individual residues in the free state of IDPs. The approach combines experimental measurements of the binding of wild-type and mutant IDPs to their partners with alchemical free energy calculations of the structured complexes. These data allow quantitative information to be deduced about the free state via a thermodynamic cycle. The approach is validated by the analysis of the effects of mutations upon the binding free energy of the ovomucoid inhibitor third binding domain to its partners and is applied to the C-terminal domain of the measles virus nucleoprotein, a 125-residue IDP involved in the RNA transcription and replication of measles virus. The analysis reveals significant inter-residue interactions in the unbound IDP and suggests a biological role for them. The work demonstrates that advances in force fields and computational hardware have now led to the point where it is possible to develop methods, which integrate experimental and computational techniques to reveal insights that cannot be studied using either technique alone.

Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions

In eukaryotes, disordered regions cover up to 50% of proteomes and mediate fundamental cellular processes. In contrast to globular domains, where about half of the amino acids are buried in the protein interior, disordered regions show higher solvent accessibility, which makes them prone to engage in non-functional interactions. Such interactions are exacerbated by the law of mass action, prompting the question of how they are minimized in abundant proteins. We find that interaction propensity or "stickiness" of disordered regions negatively correlates with their cellular abundance, both in yeast and human. Strikingly, considering yeast proteins where a large fraction of the sequence is disordered, the correlation between stickiness and abundance reaches R=-0.55. Beyond this global amino-acid composition bias, we identify three rules by which amino-acid composition of disordered regions adjusts with high abundance. First, lysines are preferred over arginines, consistent with the latter amino acid being stickier than the former. Second, compensatory effects exist, whereby a sticky region can be tolerated if it is compensated by a distal non-sticky region. Third, such compensation requires a lower average stickiness at the same abundance when compared to a scenario where stickiness is homogeneous throughout the sequence. We validate these rules experimentally, employing them as different strategies to rescue an otherwise sticky protein fragment from aggregation. Our results highlight that non-functional interactions represent a significant constraint in cellular systems and reveal simple rules by which protein sequences adapt to that constraint. Data from this work are deposited in Figshare, at https://doi.org/10.6084/m9.figshare.8068937.v3.

Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding

Intrinsically disordered proteins mediate crucial biological functions through their interactions with other proteins. Mutual synergistic folding (MSF) occurs when all interacting proteins are disordered, folding into a stable structure in the course of the complex formation. In these cases, the folding and binding processes occur in parallel, lending the resulting structures uniquely heterogeneous features. Currently there are no dedicated classification approaches that take into account the particular biological and biophysical properties of MSF complexes. Here, we present a scalable clustering-based classification scheme, built on redundancy-filtered features that describe the sequence and structure properties of the complexes and the role of the interaction, which is directly responsible for structure formation. Using this approach, we define six major types of MSF complexes, corresponding to biologically meaningful groups. Hence, the presented method also shows that differences in binding strength, subcellular localization, and regulation are encoded in the sequence and structural properties of proteins. While current protein structure classification methods can also handle complex structures, we show that the developed scheme is fundamentally different, and since it takes into account defining features of MSF complexes, it serves as a better representation of structures arising through this specific interaction mode.

The various shades of ER-phagy

Endoplasmic reticulum (ER) is a large and dynamic cellular organelle. ER morphology consists of sheets, tubules, matrixes, and contact sites shared with other membranous organelles. The capacity of the ER to fulfill its numerous biological functions depends on its continuous remodeling and the quality control of its proteome. Selective turnover of the ER by autophagy, termed ER‐phagy, plays an important role in maintaining ER homeostasis. ER network integrity and turnover rely on specific ER‐phagy receptors, which influence and coordinate alterations in ER morphology and the degradation of ER contents and membranes via the lysosome, by interacting with the LC3/GABARAP family. In this commentary, we discuss general principles and identify the major players in this recently characterized form of selective autophagy, while simultaneously highlighting open questions in the field.

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

The structural states of proteins include ordered globular domains as well as intrinsically disordered protein regions that exist as highly flexible conformational ensembles in isolation. Various computational tools have been developed to discriminate ordered and disordered segments based on the amino acid sequence. However, properties of IDRs can also depend on various conditions, including binding to globular protein partners or environmental factors, such as redox potential. These cases provide further challenges for the computational characterization of disordered segments. In this work we present IUPred2A, a combined web interface that allows to generate energy estimation based predictions for ordered and disordered residues by IUPred2 and for disordered binding regions by ANCHOR2. The updated web server retains the robustness of the original programs but offers several new features. While only minor bug fixes are implemented for IUPred, the next version of ANCHOR is significantly improved through a new architecture and parameters optimized on novel datasets. In addition, redox-sensitive regions can also be highlighted through a novel experimental feature. The web server offers graphical and text outputs, a RESTful interface, access to software download and extensive help, and can be accessed at a new location: http://iupred2a.elte.hu.

Automated feature engineering improves prediction of protein-protein interactions

Over the last decade, various machine learning (ML) and statistical approaches for protein-protein interaction (PPI) predictions have been developed to help annotating functional interactions among proteins, essential for our system-level understanding of life. Efficient ML approaches require informative and non-redundant features. In this paper, we introduce novel types of expert-crafted sequence, evolutionary and graph features and apply automatic feature engineering to further expand feature space to improve predictive modeling. The two-step automatic feature-engineering process encompasses the hybrid method for feature generation and unsupervised feature selection, followed by supervised feature selection through a genetic algorithm (GA). The optimization of both steps allows the feature-engineering procedure to operate on a large transformed feature space with no considerable computational cost and to efficiently provide newly engineered features. Based on GA and correlation filtering, we developed a stacking algorithm GA-STACK for automatic ensembling of different ML algorithms to improve prediction performance. We introduced a unified method, HP-GAS, for the prediction of human PPIs, which incorporates GA-STACK and rests on both expert-crafted and 40% of newly engineered features. The extensive cross validation and comparison with the state-of-the-art methods showed that HP-GAS represents currently the most efficient method for proteome-wide forecasting of protein interactions, with prediction efficacy of 0.93 AUC and 0.85 accuracy. We implemented the HP-GAS method as a free standalone application which is a time-efficient and easy-to-use tool. HP-GAS software with supplementary data can be downloaded from: http://www.vinca.rs/180/tools/HP-GAS.php .

Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions

A long-standing goal in biology is the complete annotation of function and structure on all protein-protein interactions, a large fraction of which is mediated by intrinsically disordered protein regions (IDRs). However, knowledge derived from experimental structures of such protein complexes is disproportionately small due, in part, to challenges in studying interactions of IDRs. Here, we introduce IDRBind, a computational method that by combining gradient boosted trees and conditional random field models predicts binding sites of IDRs with performance approaching state-of-the-art globular interface predictions, making it suitable for proteome-wide applications. Although designed and trained with a focus on molecular recognition features, which are long interaction-mediating-elements in IDRs, IDRBind also predicts the binding sites of short peptides more accurately than existing specialized predictors. Consistent with IDRBind's specificity, a comparison of protein interface categories uncovered uniform trends in multiple physicochemical properties, positioning molecular recognition feature interfaces between peptide and globular interfaces.

Predicting Functions of Disordered Proteins with MoRFpred

Intrinsically disordered proteins and regions are involved in a wide range of cellular functions, and they often facilitate protein-protein interactions. Molecular recognition features (MoRFs) are segments of intrinsically disordered regions that bind to partner proteins, where binding is concomitant with a transition to a structured conformation. MoRFs facilitate translation, transport, signaling, and regulatory processes and are found across all domains of life. A popular computational tool, MoRFpred, accurately predicts MoRFs in protein sequences. MoRFpred is implemented as a user-friendly web server that is freely available at http://biomine.cs.vcu.edu/servers/MoRFpred/ . We describe this predictor, explain how to run the web server, and show how to interpret the results it generates. We also demonstrate the utility of this web server based on two case studies, focusing on the relevance of evolutionary conservation of MoRF regions.

DIBS: a repository of disordered binding sites mediating interactions with ordered proteins

Motivation

Intrinsically Disordered Proteins (IDPs) mediate crucial protein–protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode.

Results

Here, we present DIBS, the first comprehensive, curated collection of complexes between IDPs and ordered proteins. DIBS not only describes by far the highest number of cases, it also provides the dissociation constants of their interactions, as well as the description of potential post-translational modifications modulating the binding strength and linear motifs involved in the binding. Together with the wide range of structural and functional annotations, DIBS will provide the cornerstone for structural and functional studies of IDP complexes.

Availability and implementation

DIBS is freely accessible at http://dibs.enzim.ttk.mta.hu/. The DIBS application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created.

Supplementary information

Supplementary data are available at Bioinformatics online.

Diffusion-limited association of disordered protein by non-native electrostatic interactions

Intrinsically disordered proteins (IDPs) usually fold during binding to target proteins. In contrast to interactions between folded proteins, this additional folding step makes the binding process more complex. Understanding the mechanism of coupled binding and folding of IDPs requires analysis of binding pathways that involve formation of the transient complex (TC). However, experimental characterization of TC is challenging because it only appears for a very brief period during binding. Here, we use single-molecule fluorescence spectroscopy to investigate the mechanism of diffusion-limited association of an IDP. A large enhancement of the association rate is observed due to the stabilization of TC by non-native electrostatic interactions. Moreover, photon-by-photon analysis reveals that the lifetime of TC for IDP binding is at least two orders of magnitude longer than that for binding of two folded proteins. This result suggests the long lifetime of TC is generally required for folding of IDPs during binding processes.

Intrinsically disordered proteins (IDPs) usually fold during binding to target proteins which involves the formation of a transient complex (TC). Here authors use single-molecule FRET to show that the lifetime of TC for IDP binding is very long due to the stabilization by non-native electrostatic interactions, which makes fast association possible.

MFIB: a repository of protein complexes with mutual folding induced by binding

Motivation

It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein–protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs.

Results

Here we present the Mutual Folding Induced by Binding (MFIB) database, the first systematic collection of complexes formed exclusively by IDPs. MFIB contains an order of magnitude more data than any dataset used in corresponding studies and offers a wide coverage of known IDP complexes in terms of flexibility, oligomeric composition and protein function from all domains of life. The included complexes are grouped using a hierarchical classification and are complemented with structural and functional annotations. MFIB is backed by a firm development team and infrastructure, and together with possible future community collaboration it will provide the cornerstone for structural and functional studies of IDP complexes.

Availability and implementation

MFIB is freely accessible at http://mfib.enzim.ttk.mta.hu/. The MFIB application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created.

Supplementary information

Supplementary data are available at Bioinformatics online.

Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins

Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species. Conservation signals for the maintenance and novel emergence of MAU sites are examined at 11 evolutionary levels from the whole eukaryotic domain down to the ape superfamily, in both ordered and disordered regions. We discover that MAU PTM is a major driver of conservation for arginines and lysines in both ordered and disordered regions, across the 11 levels, most significantly across the mammalian clade. Conservation of human methylatable arginines is very strongly favoured for ordered regions rather than for disordered, whereas methylatable lysines are conserved in either set of regions, and conservation of acetylatable and ubiquitinatable lysines is favoured in disordered over ordered. Notably, we find evidence for the emergence of new lysine MAU sites in disordered regions of proteins in deuterostomes and mammals, and in ordered regions after the dawn of eutherians. For histones specifically, MAU sites demonstrate an idiosyncratic significant conservation pattern that is evident since the last common ancestor of mammals. Similarly, folding-on-binding (FB) regions are highly enriched for MAU sites relative to either ordered or disordered regions, with ubiquitination sites in FBs being highly conserved at all evolutionary levels back as far as mammals. This investigation clearly demonstrates the complex patterns of PTM evolution across the human proteome and that it is necessary to consider conservation of sequence features at multiple evolutionary levels in order not to get an incomplete or misleading picture.

IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency.

The Disordered C-Terminus of Yeast Hsf1 Contains a Cryptic Low-Complexity Amyloidogenic Region

Response mechanisms to external stress rely on networks of proteins able to activate specific signaling pathways to ensure the maintenance of cell proteostasis. Many of the proteins mediating this kind of response contain intrinsically disordered regions, which lack a defined structure, but still are able to interact with a wide range of clients that modulate the protein function. Some of these interactions are mediated by specific short sequences embedded in the longer disordered regions. Because the physicochemical properties that promote functional and abnormal interactions are similar, it has been shown that, in globular proteins, aggregation-prone and binding regions tend to overlap. It could be that the same principle applies for disordered protein regions. In this context, we show here that a predicted low-complexity interacting region in the disordered C-terminus of the stress response master regulator heat shock factor 1 (Hsf1) protein corresponds to a cryptic amyloid region able to self-assemble into fibrillary structures resembling those found in neurodegenerative disorders.

Prediction of spacer-α6 complex: a novel insight into binding of ADAMTS13 with A2 domain of von Willebrand factor under forces

Force-regulated cleavage of A2 domain of von Willebrand factor (vWF) by ADAMTS13 is a key event in preventing thrombotic thrombocytopenic purpura (TTP). Recognition and cleavage depend on cooperative and modular contacts between several ADAMTS13 subdomains and discrete segments of vWF A2 domain. Spacer domain of ADAMTS13 contains an important exosite interacting with α6 helix of unfold A2 domain, but it remains unclear whether stretching of α6 regulates binding to spacer. To understand the molecular mechanism underlying the interactions between spacer and α6 under stretching, we successfully predicted spacer-α6 complex by a novel computer strategy combined the steered molecular dynamics (SMD) and flexible docking techniques. This strategy included three steps: (1) constant-velocity SMD simulation of α6; (2) zero-velocity SMD simulations of α6, and (3) flexible dockings of α6 to spacer. In our spacer-α6 complex model, 13 key residues, six in α6 and seven in spacer, were identified. Our data demonstrated a biphasic extension-regulated binding of α6 to spacer. The binding strength of the complex increased with α6 extension until it reaches its optimum of 0.25 nm, and then decreased as α6 extension further increased, meaning that spacer is in favor to binding with a partially extended α6, which may contribute to the optimal contact and proteolysis. Changes of interface area and intermolecular salt bridge may serve as the molecular basis for this characteristic. These findings provide a novel insight into mechano-chemical regulation on interaction between ADAMTS13 and vWF A2 domain under forces.

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation

Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.