pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nuclear magnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics. Predictions have been expanded to provide new types of annotation on backbone rigidity, secondary structure preference and disordered binding regions. MobiDB 3.0 contains information for the complete UniProt protein set and synchronization has been improved by covering all UniParc sequences. An advanced search function allows the creation of a wide array of custom-made datasets for download and further analysis. A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility.

Binding of Noradrenaline to Native and Intermediate States during the Fibrillation of α-Synuclein Leads to the Formation of Stable and Structured Cytotoxic Species

Parkinson's disease is characterized by the deterioration of dopaminergic neurons of substantia nigra pars compacta along with a substantial loss of noradrenergic neurons of the locus coeruleus, which is the major source of noradrenaline (NA) in the brain. We have investigated the interaction of NA with α-synuclein (α-syn), the major protein constituent of Lewy bodies that are the pathological hallmark of Parkinson's disease (PD). It is expected that NA, like dopamine, could bind to α-syn and modulate its aggregation propensity and kinetics, which could also contribute to the onset of PD. We have, thus, evaluated the thermodynamic parameters of interaction of NA with α-syn monomer as well as species formed at different stages during its fibrillation pathway and have investigated the conformational and aggregation properties using various spectroscopic and calorimetric techniques. Binding isotherms of NA with α-syn species formed at different time points in the pathway have been observed to be exothermic in nature, suggesting hydrogen bonding interactions and weak affinity with binding constants in the millimolar range in all the cases. The interaction site of NA for α-syn was determined using Förster resonance energy transfer measurements that resulted in its binding in close proximity (23 Å) of an Alexa-labeled A90C mutant of α-syn. Docking studies further suggested binding of NA to the C-terminal as well as the non-amyloid-β component (NAC) region of α-syn. We have shown that α-syn oligomerization into sodium dodecyl sulfate resistant, higher-order, β-sheet-rich species is dependent on the oxidation of NA. Under non-reducing conditions, NA was also found to disaggregate the intermediates, populated during the fibrillation pathway, which are more cytotoxic compared to amyloid fibrils, as observed by 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide cytotoxicity assay using a human neuroblastoma cell line. On the basis of these and earlier data, we propose that NA-induced formation of α-syn oligomers may contribute to the progressive loss of the noradrenergic neuronal population and the pronounced Lewy body deposition observed in patients with PD.

Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins

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

Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles

The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), ³J-couplings (³Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.

Fast NMR method to probe solvent accessibility and disordered regions in proteins

Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established ¹H-¹⁵N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.

Troubleshooting Guide to Expressing Intrinsically Disordered Proteins for Use in NMR Experiments

Intrinsically disordered proteins (IDPs) represent a structural class of proteins that do not have a well-defined, 3D fold in solution, and often have little secondary structure. To characterize their function and molecular mechanism, it is helpful to examine their structure using nuclear magnetic resonance (NMR), which can report on properties, such as residual structure (at both the secondary and tertiary levels), ligand binding affinity, and the effect of ligand binding on IDP structure, all on a per residue basis. This brief review reports on the common problems and decisions that are involved when preparing a disordered protein for NMR studies. The paper covers gene design, expression host choice, protein purification, and the initial NMR experiments that are performed. While many of these steps are essentially identical to those for ordered proteins, a few key differences are highlighted, including the extreme sensitivity of IDPs to proteolytic cleavage, the ability to use denaturing conditions without having to refold the protein, the optimal chromatographic system choice, and the challenges of quantifying an IDP. After successful purification, characterization by NMR can be done using the standard ¹⁵N-heteronuclear single quantum coherence (¹⁵N-HSQC) experiment, or the newer CON series of experiments that are superior for disordered proteins.

In Silico and In Vitro Considerations of Keratinocyte Nuclear Receptor Protein Structural Order for Improving Experimental Analysis

Nuclear receptors (NR) regulate gene expression critical in keratinocyte replication and differentiation. In addition to a ligand-binding domain, NR like other transcription factor families have a DNA-binding domain that must attain a particular conformation for effective interaction with the three-dimensional structure in promoters of target genes for control of their expression. Such protein-DNA assemblies extend the classic "lock and key" idea typified by protein-protein interactions. However, it is becoming increasingly clear that multi-subdomain transcription factors like NR frequently range along the length of the protein from structured, ordered regions expected for interaction with a preset partner to more flexible, intrinsically disordered regions which are more available for diverse posttranslational modifications and/or interaction with differing partners. The extended amino terminus of NR (the A/B subdomain) is one such intrinsically disordered region. Here we provide a primer on in silico-based recognition of amino acid composition and order associated with such conformational flexibility along with adaptations of readily accessible laboratory techniques (e.g., considerations for recombinant expression, sensitivity to protease and proteasome digestion) to facilitate initial prediction and testing for intrinsic disorder in various proteins of interest to keratinocyte biologists, like NR and other transcription factors.

Structural Basis of Small Molecule Targetability of Monomeric Tau Protein

The therapeutic targeting of intrinsically disordered proteins (IDPs) by small molecules has been a challenge due to their heterogeneous conformational ensembles. A potential therapeutic strategy to alleviate the aggregation of IDPs is to maintain them in their native monomeric state by small molecule binding. This study investigates the structural basis of small molecule druggability of native monomeric Tau whose aggregation is linked to the onset of Tauopathies such as Alzheimer's disease. Initially, two available monomeric conformational ensembles of a shorter Tau construct K18 (also termed Tau4RD) were analyzed which revealed striking structural differences between the two ensembles, while similar number of hot spots and small molecule binding sites were identified on monomeric Tau ensembles as on tertiary folded proteins of similar size. Remarkably, some critical fibril forming sequence regions of Tau (V306-K311, V275-K280) participated in hot spot formation with higher frequency compared to other regions. As an example of small molecule binding to monomeric Tau, it was shown that methylene blue (MB) bound to monomeric K18 and full-length Tau selectively with high affinity (K_d = 125.8 nM and 86.6 nM, respectively) with binding modes involving Cys291 and Cys322, previously reported to be oxidized in the presence of MB. Overall, our results provide structure-based evidence that Tau can be a viable drug target for small molecules and indicate that specific small molecules may be able to bind to monomeric Tau and influence the way in which the protein interacts among itself and with other proteins.

AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins

The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems. In this work, we introduce AWSEM-IDP, a new AWSEM branch for simulating intrinsically disordered proteins (IDPs), where the weights of the potentials determining secondary structure formation have been finely tuned, and a novel potential is introduced that helps to precisely control both the average extent of protein chain collapse and the chain's fluctuations in size. AWSEM-IDP can efficiently sample large conformational spaces, while retaining sufficient molecular accuracy to realistically model proteins. We applied this new model to two IDPs, demonstrating that AWSEM-IDP can reasonably well reproduce higher-resolution reference data, thus providing the foundation for a transferable IDP force field. Finally, we used thermodynamic perturbation theory to show that, in general, the conformational ensembles of IDPs are highly sensitive to fine-tuning of force field parameters.

Conservation of Potentially Druggable Cavities in Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) exist in highly dynamic conformational ensembles, which pose a major obstacle for drug development targeting IDPs because traditional rational drug design relies on unique three-dimensional structures. Here, we analyzed the conservation (especially structural conservation) of potentially druggable cavities in 22 ensembles of IDPs. It was found that there is considerable conservation for potentially druggable cavities within each ensemble. The average common atom percentage of potentially druggable cavities is as high as 54%. The average root-mean-squared deviation of common atoms ranges between 1 and 8 Å for multichain IDPs, and a common pocket is kept after direct alignment of cavities. In addition, the conservation of potentially druggable cavities varies among different proteins. In the comparison of multi- and single-chain IDPs, some multichain IDPs have an extremely high conservation, whereas another multichain IDPs' conservation appears worse, and the single-chain IDPs have relatively moderate conservations. This study is a new attempt to generally assess the potentially druggable cavities in IDPs for taking IDPs as druggable targets, and this work also lends support to the opinion of IDPs tending to bind to "multiconformational affinity" compounds.

Stopped-Flow Kinetic Techniques for Studying Binding Reactions of Intrinsically Disordered Proteins

Intrinsically disordered proteins are abundant in signaling processes such as transcription. Suitable binding and unbinding rates of proteins with their partners are critical for allowing them to perform their biological roles. Understanding how these are achieved, and indeed designing strategies for intervening or modulating related biological processes, therefore requires kinetic studies. In this chapter, we describe stopped-flow-based methods for determining association and dissociation rate constants for pairs of macromolecular binding partners. We describe how to select the simplest appropriate model to describe the interaction, and highlight cases where it is possible to distinguish between induced fit and conformational selection binding mechanisms. Finally, we go on to describe methods for examining the role of electrostatic forces in binding processes, and for describing the transition state for binding processes that have folding associated with them.

Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools

The structural and functional characterization of large multidomain signaling proteins containing long disordered linker regions represents special methodological and conceptual challenges. These proteins show extreme structural heterogeneity and have complex posttranslational modification patterns, due to which traditional structural biology techniques provide results that are often difficult to interpret. As demonstrated through the example of two such multidomain proteins, CREB-binding protein (CBP) and its paralogue, p300, even the expression and purification of such proteins are compromised by their extreme proteolytic sensitivity and structural heterogeneity. In this chapter, we describe the effective expression of CBP and p300 in a eukaryotic host, Sf9 insect cells, followed by their tandem affinity purification based on two terminal tags to ensure their structural integrity. The major focus of this chapter is on the development of novel accessory tools, single-domain camelid antibodies (nanobodies), for structural-functional characterization. Specific nanobodies against full-length CBP and p300 can specifically target their different regions and can be used for their marking, labeling, and structural stabilization in a broad range of in vitro and in vivo studies. Here, we describe four high-affinity nanobodies binding to the KIX and the HAT domains, either mimicking known interacting partners or revealing new functionally relevant conformations. As immunization of llamas results in nanobody libraries with a great sequence variation, deep sequencing and interaction analysis with different regions of the proteins provide a novel approach toward developing a panel of specific nanobodies.

Interplay between sequence, structure and linear motifs in the adenovirus E1A hub protein

E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery.

Conformational Ensembles Exhibit Extensive Molecular Recognition Features

Intrinsically disordered proteins (IDPs) are important for signaling and regulatory pathways. In contrast to folded proteins, they sample a diverse conformational space. IDPs have residue ranges within a sequence that have been referred to as molecular recognition features (MoRFs). A MoRF can be viewed as contiguous residues exhibiting a conformational disorder that become ordered upon binding to another protein or ligand. In this work, we introduce a structural characterization of MoRFs based on entropy and mutual information (MI). In this view, a MoRF is a set of contiguous residues that exhibit a large entropy (from rotameric residue sampling) and large MI, the latter indicating a dependence among the residues' rotameric sampling comprising the MoRF. The methodology is first applied to a number of ubiquitin ensembles that were obtained based on nuclear magnetic resonance experiments. One is a denatured Ub ensemble that has a large entropy for various unitSizes (number of contiguous residues) but essentially zero MI, indicting no dependence among the residue rotamer sampling. Another ensemble does exhibit extensive regions along the sequence where there are MoRFs centered on nonsecondary structure regions. The MoRFs are present for unitSizes 2-10. That a substantial number of MoRFs are present in Ub strongly suggests a conformational selection mechanism for this protein. Two additional ensembles for the cyclin-dependent kinase inhibitor Sic1 and for the amyloid protein α-synuclein, which have been shown to be IDPs, are also analyzed. Both exhibit MoRF-like character.

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.

Disordered peptide chains in an α-C-based coarse-grained model

We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during the course of the time evolution. The contacts may arise between the sidechains, the backbones or the sidechains and backbones of the interacting residues. The model yields results that are consistent with many all-atom and experimental data on these systems. We demonstrate that the geometrical properties of various homopeptides differ substantially in this model. In particular, the average radius of gyration scales with the sequence length in a residue-dependent manner.

Complete Coupled Binding-Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling

Intrinsically disordered proteins (IDPs) make up a large class of proteins that lack stable structures in solution, existing instead as dynamic conformational ensembles. To perform their biological functions, many IDPs bind to other proteins or nucleic acids. Although IDPs are unstructured in solution, when they interact with binding partners, they fold into defined three-dimensional structures via coupled binding-folding processes. Because they frequently underlie IDP function, the mechanisms of this coupled binding-folding process are of great interest. However, given the flexibility inherent to IDPs and the sparse populations of intermediate states, it is difficult to reveal binding-folding pathways at atomic resolution using experimental methods. Computer simulations are another tool for studying these pathways at high resolution. Accordingly, we have applied 40 μs of unbiased molecular dynamics simulations and Markov state modeling to map the complete binding-folding pathway of a model IDP, the 59-residue C-terminal portion of the DNA binding domain of Drosophila melanogaster transcription factor Brinker (BrkDBD). Our modeling indicates that BrkDBD binds to its cognate DNA and folds in ∼50 μs by an induced fit mechanism, acquiring most of its stable secondary and tertiary structure only after it reaches the final binding site on the DNA. The protein follows numerous pathways en route to its bound and folded conformation, occasionally becoming stuck in kinetic traps. Each binding-folding pathway involves weakly bound, increasingly folded intermediate states located at different sites on the DNA surface. These findings agree with experimental data and provide additional insight into the BrkDBD folding mechanism and kinetics.

Fast simulations of multidimensional NMR spectra of proteins and peptides

To simulate full multidimensional nuclear magnetic resonance spectra of peptides and proteins in a reasonable time frame, a strategy for separating the time-consuming full-density matrix calculations from the chemical shift prediction and calculation of coupling patterns is presented. The simulation setup uses SIMulation Program for SOlid-state NMR (SIMPSON) to calculate total correlation spectroscopy transfer amplitudes and average distances as a source for nuclear Overhauser effect spectroscopy transfer amplitudes. Simulated ¹ H 1D, 2D total correlation spectroscopy, and 2D nuclear Overhauser effect spectroscopy nuclear magnetic resonance spectra of peptides with sequence Pro─Ala─Gly─Tyr─Asn and Asn─Phe─Gly─Ala─Ile─Leu and of ubiquitin are presented. In all cases, the simulations lasted from a few seconds to tens of seconds on a normal laptop computer.

Targeting Intrinsically Disordered Transcription Factors: Changing the Paradigm

Increased understanding of intrinsically disordered proteins (IDPs) and protein regions has revolutionized our view of the relationship between protein structure and function. Data now support that IDPs can be functional in the absence of a single, fixed, three-dimensional structure. Due to their dynamic morphology, IDPs have the ability to display a range of kinetics and affinity depending on what the system requires, as well as the potential for large-scale association. Although several studies have shed light on the functional properties of IDPs, the class of intrinsically disordered transcription factors (TFs) is still poorly characterized biophysically due to their combination of ordered and disordered sequences. In addition, TF modulation by small molecules has long been considered a difficult or even impossible task, limiting functional probe development. However, with evolving technology, it is becoming possible to characterize TF structure-function relationships in unprecedented detail and explore avenues not available or not considered in the past. Here we provide an introduction to the biophysical properties of intrinsically disordered TFs and we discuss recent computational and experimental efforts toward understanding the role of intrinsically disordered TFs in biology and disease. We describe a series of successful TF targeting strategies that have overcome the perception of the "undruggability" of TFs, providing new leads on drug development methodologies. Lastly, we discuss future challenges and opportunities to enhance our understanding of the structure-function relationship of intrinsically disordered TFs.

HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties

Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.

Conformational sampling of the intrinsically disordered dsRBD-1 domain from Arabidopsis thaliana DCL1

Partial folding and stability of DCL1-dsRBD1.

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions

More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.

Structural database resources for biological macromolecules

This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connections to sequence and functional annotation databases. Importantly, updates of most of these databases involves steps of curation and error checks based on specific expertise about the subject molecules or interactions, and removal of sequence redundancy, both leading to better data sets for mining studies compared with the full list of raw PDB entries. The article presents the databases in groups such as those aimed to facilitate browsing through PDB entries, their molecules and their general information, those built to link protein structure with sequence and dynamics, those specific for transmembrane proteins, nucleic acids, interactions of biomacromolecules with each other and with small molecules or metal ions, and those concerning specific structural features or specific protein families. A few webservers directly connected to active databases, and a few databases that have been discontinued but would be important to have back, are also briefly commented on. Along the Briefing, sample cases where these databases have been used to aid structural studies or advance our knowledge about biological macromolecules are referenced. A few specific examples are also given where using these databases is easier and more informative than using raw PDB data.

A Small Molecule Causes a Population Shift in the Conformational Landscape of an Intrinsically Disordered Protein

Intrinsically disordered proteins (IDPs) have roles in myriad biological processes and numerous human diseases. However, kinetic and amplitude information regarding their ground-state conformational fluctuations has remained elusive. We demonstrate using nuclear magnetic resonance (NMR)-based relaxation dispersion that the D2 domain of p27Kip1, a prototypical IDP, samples multiple discrete, rapidly exchanging conformational states. By combining NMR with mutagenesis and small-angle X-ray scattering (SAXS), we show that these states involve aromatic residue clustering through long-range hydrophobic interactions. Theoretical studies have proposed that small molecules bind promiscuously to IDPs, causing expansion of their conformational landscapes. However, on the basis of previous NMR-based screening results, we show here that compound binding only shifts the populations of states that existed within the ground state of apo p27-D2 without changing the barriers between states. Our results provide atomic resolution insight into how a small molecule binds an IDP and emphasize the need to examine motions on the low microsecond time scale when probing these types of interactions.

Conformation-based assay of tau protein aggregation

Amyloid fiber-forming proteins are predominantly intrinsically disordered proteins (IDPs). The protein tau, present mostly in neurons, is no exception. There is a significant interest in the study of tau protein aggregation mechanisms, given the direct correlation between the deposit of β-sheet structured neurofibrillary tangles made of tau and pathology in several neurodegenerative diseases, including Alzheimer's disease. Among the core unresolved questions is the nature of the initial step triggering aggregation, with increasing attention placed on the question whether a conformational change of the IDPs plays a key role in the early stages of aggregation. Specifically, there is growing evidence that a shift in the conformation ensemble of tau is involved in its aggregation pathway, and might even dictate structural and pathological properties of mature fibers. Yet, because IDPs lack a well-defined 3D structure and continuously exchange between different conformers, it has been technically challenging to characterize their structural changes on-pathway to aggregation. Here, we make a case that double spin labeling of the β-sheet stacking region of tau combined with pulsed double electron-electron resonance spectroscopy is a powerful method to assay conformational changes occurring during the course of tau aggregation, by probing intramolecular distances around aggregation-prone domains. We specifically demonstrate the potential of this approach by presenting recent results on conformation rearrangement of the β-sheet stacking segment VQIINK (known as PHF6*) of tau. We highlight a canonical shift of the conformation ensemble, on-pathway and occurring at the earliest stage of aggregation, toward an opening of PHF6*. We expect this method to be applicable to other critical segments of tau and other IDPs.

Insights into the conformations and dynamics of intrinsically disordered proteins using single-molecule fluorescence

Most proteins are not static structures, but many of them are found in a dynamic state, exchanging conformations on various time scales as a key aspect of their biological function. An entire spectrum of structural disorder exists in proteins and obtaining a satisfactory quantitative description of these states remains a challenge. Single-molecule fluorescence spectroscopy techniques are uniquely suited for this task, by measuring conformations without ensemble averaging and kinetics without interference from asynchronous processes. In this paper we review some of the recent successes in applying single-molecule fluorescence to different disordered protein systems, including interactions with their cellular targets and self-aggregation processes. We also discuss the implementation of computational methods and polymer physics models that are essential for inferring global dimension parameters for these proteins from smFRET data. Regarding future directions; 3- or 4-color FRET methods can provide multiple distances within a disordered ensemble simultaneously. In addition, integrating complementary experimental data from smFRET, NMR and SAXS will provide meaningful constraints for molecular simulations and will lead to more accurate structural representations of disordered proteins. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.

Modeling disordered protein interactions from biophysical principles

Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs.

Mechanistic roles of protein disorder within transcription

Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.

Principles of protein structural ensemble determination

The biological functions of protein molecules are intimately dependent on their conformational dynamics. This aspect is particularly evident for disordered proteins, which constitute perhaps one-third of the human proteome. Therefore, structural ensembles often offer more useful representations of proteins than individual conformations. Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. These principles concern primarily how to deal with conformationally heterogeneous states, and with experimental measurements that are averaged over such states and affected by a variety of errors. We first review the growing literature of recent methods that combine experimental and computational information to model structural ensembles, highlighting their similarities and differences. We then address some conceptual problems in the determination of structural ensembles and define future goals towards the establishment of objective criteria for the comparison, validation, visualization and dissemination of such ensembles.

Conformational Dynamics of Intracellular Tau Protein Revealed by CD and SAXS

A native conformation of a protein is essential for its biological role. In certain conditions, some proteins show non-native conformations, leading to aggregation, which in turn may produce severe pathologies. Such physiological conditions are classified as protein misfolding diseases. Alzheimer's disease (AD) is the most common form of dementia. Extracellular senile plaques formed by Amyloid β and intracellular aggregates formed by microtubule-associated protein Tau (MAPT) are the hallmarks of AD. Physiological role of MAPT is to maintain the integrity and stability of microtubules, however it tends to self-aggregate forming intracellular paired helical filaments (PHFs) during AD. MAPT is also subjected to various post-translational modifications such as phosphorylation, glycosylation, truncation, and acetylation. Being natively unfolded, MAPT is prone to full characterization at atomic level. Small-angle X-ray scattering (SAXS) is often applied in combination with other biophysical methods, like nuclear magnetic resonance (NMR), circular dichroism (CD), fluorescence spectroscopy, analytical ultracentrifugation (AUC), or dynamic light scattering (DLS) to characterize natively unfolded systems. Here we describe the practical aspects of MAPT characterization by SAXS and CD in detail as well as outline the inferred structural and functional implications.

How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe

In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins lack a stable 3D structure, are ubiquitous and fulfill essential biological functions. Their conformational heterogeneity is encoded in their amino acid sequences, thereby allowing intrinsically disordered proteins or regions to be recognized based on properties of these sequences. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray crystallization. This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved in induced folding. It also provides a set of detailed instructions that should be followed to perform computational analysis of disorder.

DisProt 7.0: a major update of the database of disordered proteins

The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

FuzDB (http://protdyn-database.org) compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database have both (i) structural evidence demonstrating the structural multiplicity or dynamic disorder of the ID region(s) in the partner bound form of the protein and (ii) in vitro or in vivo biological evidence that indicates the significance of the fuzzy region(s) in the formation, function or regulation of the assembly. Unlike the other intrinsically disordered or unfolded protein databases, FuzDB focuses on ID regions within a biological context, including higher-order assemblies and presents a detailed analysis of the structural and functional data. FuzDB also provides interpretation of experimental results to elucidate the molecular mechanisms by which fuzzy regions-classified on the basis of topology and mechanism-interfere with the structural ensembles and activity of protein assemblies. Regulatory sites generated by alternative splicing (AS) or post-translational modifications (PTMs) are also collected. By assembling all this information, FuzDB could be utilized to develop stochastic structure-function relationships for proteins and could contribute to the emergence of a new paradigm.

Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy

Here, we present a structural and dynamic description of CBP-ID4 at atomic resolution. ID4 is the fourth intrinsically disordered linker of CREB-binding protein (CBP). In spite of the largely disordered nature of CBP-ID4, NMR chemical shifts and relaxation measurements show a significant degree of α-helix sampling in the protein regions encompassing residues 2-25 and 101-128 (1852-1875 and 1951-1978 in full-length CBP). Proline residues are uniformly distributed along the polypeptide, except for the two α-helical regions, indicating that they play an active role in modulating the structural features of this CBP fragment. The two helical regions are lacking known functional motifs, suggesting that they represent thus-far uncharacterized functional modules of CBP. This work provides insights into the functions of this protein linker that may exploit its plasticity to modulate the relative orientations of neighboring folded domains of CBP and fine-tune its interactions with a multitude of partners.

Origin of a folded repeat protein from an intrinsically disordered ancestor

Repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. Many of these originated in a non-repetitive context as cofactors of RNA-based replication and catalysis, and required the RNA to assume their active conformation. In search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (TPR), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the putatively ancient ribosomal protein S20 (RPS20), which only becomes structured in the context of the ribosome. We evaluated the ability of the RPS20 hairpin to form a TPR fold by amplification and obtained structures identical to natural TPRs for variants with 2-5 point mutations per repeat. The mutations were neutral in the parent organism, suggesting that they could have been sampled in the course of evolution. TPRs could thus have plausibly arisen by amplification from an ancestral helical hairpin.

Finding Our Way in the Dark Proteome

The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.