Relating sequence encoded information to form and function of intrinsically disordered proteins

Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo

Compartmentalization of multiple enzymes in cellulo and in vitro is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid-liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows in vitro and in vivo regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies in vitro and in cellulo. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.

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

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

Characterization and Expression Analysis of the ALOG Gene Family in Rice (Oryza sativa L.)

ALOG (Arabidopsis LSH1 and Oryza G1) proteins constitute a plant-specific family of transcription factors that play crucial roles in lateral organ development across land plants. Initially identified through forward genetic studies of Arabidopsis LSH1 and rice G1 proteins, ALOG family members have since been functionally characterized in various plant species. However, research focusing on the characteristics and expression patterns of all ALOG family members in rice remains relatively limited. In this study, we systematically characterized OsALOG family genes in rice. Compared to other genes in rice and Arabidopsis, the ALOG family genes have a relatively simple structure. The alignment of OsALOG amino acid sequences and analysis of disorder predictions reveal that all members possess conserved ALOG domains, while the conservation of intrinsically disordered regions (IDRs) is relatively low. Four amino acids-alanine, glycine, proline, and serine-are significantly enriched in the IDRs of each ALOG protein. Synteny analysis indicates that most OsALOG genes have undergone considerable divergence compared to their counterparts in Arabidopsis. Bioinformatic analysis of cis-regulatory elements predicts that OsALOG family genes contain elements responsive to ABA, light, and methyl jasmonate, although the abundance and composition of these elements vary among different members. The expression patterns associated with the rice floral development of OsALOG genes can be broadly categorized into two types; however, even within the same type, differences in expression levels, as well as the initiation time and duration of expression, were observed. These results provide a comprehensive understanding of the structural characteristics and expression patterns of OsALOG members in rice.

Applications of Liquid-Liquid Phase Separation in Biosensing

Phase separation, particularly liquid-liquid phase separation (LLPS), has emerged as a powerful tool in biological research, offering unique advantages for visualizing and analyzing biomolecular interactions. This review highlights recent advances in leveraging LLPS to develop experimental techniques for studying protein-protein interactions (PPIs), protein-RNA interactions, and enzyme activity. The integration of LLPS with advanced techniques has expanded its applications, offering new possibilities for unraveling the complexities of cellular function and disease mechanisms. Looking forward, the development of more versatile, sensitive, and targeted LLPS-based methods is poised to transform molecular biology, providing deeper insights into cellular dynamics and facilitating therapeutic advancements.

Structural Context Modulates the Conformational Ensemble of the Intrinsically Disordered Amino Terminus of α-Synuclein

Regions of intrinsic disorder play crucial roles in biological systems, yet they often elude characterization by conventional biophysical techniques. To capture conformational distributions across different time scales, we employed a freezing approach coupled with solid-state NMR analysis. Using segmentally isotopically labeled α-synuclein (α-syn), we investigated the conformational ensembles of the six alanines, three glycines, and a single site (L8) in the disordered amino terminus under three distinct conditions: in 8 M urea, as a frozen monomer in buffer, and within the disordered regions flanking the amyloid core. The experimental spectra varied significantly among these conditions and deviated from those of a statistical coil. In 8 M urea, monomeric α-syn exhibited the most restricted conformational sampling, rarely accessing chemical shifts characteristic of α-helices or β-strands. In buffer, monomeric α-syn showed a broader conformational sampling, favoring α-helical conformations and, to a lesser extent, random coil states. Notably, amino acids in the disordered regions flanking the amyloid core demonstrated the most extensive conformational sampling, with broad peaks encompassing the entire range of possible chemical shifts and a marked increase in highly extended β-strand conformations. Collectively, this work demonstrates that intrinsically disordered regions exhibit distinct conformational ensembles, which are influenced not only by the chemical environment but also by the conformations of adjacent protein sequences. The differences in the conformational ensembles of the disordered amino terminus may explain why the monomer and the amyloid form of α-syn interact with different biomolecules inside cells.

Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins

The preponderance of intrinsically disordered proteins (IDPs) in the eukaryotic proteome, and their ability to interact with each other, and with folded proteins, RNA, and DNA for functional purposes, have made it important to quantitatively characterize their biophysical properties. Toward this end, we developed the transferable self-organized polymer (SOP-IDP) model to calculate the properties of several IDPs. The values of the radius of gyration (R g $$ {R}_g $$ ) obtained from SOP-IDP simulations are in excellent agreement (correlation coefficient of 0.96) with those estimated from SAXS experiments. For AP180 and Epsin, the predicted values of the hydrodynamic radii (R h s $$ {R}_h\mathrm{s} $$ ) are in nearly quantitative agreement with those from fluorescence correlation spectroscopy (FCS) experiments. Strikingly, the calculated SAXS profiles for 36 IDPs are also nearly superimposable on the experimental profiles. The dependence ofR g $$ {R}_g $$ and the mean end-to-end distance (R ee $$ {R}_{ee} $$ ) on chain length,N $$ N $$ , follows Flory's scaling law,R α ≈ a α N 0.588 $$ {R}_{\alpha}\approx {a}_{\alpha }{N}^{0.588} $$ (α = g , $$ \alpha =g, $$ ande $$ e $$ ), suggesting that globally IDPs behave as synthetic polymers in a good solvent. This finding depends on the solvent quality, which can be altered by changing variables such as pH and salt concentration. The values ofa g $$ {a}_g $$ anda e $$ {a}_e $$ are 0.20 and 0.48 nm, respectively. Surprisingly, finite size corrections to scaling, expected on theoretical grounds, are negligible forR g $$ {R}_g $$ andR ee $$ {R}_{ee} $$ . In contrast, only by accounting for the finite sizes of the IDPs, the dependence of experimentally measurableR h $$ {R}_h $$ onN $$ N $$ can be quantitatively explained usingν = 0.588 $$ \nu =0.588 $$ . Although Flory scaling law captures the estimates forR g $$ {R}_g $$ ,R ee $$ {R}_{ee} $$ , andR h $$ {R}_h $$ accurately, the spread of the simulated data around the theoretical curve is suggestive of of sequence-specific features that emerge through a fine-grained analysis of the conformational ensembles using hierarchical clustering. Typically, the ensemble of conformations partitions into three distinct clusters, having different equilibrium populations and structural properties. Without any further readjustments to the parameters of the SOP-IDP model, we also obtained nearly quantitative agreement with paramagnetic relaxation enhancement (PRE) measurements for α-synuclein. The transferable SOP-IDP model sets the stage for several applications, including the study of phase separation in IDPs and interactions with nucleic acids.

Accuracy of distance distributions and dynamics from single-molecule FRET

Single-molecule spectroscopy combined with Förster resonance energy transfer is widely used to quantify distance dynamics and distributions in biomolecules. Most commonly, measurements are interpreted using simple analytical relations between experimental observables and the underlying distance distributions. However, these relations make simplifying assumptions, such as a separation of timescales between interdye distance dynamics, fluorescence lifetimes, and dye reorientation, the validity of which is notoriously difficult to assess from experimental data alone. Here, we use experimentally validated long-timescale, all-atom explicit-solvent molecular dynamics simulations of a disordered peptide with explicit fluorophores for testing these assumptions, in particular the separation of the relevant timescales and the description of chain dynamics in terms of diffusion in a potential of mean force. Our results allow us to quantitatively assess the resulting errors; they indicate that, even outside the simple limiting regimes, the errors from common approximations in data analysis are generally smaller than the systematic uncertainty limiting the accuracy of Förster resonance energy transfer efficiencies. We also illustrate how the direct comparison between measured and simulated experimental data can be employed to optimize force field parameters and develop increasingly realistic simulation models.

Disentangling Folding from Energetic Traps in Simulations of Disordered Proteins

Protein conformational heterogeneity plays an essential role in a myriad of different biological processes. Extensive conformational heterogeneity is especially characteristic of intrinsically disordered proteins and protein regions (collectively IDRs), which lack a well-defined three-dimensional structure and instead rapidly exchange between a diverse ensemble of configurations. An emerging paradigm recognizes that the conformational biases encoded in IDR ensembles can play a central role in their biological function, necessitating understanding these sequence-ensemble relations. All-atom simulations have provided critical insight into our modern understanding of the solution behavior of IDRs. However, effectively exploring the accessible conformational space associated with large, heterogeneous ensembles is challenging. In particular, identifying poorly sampled or energetically trapped regions of disordered proteins in simulations often relies on qualitative assessment based on visual inspection of simulations and/or analysis data. These approaches, while convenient, run the risk of masking poorly sampled simulations. In this work, we present an algorithm for quantifying per-residue local conformational heterogeneity in protein simulations. Our work builds on prior work and compares the similarity between backbone dihedral angle distributions generated from molecular simulations in a limiting polymer model and across independent all-atom simulations. In this regime, the polymer model serves as a statistical reference model for extensive conformational heterogeneity in a real chain. Quantitative comparisons of probability vectors generated from these simulations reveal the extent of conformational sampling in a simulation, enabling us to distinguish between situations in which protein regions are well-sampled, poorly sampled, or folded. To demonstrate the effectiveness of this approach, we apply our algorithm to several toy, synthetic, and biological systems. Accurately assessing local conformational sampling in simulations of IDRs will help better quantify new enhanced sampling methods, ensure force field comparisons are equivalent, and provide confidence that conclusions drawn from simulations are robust.

Accurate prediction of thermoresponsive phase behavior of disordered proteins

Protein responses to environmental stress, particularly temperature fluctuations, have long been a subject of investigation, with a focus on how proteins maintain homeostasis and exhibit thermoresponsive properties. While UCST-type (upper critical solution temperature) phase behavior has been studied extensively and can now be predicted reliably using computational models, LCST-type (lower critical solution temperature) phase transitions remain less explored, with a lack of computational models capable of accurate prediction. This gap limits our ability to probe fully how proteins undergo phase transitions in response to temperature changes. Here, we introduce Mpipi-T, a residue-level coarse-grained model designed to predict LCST-type phase behavior of proteins. Parametrized using both atomistic simulations and experimental data, Mpipi-T accounts for entropically driven protein phase separation that occurs upon heating. Accordingly, Mpipi-T predicts temperature-driven protein behavior quantitatively in both single- and multi-chain systems. Beyond its predictive capabilities, we demonstrate that Mpipi-T provides a framework for uncovering the molecular mechanisms underlying heat stress responses, offering new insights into how proteins sense and adapt to thermal changes in biological systems.

Predicting Heteropolymer Phase Separation Using Two-Chain Contact Maps

Phase separation in polymer solutions often correlates with single-chain and two-chain properties, such as the single-chain radius of gyration,R g , and the pairwise second virial coefficient,B 22 . However, recent studies have shown that these metrics can fail to distinguish phase-separating from non-phase-separating heteropolymers, including intrinsically disordered proteins (IDPs). Here we introduce an approach to predict heteropolymer phase separation from two-chain simulations by analyzing contact maps, which capture how often specific monomers from the two chains are in physical proximity. WhereasB 22 summarizes the overall attraction between two chains, contact maps preserve spatial information about their interactions. To compare these metrics, we train phase-separation classifiers for both a minimal heteropolymer model and a chemically specific, residue-level IDP model. Remarkably, simple statistical properties of two-chain contact maps predict phase separation with high accuracy, vastly outperforming classifiers based onR g andB 22 alone. Our results thus establish a transferable and computationally efficient method to uncover key driving forces of IDP phase behavior based on their physical interactions in dilute solution.

Peptide-mediated liquid-liquid phase separation and biomolecular condensates

Liquid-liquid phase separation (LLPS) is a cornerstone of cellular organization, driving the formation of biomolecular condensates that regulate diverse biological processes and inspire innovative applications. This review explores the molecular mechanisms underlying peptide-mediated LLPS, emphasizing the roles of intermolecular interactions such as hydrophobic effects, electrostatic interactions, and π-π stacking in phase separation. The influence of environmental factors, such as pH, temperature, ionic strength, and molecular crowding on the stability and dynamics of peptide coacervates is examined, highlighting their tunable properties. Additionally, the unique physicochemical properties of peptide coacervates, including their viscoelastic behavior, interfacial dynamics, and stimuli-responsiveness, are discussed in the context of their biological relevance and engineering potential. Peptide coacervates are emerging as versatile platforms in biotechnology and medicine, particularly in drug delivery, tissue engineering, and synthetic biology. By integrating fundamental insights with practical applications, this review underscores the potential of peptide-mediated LLPS as a transformative tool for advancing science and healthcare.

Low-complexity regions in fungi display functional groups and are depleted in positively charged amino acids

Reports on the diversity and occurrence of low-complexity regions (LCR) in Eukaryota are limited. Some studies have provided a more extensive characterization of LCR proteins in prokaryotes. There is a growing body of knowledge about a plethora of biological functions attributable to LCRs. However, it is hard to determine to what extent observed phenomena apply to fungi since most studies of fungal LCRs were limited to model yeasts. To fill this gap, we performed a survey of LCRs in proteins across all fungal tree of life branches. We show that the abundance of LCRs and the abundance of proteins with LCRs are positively correlated with proteome size. We observed that most LCRs are present in proteins with protein domains but do not overlap with the domain regions. LCRs are associated with many duplicated protein domains. The quantity of particular amino acids in LCRs deviates from the background frequency with a clear over-representation of amino acids with functional groups and a negative charge. Moreover, we discovered that each lineage of fungi favors distinct LCRs expansions. Early diverging fungal lineages differ in LCR abundance and composition pointing at a different evolutionary trajectory of each fungal group.

Context-dependent effect of polyethylene glycol on the structure and dynamics of hirudin

Hirudin is a bioactive small protein that binds thrombin to interrupt the blood clotting cascade. It contains an ordered and a disordered (IDR) region. Conjugating with polyethylene glycol (PEGylation) is an important modification of biopharmaceuticals to improve their lifetime and retention. Here, we studied by molecular dynamics (MD) simulation how hirudin P18 and its PEGylated variant differ in their structural flexibility depending on binding to thrombin and charge screening by NaCl. We also compare with glycated hirP18 and the hirV1 variant to assess effects of different polar attachments and sequence variability. First, we synthesized unlabeled and PEG-labeled hirP18 followed by an activity assay to ascertain that the peptide-PEG conjugate retains anticoagulant activity. Next, we carried 16 different microsecond MD simulations of the different proteins, bound and unbound, for 2 sequences and different salt conditions. Simulations were analyzed in terms of scaling exponents to study the effect of ionic strength on hirudin size and solvent-exposed surface area. We conclude that charge patterning of the sequence and the presence of arginine are 2 important features for how PEG interacts with the protein folded and intrinsically disordered regions. Specifically, PEG can screen end-to-end electrostatic interactions by "hiding" a positively charged region of hirudin, whereas hirV1 is less sticky than hirP18 due to different PEG-hirudin hydrophobic interactions and the presence of an arginine in hirP18. Conjugation with either PEG or a glycan significantly reduces solvent-exposed area of hirudin, but PEG interacts more efficiently with surface residues than does glycan due to its narrower chain that can fit in surface grooves, and alternation of polar (oxygen) and nonpolar (CH2-CH2) groups that interact favorably with charged and hydrophobic surface patches.

Regulation of physiological and pathological condensates by molecular chaperones

Biomolecular condensates are dynamic membraneless compartments that regulate a myriad of cellular functions. A particular type of physiological condensate called stress granules (SGs) has gained increasing interest due to its role in the cellular stress response and various diseases. SGs, composed of several hundred RNA-binding proteins, form transiently in response to stress to protect mRNAs from translation and disassemble when the stress subsides. Interestingly, SGs contain several aggregation-prone proteins, such as TDP-43, FUS, hnRNPA1, and others, which are typically found in pathological inclusions seen in autopsy tissues from amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients. Moreover, mutations in these genes lead to the familial form of ALS and FTD. This has led researchers to propose that pathological aggregation is seeded by aberrant SGs: SGs that fail to properly disassemble, lose their dynamic properties, and become pathological condensates which finally 'mature' into aggregates. Here, we discuss the evidence supporting this model for various ALS/FTD-associated proteins. We further continue to focus on molecular chaperone-mediated regulation of ALS/FTD-associated physiological condensates on one hand, and pathological condensates on the other. In addition to SGs, we review ALS/FTD-relevant nuclear condensates, namely paraspeckles, anisosomes, and nucleolar amyloid bodies, and discuss their emerging regulation by chaperones. As the majority of chaperoning mechanisms regulate physiological condensate disassembly, we highlight parallel themes of physiological and pathological condensation regulation across different chaperone families, underscoring the potential for early disease intervention.

piRNA processing within non-membrane structures is governed by constituent proteins and their functional motifs

Discovered two decades ago, PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements (TEs) in animal gonads, thereby protecting the germline genome from harmful transposition, and ensuring species continuity. Silencing of TEs is achieved through transcriptional and post-transcriptional suppression by piRNAs and the PIWI clade of Argonaute proteins within non-membrane structured organelle. These structures are composed of proteins involved in piRNA processing, including PIWIs and other proteins by distinct functional motifs such as the Tudor domain, LOTUS, and intrinsic disordered regions (IDRs). This review highlights recent advances in understanding the roles of these conserved proteins and structural motifs in piRNA biogenesis. We explore the molecular mechanisms of piRNA biogenesis, with a primary focus on Drosophila as a model organism, identifying common themes and species-specific variations. Additionally, we extend the discussion to the roles of these components in nongonadal tissues.

Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure

Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ) as a model system, revealing how its material properties and cellular function depend on its ultrastructure. We revealed PopZ's hierarchical assembly into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques, and molecular dynamics simulations. The helical domain drives filamentation and condensation, while the disordered domain inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client binding sites in the dense phase. These findings establish a multiscale framework that links molecular interactions and condensate ultrastructure to macroscopic material properties that drive cellular function.

Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations

It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facilitate a systematic investigation of these sequence-ensemble relationships, we selected a set of 16 naturally occurring intrinsically disordered regions of identical length but with large differences in amino acid composition, hydrophobicity, and charge patterning. We probed their conformational ensembles with single-molecule Förster resonance energy transfer (FRET), complemented by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as small-angle X-ray scattering (SAXS). The set of disordered proteins shows a strong dependence of the chain dimensions on sequence composition, with chain volumes differing by up to a factor of 6. The residue-specific intrachain interaction networks that underlie these pronounced differences were identified using atomistic simulations combined with ensemble reweighting, revealing the important role of charged, aromatic, and polar residues. To advance a transferable description of disordered protein regions, we further employed the experimental data to parametrize a coarse-grained model for disordered proteins that includes an explicit representation of the FRET fluorophores and successfully describes experiments with different dye pairs. Our findings demonstrate the value of integrating experiments and simulations for advancing our quantitative understanding of the sequence features that determine the conformational ensembles of intrinsically disordered proteins.

A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) adopt ensembles of rapidly fluctuating heterogeneous conformations, influencing their binding capabilities and supramolecular transitions. The primary conformational descriptors for understanding IDP ensembles-the radius of gyration (RG), measured by small-angle X-ray scattering (SAXS), and the root mean square (rms) end-to-end distance (RE), probed by fluorescent resonance energy transfer (FRET)-are often reported to produce inconsistent results regarding IDP expansion as a function of denaturant concentration in the buffer. This ongoing debate surrounding the FRET-SAXS discrepancy raises questions about the overall reliability of either method for quantitatively studying IDP properties. To address this discrepancy, we introduce a genetically encoded anomalous SAXS (ASAXS) ruler, enabling simultaneous and direct measurements of RG and RE without assuming a specific structural model. This ruler utilizes a genetically encoded noncanonical amino acid with two bromine atoms, providing an anomalous X-ray scattering signal for precise distance measurements. Through this approach, we experimentally demonstrate that the ratio between RE and RG varies under different denaturing conditions, highlighting the intrinsic properties of IDPs as the primary source of the observed SAXS-FRET discrepancy rather than shortcomings in either of the two established methods. The developed genetically encoded ASAXS ruler emerges as a versatile tool for both IDPs and folded proteins, providing a unified approach for obtaining complementary and site-specific conformational information in scattering experiments, thereby contributing to a deeper understanding of protein functions.

Emergent microenvironments of nucleoli

In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.

Survey of the Aβ-peptide structural diversity: molecular dynamics approaches

The review deals with the application of Molecular Dynamics (MD) to the structure modeling of beta-amyloids (Aβ), currently classified as intrinsically disordered proteins (IDPs). In this review, we strive to relate the main advances in this area but specifically focus on the approaches and methodology. All relevant papers on the Aβ modeling are cited in the Tables in Supplementary Data, including a concise description of the applied approaches, sorted according to the types of the studied systems: modeling of the monomeric Aβ and Aβ aggregates. Similar sections focused according to the type of modeled object are present in the review. In the final part of the review, novel methods of general IDP modeling not confined to Aβ are described.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-024-01253-y.

Likely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water

Recent years have witnessed drastic improvements in general-purpose explicit solvent protein force fields, partially driven by the need to study intrinsically disordered proteins (IDPs), and yet the state-of-the-art force fields such as CHARMM36m (c36m) and a99SB-disp still provide different performances in simulating disordered protein states, where c36m has a bias toward overcompaction for large IDPs. Here, we examine the performance of c36m and a99SB-disp in describing the stabilities of a set of 46 amino acid backbone and side chain pairs in various configurations. The free energy results show that c36m systematically predicts stronger interactions compared to a99SB-disp by an average of 0.2 kcal/mol for nonpolar pairs, 0.6 kcal/mol for polar pairs, and 0.8 kcal/mol for salt bridges. The most severe overstabilization in c36m is observed for charged pairs involving the Arg and Glu side chains by up to 2.9 kcal/mol. Importantly, the systematic overstabilization of c36m is only marginally alleviated by c36mw, an ad hoc patch to c36m that increases the dispersion interactions between TIP3P hydrogens and protein atoms. Guided by free energy decomposition, we evaluated if revising the charges alone could alleviate the severe overstabilization of salt bridges of c36m(w) vs a99SB-disp. The results suggested that the direct modification of protein-water interactions is also necessary. Toward this end, we proposed a tentative modification to c36m, referred to as c36mrb-disp, which combines modified Arg side chain charges, retuned backbone hydrogen bonding strength, and the a99SB-disp water model. The modified force field successfully reproduces the secondary structures of several intrinsically disordered peptides and proteins including (AAQAA)3, GB1p, and p53 transactivation domain, while maintaining the stability of a set of folded proteins. This work provides a set of useful systems for benchmarking and optimizing protein force fields and highlights the importance of balancing protein-protein and protein-water electrostatic interactions for accurately describing both folded and disordered proteins.

Physics-Based Machine Learning Trains Hamiltonians and Decodes the Sequence-Conformation Relation in the Disordered Proteome

Intrinsically disordered proteins and regions (IDPs) are involved in vital biological processes. To understand the IDP function, often controlled by conformation, we need to find the link between sequence and conformation. We decode this link by integrating theory, simulation, and machine learning (ML) where sequence-dependent electrostatics is modeled analytically while nonelectrostatic interaction is extracted from simulations for many sequences and subsequently trained using ML. The resulting Hamiltonian, combining physics-based electrostatics and machine-learned nonelectrostatics, accurately predicts sequence-specific global and local measures of conformations beyond the original observable used from the simulation. This is in contrast to traditional ML approaches that train and predict a specific observable, not a Hamiltonian. Our formalism reproduces experimental measurements, predicts multiple conformational features directly from sequence with high throughput that will give insights into IDP design and evolution, and illustrates the broad utility of using physics-based ML to train unknown parts of a Hamiltonian, rather than a specific observable, in combination with known physics.

Disordered proteins interact with the chemical environment to tune their protective function during drying

The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins, combined with the exposure of their residues, accounts for this sensitivity. One context in which IDPs play important roles that are concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat-soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results suggest that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet the mechanisms underlying this synergy differ between IDP families.

A High-Throughput Workflow to Analyze Sequence-Conformation Relationships and Explore Hydrophobic Patterning in Disordered Peptoids

Understanding how a macromolecule's primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using MALDI-MS/MS, and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived 'motifs' to inform a machine learning algorithm towards conformation prediction. This multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.

Structural context modulates the conformational ensemble of the intrinsically disordered amino terminus of α-synuclein

Regions of intrinsic disorder play crucial roles in biological systems, yet they often elude characterization by conventional biophysical techniques. To capture conformational distributions across different timescales, we employed a freezing approach coupled with solid-state NMR analysis. Using segmentally isotopically labeled α-synuclein (α-syn), we investigated the conformational preferences of the six alanines, three glycines, and a single site (L8) in the disordered amino terminus under three distinct conditions: in 8 M urea, as a frozen monomer in buffer, and within the disordered regions flanking the amyloid core. The experimental spectra varied significantly among these conditions and deviated from those of a statistical coil. In 8 M urea, monomeric α-syn exhibited the most restricted conformational sampling, rarely accessing chemical shifts characteristic of α-helices or β-strands. In buffer, monomeric α-syn showed broader conformational sampling, favoring α-helical conformations and, to a lesser extent, random coil states. Notably, amino acids in the disordered regions flanking the amyloid core demonstrated the most extensive conformational sampling, with broad peaks encompassing the entire range of possible chemical shifts and a marked preference for highly extended β-strand conformations. Collectively, this work demonstrates that intrinsically disordered regions exhibit distinct conformational preferences, which are influenced not only by the chemical environment but also by the conformations of adjacent protein sequences. The differences in the conformational ensembles of the disordered amino terminus may explain why the monomer and the amyloid form of α-syn interact with different biomolecules inside cells.

Sequence Length Controls Coil-to-Globule Transition in Elastin-like Polypeptides

It appeared certain that elastin condensates retain liquid-like properties. However, a recent experimental study demonstrated that their aggregate states might depend on the length of hydrophobic domains. To gain microscopic insight into this behavior, we employ atomistic modeling to assess the conformational properties of hydrophobic elastin-like polypeptides (ELPs). We find that short ELPs always remain in coil-like conformations, while the longer ones prefer globule states. While the former engages in intrapeptide hydrogen bonds temporarily, retaining their liquid-like properties, the latter forms hundreds of nanosecond-long intrapeptide hydrogen bonds attributed to ordered secondary structure motifs. Our work demonstrates that the sequence length modulates the material properties of elastin condensates.

Acetylation-Dependent Compaction of the Histone H4 Tail Ensemble

Acetylation of the histone H4 tail (H4Kac) has been established as a significant regulator of chromatin architecture and accessibility; however, the molecular mechanisms that underlie these observations remain elusive. Here, we characterize the ensemble features of the histone H4 tail and determine how they change following acetylation on specific sets of lysine residues. Our comprehensive account is enabled by a robust combination of experimental and computational biophysical methods that converge on molecular details including conformer size, intramolecular contacts, and secondary structure propensity. We find that acetylation significantly alters the chemical environment of basic patch residues (16-20) and leads to tail compaction that is partially mediated by transient intramolecular contacts established between the basic patch and N-terminal amino acids. Beyond acetylation, we identify that the protonation state of H18, which is affected by the acetylation state, is a critical regulator of ensemble characteristics, highlighting the potential for interplay between the sequence context and post-translational modifications to define the ensemble features of intrinsically disordered regions. This study elucidates molecular details that could link H4Kac with the regulation of chromatin architecture, illuminating a small piece of the complex network of molecular mechanisms underlying the histone code hypothesis.

Biomolecular condensates in plant cells: Mediating and integrating environmental signals and development

In response to the spatiotemporal coordination of various biochemical reactions and membrane-encapsulated organelles, plants appear to provide another effective mechanism for cellular organization by phase separation that allows the internal compartmentalization of cells to form a variety of membrane-less organelles. Most of the research on phase separation has centralized in various non-plant systems, such as yeast and animal systems. Recent studies have shown a remarkable correlation between the formation of condensates in plant systems and the formation of condensates in these systems. Moreover, the last decade has made new advances in phase separation research in the context of plant biology. Here, we provide an overview of the physicochemical forces and molecular factors that drive liquid-liquid phase separation in plant cells and the biochemical characterization of condensates. We then explore new developments in phase separation research specific to plants, discussing examples of condensates found in green plants and detailing their role in plant growth and development. We propose that phase separation may be a conserved organizational mechanism in plant evolution to help plants respond rapidly and effectively to various environmental stresses as sessile organisms.

Unravelling the involvement of protein disorder in cyanobacterial stress responses

This study has explored the involvement of Intrinsically Disordered Proteins (IDPs) in cyanobacterial stress response. IDPs possess distinct physicochemical properties, which allow them to execute diverse functions. Anabaena PCC 7120, the model photosynthetic, nitrogen-fixing cyanobacterium encodes 688 proteins (11 % of the total proteome) with at least one intrinsically disordered region (IDR). Of these, 130 proteins that showed >30 % overall disorder were designated as IDPs. Physico-chemical analysis, showed these IDPs to adopt shapes ranging from 'globular' to 'tadpole-like'. Upon exposure to NaCl, 41 IDP-encoding genes were found to be differentially expressed. Surprisingly, most of these were induced, indicating the importance of IDP-accumulation in overcoming salt stress. Subsequently, six IDPs were identified to be induced by multiple stresses (salt, ammonium and selenite). Interestingly, the presence of these 6-multiple stress-induced IDPs was conserved in filamentous cyanobacteria. Utilizing the experimental proteomic data of Anabaena, these 6 IDPs were found to interact with many proteins involved in diverse pathways, underscoring their physiological importance as protein hubs. This study lays the framework for IDP-related research in Anabaena by (a) identifying, as well as physiochemically characterizing, all the disordered proteins and (b) uncovering a subset of IDPs that are likely to be critical in adaptation to environmental stresses.

Intrinsic disorder and salt-dependent conformational changes of the N-terminal region of TFIP11 splicing factor

Tuftelin Interacting Protein 11 (TFIP11) was identified as a critical human spliceosome assembly regulator, interacting with multiple proteins and localising in membrane-less organelles. However, a lack of structural information on TFIP11 limits the rationalisation of its biological role. TFIP11 is predicted as an intrinsically disordered protein (IDP), and more specifically concerning its N-terminal (N-TER) region. IDPs lack a defined tertiary structure, existing as a dynamic conformational ensemble, favouring protein-protein and protein-RNA interactions. IDPs are involved in liquid-liquid phase separation (LLPS), driving the formation of subnuclear compartments. Combining disorder prediction, molecular dynamics, and spectroscopy methods, this contribution shows the first evidence TFIP11 N-TER is a polyampholytic IDP, exhibiting a structural duality with the coexistence of ordered and disordered assemblies, depending on the ionic strength. Increasing the salt concentration enhances the protein conformational flexibility, presenting a more globule-like shape, and a fuzzier unstructured arrangement that could favour LLPS and protein-RNA interaction. The most charged and hydrophilic regions are the most impacted, including the G-Patch domain essential to TFIP11 function. This study gives a better understanding of the salt-dependent conformational behaviour of the N-TER TFIP11, supporting the hypothesis of the formation of different types of protein assembly, in line with its multiple biological roles.

Disorder-mediated interactions target proteins to specific condensates

Selective compartmentalization of cellular contents is fundamental to the regulation of biochemistry. Although membrane-bound organelles control composition by using a semi-permeable barrier, biomolecular condensates rely on interactions among constituents to determine composition. Condensates are formed by dynamic multivalent interactions, often involving intrinsically disordered regions (IDRs) of proteins, yet whether distinct compositions can arise from these dynamic interactions is not known. Here, by comparative analysis of proteins differentially partitioned by two different condensates, we find that distinct compositions arise through specific IDR-mediated interactions. The IDRs of differentially partitioned proteins are necessary and sufficient for selective partitioning. Distinct sequence features are required for IDRs to partition, and swapping these sequence features changes the specificity of partitioning. Swapping whole IDRs retargets proteins and their biochemical activity to different condensates. Our results demonstrate that IDR-mediated interactions can target proteins to specific condensates, enabling the spatial regulation of biochemistry within the cell.

Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins

Conformations and dynamics of an intrinsically disordered protein (IDP) depend on its composition of charged and uncharged amino acids, and their specific placement in the protein sequence. In general, the charge (positive or negative) on an amino acid residue in the protein is not a fixed quantity. Each of the ionizable groups can exist in an equilibrated distribution of fully ionized state (monopole) and an ion-pair (dipole) state formed between the ionizing group and its counterion from the background electrolyte solution. The dipole formation (counterion condensation) depends on the protein conformation, which in turn depends on the distribution of charges and dipoles on the molecule. Consequently, effective charges of ionizable groups in the IDP backbone may differ from their chemical charges in isolation-a phenomenon termed charge-regulation. Accounting for the inevitable dipolar interactions, that have so far been ignored, and using a self-consistent procedure, we present a theory of charge-regulation as a function of sequence, temperature, and ionic strength. The theory quantitatively agrees with both charge reduction and salt-dependent conformation data of Prothymosin-alpha and makes several testable predictions. We predict charged groups are less ionized in sequences where opposite charges are well mixed compared to sequences where they are strongly segregated. Emergence of dipolar interactions from charge-regulation allows spontaneous coexistence of two phases having different conformations and charge states, sensitively depending on the charge patterning. These findings highlight sequence dependent charge-regulation and its potential exploitation by biological regulators such as phosphorylation and mutations in controlling protein conformation and function.

Design of intrinsically disordered protein variants with diverse structural properties

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

Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes

Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through -1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the -1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.

Disordered proteins interact with the chemical environment to tune their protective function during drying

The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results suggest that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.

Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation

Intrinsically disordered regions (IDRs) are critical for cellular function yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. Here, we focus on the first two domains of coronavirus nucleocapsid proteins: the disordered N-terminal domain (NTD) and the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system for exploring the interplay between an IDR adjacent to a folded domain and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved dynamic and disordered RNA:protein complex is found across nucleocapsid protein orthologs despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.

The Streptococcus phage protein paratox is an intrinsically disordered protein

The bacteriophage protein paratox (Prx) blocks quorum sensing in its streptococcal host by directly binding the signal receptor and transcription factor ComR. This reduces the ability of Streptococcus to uptake environmental DNA and protects phage DNA from damage by recombination. Past work characterizing the Prx:ComR molecular interaction revealed that paratox adopts a well-ordered globular fold when bound to ComR. However, solution-state biophysical measurements suggested that Prx may be conformationally dynamic. To address this discrepancy, we investigated the stability and dynamic properties of Prx in solution using circular dichroism, nuclear magnetic resonance, and several fluorescence-based protein folding assays. Our work shows that under dilute buffer conditions Prx is intrinsically disordered. We also show that the addition of kosmotropic salts or protein stabilizing osmolytes induces Prx folding. However, the solute stabilized fold is different from the conformation Prx adopts when it is bound to ComR. Furthermore, we have characterized Prx folding thermodynamics and folding kinetics through steady-state fluorescence and stopped flow kinetic measurements. Our results show that Prx is a highly dynamic protein in dilute solution, folding and refolding within the 10 ms timescale. Overall, our results demonstrate that the streptococcal phage protein Prx is an intrinsically disordered protein in a two-state equilibrium with a solute-stabilized folded form. Furthermore, the solute-stabilized fold is likely the predominant form of Prx in a solute-crowded bacterial cell. Finally, our work suggests that Prx binds and inhibits ComR, and thus quorum sensing in Streptococcus, by a combination of conformational selection and induced-fit binding mechanisms.

Solutes unmask differences in clustering versus phase separation of FET proteins

Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.

Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates

Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.

Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.

Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life

Low-complexity domains (LCDs) in proteins are typically enriched in one or two predominant amino acids. As a result, LCDs often exhibit unusual structural/biophysical tendencies and can occupy functional niches. However, for each organism, protein sequences must be compatible with intracellular biomolecules and physicochemical environment, both of which vary from organism to organism. This raises the possibility that LCDs may occupy sequence spaces in select organisms that are otherwise prohibited in most organisms. Here, we report a comprehensive survey and functional analysis of LCDs in all known reference proteomes (>21k organisms), with added focus on rare and unusual types of LCDs. LCDs were classified according to both the primary amino acid and secondary amino acid in each LCD sequence, facilitating detailed comparisons of LCD class frequencies across organisms. Examination of LCD classes at different depths (i.e., domain of life, organism, protein, and per-residue levels) reveals unique facets of LCD frequencies and functions. To our surprise, all 400 LCD classes occur in nature, although some are exceptionally rare. A number of rare classes can be defined for each domain of life, with many LCD classes appearing to be eukaryote-specific. Certain LCD classes were consistently associated with identical functions across many organisms, particularly in eukaryotes. Our analysis methods enable simultaneous, direct comparison of all LCD classes between individual organisms, resulting in a proteome-scale view of differences in LCD frequencies and functions. Together, these results highlight the remarkable diversity and functional specificity of LCDs across all known life forms.

How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.

HYPK: A marginally disordered protein sensitive to charge decoration

Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky's charge-hydropathy plot may behave as "marginal IDPs" and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK's sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning.

Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A

The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations.

Intrinsic disorder: A term to define the specific physicochemical characteristic of protein conformational heterogeneity

In his commentary in this issue of Molecular Cell,1 Struhl reasons that the term "intrinsically disordered regions" represents a vague and confusing concept for protein function. However, the term "intrinsically disordered" highlights the important physicochemical characteristic of conformational heterogeneity. Thus, "intrinsically disordered" is the counterpart to the term "folded, " with neither term having specific functional implications.

Cell-specific polymerization-driven biomolecular condensate formation fine-tunes root tissue morphogenesis

Formation of biomolecular condensates can be driven by weak multivalent interactions and emergent polymerization. However, the mechanism of polymerization-mediated condensate formation is less studied. We found lateral root cap cell (LRC)-specific SUPPRESSOR OF RPS4-RLD1 (SRFR1) condensates fine-tune primary root development. Polymerization of the SRFR1 N-terminal domain is required for both LRC condensate formation and optimal root growth. Surprisingly, the first intrinsically disordered region (IDR1) of SRFR1 can be functionally substituted by a specific group of intrinsically disordered proteins known as dehydrins. This finding facilitated the identification of functional segments in the IDR1 of SRFR1, a generalizable strategy to decode unknown IDRs. With this functional information we further improved root growth by modifying the SRFR1 condensation module, providing a strategy to improve plant growth and resilience.

Direct prediction of intrinsically disordered protein conformational properties from sequence

Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence-ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.

The molecular basis for cellular function of intrinsically disordered protein regions

Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.