Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates

Condensation and aggregation of disordered proteins in cellular non-equilibrium environments are shaped decisively by enzymes. Enzymes called kinases phosphorylate proteins, consuming the chemical fuel ATP. Protein phosphorylation by kinases such as Casein kinase 1 delta (CK1δ) determines the interactions of neurodegeneration-linked proteins such as TDP-43. Hyperphosphorylation of TDP-43 by CK1δ may be a cytoprotective mechanism for neurons, but how CK1δ interacts with protein condensates is not known. Molecular dynamics simulations hold the promise to resolve how kinases interact with disordered proteins and their condensates, and how this shapes the phosphorylation dynamics. In practice, it is difficult to verify whether implementations of chemical-fuel driven coarse-grained simulations are thermodynamically consistent, which we address by a generally applicable and automatic Markov state modeling approach. In this work, we thus elucidate with coarse-grained simulations, drivers of how TDP-43 is phosphorylated by CK1δ and how this leads to the dissolution of TDP-43 condensates upon hyperphosphorylation.

Nanopores with an Engineered Selective Entropic Gate Detect Proteins at Nanomolar Concentration in Complex Biological Sample

Biological nanopores enable the electrical detection of biomolecules, making them ideal sensors for use in health-monitoring devices. Proteins are widely recognized as biomarkers for various diseases, but they present a unique challenge due to their vast diversity and concentration range in biological samples. Here, inspired by the nuclear pore complex, we incorporated a layer of disordered polypeptides into the biological nanopore YaxAB. This polypeptide mesh formed an entropic gate, significantly reducing the entry of proteins from a highly concentrated mixture, including blood. The introduction of a specific recognition element within the disordered polypeptides allowed targeted proteins to penetrate through the nanopores, where they were recognized by specific current signatures. This biosensing approach allowed for the recognition of nanomolar proteins directly from blood samples without prior sample preparation. This work paves the way for the next generation of nanopore sensors for the real-time detection of proteins in blood.

Transient Interdomain Interactions Modulate the Monomeric Structural Ensemble and Self-Assembly of Huntingtin Exon 1

Polyglutamine (polyQ) tract length expansion (≥ 36 residues) within the N-terminal exon-1 of Huntingtin (Httex1) leads to Huntington's disease, a neurodegenerative condition marked by the presence of intranuclear Htt inclusions. Notably, the polyQ tract in Httex1 is flanked by an N-terminal coiled-coil domain -N17 (17 amino acids), which promotes the formation of soluble oligomers and brings the aggregation-prone polyQ tracts in close proximity. However, the molecular mechanisms underlying the conversion of soluble oligomers into insoluble β-rich aggregates with increasing polyQ length, remain unclear. In this study, extensive atomistic molecular dynamics (MD) simulations (aggregate time ≈0.7 milliseconds) are performed to uncover the interplay between structural transformation and domain "cross-talk" on the conformational ensemble and oligomerization of Httex1 due to polyQ expansion. Notably, MD-derived ensembles of N17-Qn-P5 monomers validated against NMR indicated that in addition to elevated α-helicity, polyQ expansion also favored transient, interdomain (N17/polyQ) interactions which resulted in the emergence of β-sheet conformations. Further, interdomain interactions modulated the stability of N17-mediated polyQ dimers and promoted a heterogeneous dimerization landscape. Finally, it is observed that the intact C-terminal proline-rich domain (PRD) promoted condensation of Httex1 through self-interactions involving its P10/P11 tracts while also interacting with N17 to suppress its α-helicity.

Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates

Protein-RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models of intrinsically disordered proteins have been developed to shed light on and predict single-chain properties and phase separation. An RNA model compatible with such models for disordered proteins would enable the study of complex biomolecular mixtures involving RNA. Here, we present a sequence-independent coarse-grained, two-beads-per-nucleotide model of disordered, flexible RNA based on a hydropathy scale. We parametrize the model, which we term CALVADOS-RNA, using a combination of bottom-up and top-down approaches to reproduce local RNA geometry and intramolecular interactions based on atomistic simulations and in vitro experiments. The model semiquantitatively captures several aspects of RNA-RNA and RNA-protein interactions. We examined RNA-RNA interactions by comparing calculated and experimental virial coefficients and nonspecific RNA-protein interaction by studying the reentrant phase behavior of protein-RNA mixtures. We demonstrate the utility of the model by simulating the formation of mixed condensates consisting of the disordered region of MED1 and RNA chains and the selective partitioning of disordered regions from transcription factors into these and compare the results to experiments. Despite the simplicity of our model, we show that it captures several key aspects of protein-RNA interactions and may therefore be used as a baseline model to study several aspects of the biophysics and biology of protein-RNA condensates.

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

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.

Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins

MOTIVATION

Characterizing the structure of flexible proteins, particularly within the realm of intrinsic disorder, presents a formidable challenge due to their high conformational variability. Currently, their structural representation relies on (possibly large) conformational ensembles derived from a combination of experimental and computational methods. The detailed structural analysis of these ensembles is a difficult task, for which existing tools have limited effectiveness.

RESULTS

This study proposes an innovative extension of the concept of contact maps to the ensemble framework, incorporating the intrinsic probabilistic nature of disordered proteins. Within this framework, a conformational ensemble is characterized through a weighted family of contact maps. To achieve this, conformations are first described using a refined definition of contact that appropriately accounts for the geometry of the inter-residue interactions and the sequence context. Representative structural features of the ensemble naturally emerge from the subsequent clustering of the resulting contact-based descriptors. Importantly, transiently populated structural features are readily identified within large ensembles. The performance of the method is illustrated by several use cases and compared with other existing approaches, highlighting its superiority in capturing relevant structural features of highly flexible proteins.

AVAILABILITY AND IMPLEMENTATION

An open-source implementation of the method is provided together with an easy-to-use Jupyter notebook, available at https://gitlab.laas.fr/moma/WARIO.

Inhibition of Aβ16-22 Aggregation by [TEA]+[Ms]- Follows Weakening of the Hydrophobic Core and Sequestration of Peptides in Ionic Liquid Nanodomains

We developed a coarse-grained model for the protic ionic liquid, triethylammonium mesylate ([TEA]+[Ms]-), to characterize its inhibitory effects on amyloid aggregation using the K16LVFFAE22 fragment of the amyloid-β (Aβ16-22) as a model amyloidogenic peptide. In agreement with previous experiments, coarse-grained molecular dynamics simulations showed that increasing concentrations of [TEA]+[Ms]- in aqueous media led to increasingly small Aβ16-22 aggregates with low beta-sheet contents. The cause of [TEA]+[Ms]-'s inhibition of peptide aggregation was found to be a result of two interrelated effects. At a local scale, the enrichment of interactions between [TEA]+ cations and hydrophobic phenylalanine side chains weakened the hydrophobic cores of amyloid aggregates, resulting in poorly ordered structures. At a global level, peptides tended to localize at the interfaces of IL-rich nanostructures with water. At high IL concentrations, when the IL-water interface was large or fragmented, Aβ16-22 peptides were dispersed in the simulation cell, sometimes sequestered at unaggregated monomeric states. Together, these phenomena underlie [TEA]+[Ms]-'s inhibition of amyloid aggregation. This work addresses the critical lack of knowledge on the mechanisms of protein-ionic liquid interactions and may have broader implications for industrial applications.

Backbone interactions and secondary structures in phase separation of disordered proteins

Intrinsically disordered proteins (IDPs) are one of the major drivers behind the formation and characteristics of biomolecular condensates. Due to their inherent flexibility, the backbones of IDPs are significantly exposed, rendering them highly influential and susceptible to biomolecular phase separation. In densely packed condensates, exposed backbones have a heightened capacity to interact with neighboring protein chains, which might lead to strong coupling between the secondary structures and phase separation and further modulate the subsequent transitions of the condensates, such as aging and fibrillization. In this mini-review, we provide an overview of backbone-mediated interactions and secondary structures within biomolecular condensates to underscore the importance of protein backbones in phase separation. We further focus on recent advances in experimental techniques and molecular dynamics simulation methods for probing and exploring the roles of backbone interactions and secondary structures in biomolecular phase separation involving IDPs.

Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation

Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.

Structure-function relationships in protein homorepeats

Homorepeats (or polyX), protein segments containing repetitions of the same amino acid, are abundant in proteomes from all kingdoms of life and are involved in crucial biological functions as well as several neurodegenerative and developmental diseases. Mainly inserted in disordered segments of proteins, the structure/function relationships of homorepeats remain largely unexplored. In this review, we summarize present knowledge for the most abundant homorepeats, highlighting the role of the inherent structure and the conformational influence exerted by their flanking regions. Recent experimental and computational methods enable residue-specific investigations of these regions and promise novel structural and dynamic information for this elusive group of proteins. This information should increase our knowledge about the structural bases of phenomena such as liquid-liquid phase separation and trinucleotide repeat disorders.

Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation

Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space using either experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with 2-heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in nonphosphorylated CTD models, and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination, and interactions with the nearby residues.

Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation

Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.

Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations

"Membraneless organelles," also referred to as biomolecular condensates, perform a variety of cellular functions and their dysregulation is implicated in cancer and neurodegeneration. In the last two decades, liquid-liquid phase separation (LLPS) of intrinsically disordered and multidomain proteins has emerged as a plausible mechanism underlying the formation of various biomolecular condensates. Further, the occurrence of liquid-to-solid transitions within liquid-like condensates may give rise to amyloid structures, implying a biophysical link between phase separation and protein aggregation. Despite significant advances, uncovering the microscopic details of liquid-to-solid phase transitions using experiments remains a considerable challenge and presents an exciting opportunity for the development of computational models which provide valuable, complementary insights into the underlying phenomenon. In this review, we first highlight recent biophysical studies which provide new insights into the molecular mechanisms underlying liquid-to-solid (fibril) phase transitions of folded, disordered and multi-domain proteins. Next, we summarize the range of computational models used to study protein aggregation and phase separation. Finally, we discuss recent computational approaches which attempt to capture the underlying physics of liquid-to-solid transitions along with their merits and shortcomings.

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery

Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.

Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining

Biomolecular condensation, especially liquid-liquid phase separation, is an important physical process with relevance for a number of different aspects of biological functions. Key questions of what drives such condensation, especially in terms of molecular composition, can be addressed via computer simulations, but the development of computationally efficient yet physically realistic models has been challenging. Here, the coarse-grained model COCOMO is introduced that balances the polymer behavior of peptides and RNA chains with their propensity to phase separate as a function of composition and concentration. COCOMO is a residue-based model that combines bonded terms with short- and long-range terms, including a Debye-Hückel solvation term. The model is highly predictive of experimental data on phase-separating model systems. It is also computationally efficient and can reach the spatial and temporal scales on which biomolecular condensation is observed with moderate computational resources.