Computational Studies of Intrinsically Disordered Proteins

Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences

We apply methods of Artificial Intelligence and Machine Learning to protein dynamic bioinformatics. We rewrite the sequences of a large protein data set, containing both folded and intrinsically disordered molecules, using a representation developed previously, which encodes the intrinsic dynamic properties of the naturally occurring amino acids. We Fourier analyze the resulting sequences. It is demonstrated that classification models built using several different supervised learning methods are able to successfully distinguish folded from intrinsically disordered proteins from sequence alone. It is further shown that the most important sequence property for this discrimination is the sequence mobility, which is the sequence averaged value of the residue-specific average alpha carbon B factor. This is in agreement with previous work, in which we have demonstrated the central role played by the sequence mobility in protein dynamic bioinformatics and biophysics. This finding opens a path to the application of dynamic bioinformatics, in combination with machine learning algorithms, to a range of significant biomedical problems.

Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox

Pioneer transcription factors (PTFs) have the remarkable ability to directly bind to chromatin to stimulate vital cellular processes. In this work, we dissect the universal binding mode of Sox PTF by combining extensive molecular simulations and physiochemistry approaches, along with DNA footprinting techniques. As a result, we show that when Sox consensus DNA is located at the solvent-facing DNA strand, Sox binds to the compact nucleosome without imposing any significant conformational changes. We also reveal that the base-specific Sox:DNA interactions (base reading) and Sox-induced DNA changes (shape reading) are concurrently required for sequence-specific nucleosomal DNA recognition. Among three different nucleosome positions located on the positive DNA arm, a sequence-specific reading mechanism is solely satisfied at the superhelical location 2 (SHL2). While SHL2 acts transparently for solvent-facing Sox binding, among the other two positions, SHL4 permits only shape reading. The final position, SHL0 (dyad), on the other hand, allows no reading mechanism. These findings demonstrate that Sox-based nucleosome recognition is essentially guided by intrinsic nucleosome properties, permitting varying degrees of DNA recognition.

Modeling structural interconversion in Alzheimers' amyloid beta peptide with classical and intrinsically disordered protein force fields

A comprehensive understanding of the aggregation mechanism in amyloid beta 42 (Aβ42) peptide is imperative for developing therapeutic drugs to prevent or treat Alzheimer's disease. Because of the high flexibility and lack of native tertiary structures of Aβ42, molecular dynamics (MD) simulations may help elucidate the peptide's dynamics with atomic details and collectively improve ensembles not seen in experiments. We applied microsecond-timescale MD simulations to investigate the dynamics and conformational changes of Aβ42 by using a newly developed Amber force field (ff14IDPSFF). We compared the ff14IDPSFF and the regular ff14SB force field by examining the conformational changes of two distinct Aβ42 monomers in explicit solvent. Conformational ensembles obtained by simulations depend on the force field and initial structure, Aβ42^α-helix or Aβ42^β-strand. The ff14IDPSFF sampled a high ratio of disordered structures and diverse β-strand secondary structures; in contrast, ff14SB favored helicity during the Aβ42^α-helix simulations. The conformations obtained from Aβ42^β-strand simulations maintained a balanced content in the disordered and helical structures when simulated by ff14SB, but the conformers clearly favored disordered and β-sheet structures simulated by ff14IDPSFF. The results obtained with ff14IDPSFF qualitatively reproduced the NMR chemical shifts well. In-depth peptide and cluster analysis revealed some characteristic features that may be linked to early onset of the fibril-like structure. The C-terminal region (mainly M35-V40) featured in-registered anti-parallel β-strand (β-hairpin) conformations with tested systems. Our work should expand the knowledge of force field and structure dependency in MD simulations and reveals the underlying structural mechanism-function relationship in Aβ42 peptides. Communicated by Ramaswamy H. Sarma.

Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations

Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We, therefore, used molecular dynamics to examine the structures of salmon, bull P1, and human P1 protamines. The sizes and shapes of each protamine varied widely, indicating that they were disordered with structures covering a broad conformational landscape, from hairpin loop structures to extended coils. Despite their general disorder, the protamines did form secondary structures, including helices and hairpin loops. In eutherians, hairpins may promote disulfide bonding that facilitates protamine-DNA condensation, but the specifics of this bonding is not well established. We examined inter-residue distances in the simulations to predict residue pairs likely to form intramolecular bonds, leading to the identification of bonding pairs consistent with previous results in bull and human. These results support a model for eutherian protamine structures where a highly charged center is surrounded by disulfide-bond-stabilized loops.

OCT4 interprets and enhances nucleosome flexibility

Pioneer transcription factors are proteins that induce cellular identity transitions by binding to inaccessible regions of DNA in nuclear chromatin. They contribute to chromatin opening and recruit other factors to regulatory DNA elements. The structural features and dynamics modulating their interaction with nucleosomes are still unresolved. From a combination of experiments and molecular simulations, we reveal here how the pioneer factor and master regulator of pluripotency, Oct4, interprets and enhances nucleosome structural flexibility. The magnitude of Oct4’s impact on nucleosome dynamics depends on the binding site position and the mobility of the unstructured tails of nucleosomal histone proteins. Oct4 uses both its DNA binding domains to propagate and stabilize open nucleosome conformations, one for specific sequence recognition and the other for nonspecific interactions with nearby regions of DNA. Our findings provide a structural basis for the versatility of transcription factors in engaging with nucleosomes and have implications for understanding how pioneer factors induce chromatin dynamics.

Molecular dynamics simulations of an α-synuclein NAC domain fragment with a ff14IDPSFF IDP-specific force field suggest β-sheet intermediate states of fibrillation

For the discovery of treatments against synucleinopathies, it is necessary to unravel and fully understand the mechanism of fibrillation of proteins involved. Among them, α-synuclein (αS) plays a key role in the development of these diseases through its aggregation into oligomers found in Lewy bodies. However, its structural disorder as an intrinsically disordered protein (IDP) makes its characterization by experimental techniques arduously difficult. Atomistic simulations aim to provide insights into this blank canvas and, fortunately, some studies have already suggested promising mechanisms. Still, it is urgent to consider the IDP features in simulations, so recently a lot of force fields designed to deal with IDPs have been developed. In this study, we have carried out a total of 12 μs simulations of an αS core fragment using a popular ff14SB AMBER force field and the ff14IDPSFF variation that includes a grid-based energy correction map (CMAP) method. The predicted chemical shifts from the simulations and those measured from the αS protein in the NMR solution indicate that ff14IDPSFF reproduces the experimental data more accurately. Moreover, structural analysis exhibits opposite trends between secondary structure propensities. The ff14SB force field preserves the α-helices found in the micelle-bound αS structure, which is used as an initial conformation, while ff14IDPSFF stands out with increased structural disorder and the formation of β-sheets, which suggests that the IDP-specific force field can capture more suitable conformations representing the possible intermediate states of the fibrillation process.

Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein

We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.Communicated by Ramaswamy H. Sarma.

Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method

The amyloid-β (Aβ) monomer, an intrinsically disordered peptide, is produced by the cleavage of the amyloid precursor protein, leading to Aβ-40 and Aβ-42 as major products. These two isoforms generate pathological aggregates, whose accumulation correlates with Alzheimer's disease (AD). Experiments have shown that even though the natural abundance of Aβ-42 is smaller than that for Aβ-40, the Aβ-42 is more aggregation-prone compared to Aβ-40. Moreover, several single-point mutations are associated with early onset forms of AD. This work analyzes coarse-grained associative-memory, water-mediated, structure and energy model (AWSEM) simulations of normal Aβ-40 and Aβ-42 monomers, along with six single-point mutations associated with early onset disease. We analyzed the simulations using the energy landscape visualization method (ELViM), a reaction-coordinate-free approach suited to explore the frustrated energy landscapes of intrinsically disordered proteins. ELViM is shown to distinguish the monomer ensembles of variants that rapidly form fibers from those that do not form fibers as readily. It also delineates the amino acid contacts characterizing each ensemble. The results shed light on the potential of ELViM to probe intrinsically disordered proteins.

Histone tails cooperate to control the breathing of genomic nucleosomes

Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 145–147 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and inter-nucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 24 μs. Transitions between open and closed nucleosome conformations were mediated by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Removing the histone tails resulted in a large increase of the amplitude of nucleosome breathing but did not change the sequence dependent pattern of the motions. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics with important implications for epigenetic regulation.

In the cell, the DNA is packed in chromatin. Chromatin is a highly dynamic fiber structure made of arrays of nucleosomes with different degrees of compaction. Each nucleosome has 145–147 basepairs of DNA wrapped around a protein octamer made of four unique histone proteins. Each histone is present twice and has a structured part and one or two disordered terminal tails. The regulation of gene expression in the cell and during cellular transitions depends on dynamic changes in chromatin structure. Chromatin dynamics are modulated by intra and inter nucleosome motions and by posttranslational chemical modifications of the histone tails. Here we reveal how histone tails control the intra nucleosome dynamics at atomic resolution. From extensive sampling of nucleosome dynamics in atomistic molecular simulations, we show that genomic nucleosomes breath more extensively than engineered ones and we describe how two histone tails cooperate to control nucleosome breathing through interactions between clusters of positively charged residues and the DNA. Nucleosome conformations with different degrees of opening are associated with different conformations, positions, and DNA interaction patterns of the tails. With this mechanism, we contribute to the understanding of chromatin dynamics at atomic resolution.

Quality of force fields and sampling methods in simulating pepX peptides: a case study for intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are a group of proteins that lack well-defined structures under native conditions and carry out crucial physiological functions in various biochemical pathways. Due to the heterogeneous nature of IDPs, molecular dynamics simulations have been extensively adopted to investigate the conformational ensembles and dynamic properties of these proteins. However, their accuracy remains limited by the development of force fields and sampling algorithms. Here, we evaluated the quality of both force fields and enhanced sampling algorithms based on five short pepX peptides. Our results show that the more extended conformational ensembles sampled by the AMOEBA polarizable force field present a higher ability to reproduce experimental NMR observables than AMBER and CHARMM classical force fields. Moreover, a better agreement with experiments is achieved in the simulation of IaMD (integrated accelerated molecular dynamics) than in aMD (accelerated molecular dynamics). The results together indicate that the combination of AMOEBA force field and IaMD enhanced sampling might be a better choice for simulating IDPs. This work may provide important clues for developments and applications of force fields and enhanced sampling methods in future simulations of IDPs.

Folding and self-assembly of short intrinsically disordered peptides and protein regions

Proteins and peptide fragments are highly relevant building blocks in self-assembly for nanostructures with plenty of applications. Intrinsically disordered proteins (IDPs) and protein regions (IDRs) are defined by the absence of a well-defined secondary structure, yet IDPs/IDRs show a significant biological activity. Experimental techniques and computational modelling procedures for the characterization of IDPs/IDRs are discussed. Directed self-assembly of IDPs/IDRs allows reaching a large variety of nanostructures. Hybrid materials based on the derivatives of IDPs/IDRs show a promising performance as alternative biocides and nanodrugs. Cell mimicking, in vivo compartmentalization, and bone regeneration are demonstrated for IDPs/IDRs in biotechnological applications. The exciting possibilities of IDPs/IDRs in nanotechnology with relevant biological applications are shown.

Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) play important roles in cellular functions. The inherent structural heterogeneity of IDPs makes the high-resolution experimental characterization of IDPs extremely difficult. Molecular dynamics (MD) simulation could provide the atomic-level description of the structural and dynamic properties of IDPs. This perspective reviews the recent progress in atomic MD simulation studies of IDPs, including the development of force fields and sampling methods, as well as applications in IDP-involved protein-protein interactions. The employment of large-scale simulations and advanced sampling techniques allows more accurate estimation of the thermodynamics and kinetics of IDP-mediated protein interactions, and the holistic landscape of the binding process of IDPs is emerging.

Breaths, Twists, and Turns of Atomistic Nucleosomes

Gene regulation programs establish cellular identity and rely on dynamic changes in the structural packaging of genomic DNA. The DNA is packaged in chromatin, which is formed from arrays of nucleosomes displaying different degree of compaction and different lengths of inter-nucleosomal linker DNA. The nucleosome represents the repetitive unit of chromatin and is formed by wrapping 145-147 basepairs of DNA around an octamer of histone proteins. Each of the four histones is present twice and has a structured core and intrinsically disordered terminal tails. Chromatin dynamics are triggered by inter- and intra-nucleosome motions that are controlled by the DNA sequence, the interactions between the histone core and the DNA, and the conformations, positions, and DNA interactions of the histone tails. Understanding chromatin dynamics requires studying all these features at the highest possible resolution. For this, molecular dynamics simulations can be used as a powerful complement or alternative to experimental approaches, from which it is often very challenging to characterize the structural features and atomic interactions controlling nucleosome motions. Molecular dynamics simulations can be performed at different resolutions, by coarse graining the molecular system with varying levels of details. Here we review the successes and the remaining challenges of the application of atomic resolution simulations to study the structure and dynamics of nucleosomes and their complexes with interacting partners.

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as K→Q. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins. Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state (q=+8) is essentially a random coil, hyper-acetylated H4 (q=+3) is virtually as compact and stable as a globular protein of the same number of amino-acids. Conformational ensembles of acetylated H4 match the corresponding K→X substitutions only approximately: based on the ensemble similarity, we propose K→M as a possible alternative to the commonly used K→Q. Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.

Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are molecules without a fixed tertiary structure, exerting crucial roles in cellular signalling, growth and molecular recognition events. Due to their high plasticity, IDPs are very challenging in experimental and computational structural studies. To provide detailed atomic insight in IDPs' dynamics governing their functional mechanisms, all-atom molecular dynamics (MD) simulations are widely employed. However, the current generalist force fields and solvent models are unable to generate satisfactory ensembles for IDPs when compared to existing experimental data. In this work, we present a new solvation model, denoted as the Charge-Augmented Three-Point Water Model for Intrinsically Disordered Proteins (CAIPi3P). CAIPi3P has been generated by performing a systematic scan of atomic partial charges assigned to the widely popular molecular scaffold of the three-point TIP3P water model. We found that explicit solvent MD simulations employing CAIPi3P solvation considerably improved the small-angle X-ray scattering (SAXS) scattering profiles for three different IDPs. Not surprisingly, this improvement was further enhanced by using CAIPi3P water in combination with the protein force field parametrized for IDPs. We also demonstrated the applicability of CAIPi3P to molecular systems containing structured as well as intrinsically disordered regions/domains. Our results highlight the crucial importance of solvent effects for generating molecular ensembles of IDPs which reproduce the experimental data available. Hence, we conclude that our newly developed CAIPi3P solvation model is a valuable tool for molecular simulations of intrinsically disordered proteins and assessing their molecular dynamics.

Structural ensemble and biological activity of DciA intrinsically disordered region

DciA is a newly discovered bacterial protein involved in loading the replicative helicase DnaB onto DNA at the initiation step of chromosome replication. Its three-dimensional structure is composed of a folded N-terminal domain (residues 1-111) resembling K Homology domains and a long disordered C-terminal tail (residues 112-157) which structure-activity relationship remains to be elucidated. In the present study on Vibrio cholerae DciA, we emphasize the importance of its disordered region to load DnaB onto DNA using surface plasmon resonance (SPR) and isothermal titration microcalorimetry (ITC). Then we characterize the conformational ensemble of the full-length protein using a combination of circular dichroism (CD), small angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations. The atomic-level structural ensemble generated by MD simulations is in very good agreement with SAXS data. From initial conformations of the C-terminal tail without any secondary structure, our simulations bring to light several transient helical structures in this segment, which might be molecular recognition features (MoRFs) for the binding to DnaB and its recruitment and loading onto DNA.

Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins

The need for accurate and efficient force fields for modeling 3D structures of macrobiomolecules and in particular intrinsically disordered proteins (IDPs) has increased with recent findings to associate IDPs and human diseases. However, most conventional protein force fields and recent IDP-specific force fields are limited in reproducing accurate structural features of IDPs. Here, we present an environmental specific precise force field (ESFF1) based on CMAP corrections of 71 different sequence environments to improve the accuracy and efficiency of MD simulation for both IDPs and folded proteins. MD simulations of 84 different short peptides, IDPs, and structured proteins show that ESFF1 can accurately reproduce spectroscopic properties for different peptides and proteins whether they are disordered or ordered. The successful ab initio folding of five fast-folding proteins further supports the reliability of ESFF1. The extensive analysis documented here shows that ESFF1 is able to achieve a reasonable balance between ordered and disordered states in protein simulations.

Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding

Transcription factor (TF) proteins bind to DNA to regulate gene expression. Normally, accessibility to DNA is required for their function. However, in the nucleus, the DNA is often inaccessible, wrapped around histone proteins in nucleosomes forming the chromatin. Pioneer TFs are thought to induce chromatin opening by recognizing their DNA binding sites on nucleosomes. For example, Oct4, a master regulator and inducer of stem cell pluripotency, binds to DNA in nucleosomes in a sequence-specific manner. Here, we reveal the structural dynamics of nucleosomes that mediate Oct4 binding from molecular dynamics simulations. Nucleosome flexibility and the amplitude of nucleosome motions such as breathing and twisting are enhanced in nucleosomes with multiple TF binding sites. Moreover, the regions around the binding sites display higher local structural flexibility. Probing different structures of Oct4-nucleosome complexes, we show that alternative configurations in which Oct4 recognizes partial binding sites display stable TF-DNA interactions similar to those observed in complexes with free DNA and compatible with the DNA curvature and DNA-histone interactions. Therefore, we propose a structural basis for nucleosome recognition by a pioneer TF that is essential for understanding how chromatin is unraveled during cell fate conversions.

Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils - a comparative study using MD simulations of 17-42 residues

Extracellular plaques, the hallmark of Alzheimer's disease brains, consist of insoluble amyloid fibrils that result from the aggregation of amyloid beta peptides. None of the few therapeutic options currently adopted, address the cause of the disease. Instead, they reduce symptom of the disease. Inhibition of aggregation or destabilization of aggregates therefore, emerges as a preferable therapeutic approach. Designing inhibitors or destabilizers demands comprehensive knowledge of the residues of amyloid beta responsible for the phenomenal structural stability of the aggregate. For the purpose, we have compared the effect on structural destabilization of 13 in silico mutations (single and double) with the wild type counterpart of beta-strand-turn-beta-strand motif of the amyloid beta protofibrils by molecular dynamics simulation. Besides the already known salt bridge interaction between K28 and D23, our analyses expose more significant role of K28 as the only positive charge present in the vicinity. Amongst the two consecutive aromatic residues, F19 is involved in stacking interaction; although effect of F20 mutation is more pronounced. Face to face arrangement of A21 and V36 acts as a pillar maintaining the necessary optimum distance between consecutive chains to promote stabilizing interactions. In addition to providing stability to the first beta-strand, large sized negatively charged E22 facilitates salt bridge formation by ensuring fixed relative position of D23 and in turn K28. Likewise, the hydrophobic residues I32 and L34 pack the protofibril core, once again fostering salt bridge interaction. Prospectively, these findings may be compiled for efficient identification or design of scaffolds accountable for protofibril destabilization.Communicated by Ramaswamy H. Sarma.

Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins

Molecular dynamics simulation as an important complement of experiment is widely used to study protein structures and functions. However, previous studies indicate that the current force fields cannot, simultaneously, provide accurate descriptions of folded proteins and intrinsically disordered proteins (IDPs). Therefore, a correction maps (CMAP)-optimized force field based on the Amber ff03 force field (termed ff03CMAP herein) was developed for a balanced sampling of folded proteins and IDPs. Extensive validations of short peptides, folded proteins, disordered proteins, and fast-folding proteins show that simulated chemical shifts, J-coupling constants, order parameters, and residual dipolar couplings (RDCs) with the ff03CMAP force field are in very good agreement with nuclear magnetic resonance measurements and are more accurate than other ff03-series force fields. The influence of solvent models was also investigated. It was found that the combination of ff03CMAP/TIP4P-Ew is suitable for folded proteins, and that of ff03CMAP/TIP4PD is better for disordered proteins. These findings confirm that the newly developed force field ff03CMAP can improve the balance of conformer sampling between folded proteins and IDPs.

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins

Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP) remain a challenge: widely used, "general purpose" water models tend to favor overly compact structures relative to experiment. Here we have performed a total of 93 μs of unrestrained MD simulations to explore, in the context of IDPs, a recently developed "general-purpose" 4-point rigid water model OPC, which describes liquid state of water close to experiment. We demonstrate that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks: 55-residue apo N-terminal zinc-binding domain of HIV-1 integrase ("protein IN"), amyloid β-peptide (Aβ₄₂) (residues 1-42), and 26-reside H4 histone tail. As a negative control, computed folding profile of a regular globular miniprotein (CLN025) in OPC water is in appreciably better agreement with experiment than that obtained in TIP3P, which tends to overstabilize the compact native state relative to the extended conformations. We employed Aβ₄₂ peptide to investigate the possible influence of the solvent box size on simulation outcomes. We advocate a cautious approach for simulations of IDPs: we suggest that the solvent box size should be at least four times the radius of gyration of the random coil corresponding to the IDP. The computed free energy landscape of protein IN in OPC resembles a shallow "tub" - conformations with substantially different degrees of compactness that are within 2 k_B T of each other. Conformations with very different secondary structure content coexist within 1 k_B T of the global free energy minimum. States with higher free energy tend to have less secondary structure. Computed low helical content of the protein has virtually no correlation with its degree of compactness, which calls into question the possibility of using the helicity as a metric for assessing performance of water models for IDPs, when the helicity is low. Predicted radius of gyration ( R _g) of H4 histone tail in OPC water falls in-between that of a typical globular protein and a fully denatured protein of the same size; the predicted R _g is consistent with two independent predictions. In contrast, H4 tail in TIP3P water is as compact as the corresponding globular protein. The computed free energy landscape of H4 tail in OPC is relatively flat over a significant range of compactness, which, we argue, is consistent with its biological function as facilitator of internucleosome interactions.

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

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