Molecular dynamics simulation of phosphorylated KID post-translational modification

Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ

The N-terminal transactivation domain (TAD) of p53 is a disordered region with multiple phosphorylation sites. Phosphorylation at Thr18 is crucial for the release of p53 from its negative regulator, MDM2. In stressed cells, CK1δ is responsible for phosphorylating Thr18, but requires Ser15 to be phosphorylated. To understand the mechanistic underpinnings of this sequential phosphorylation, molecular modeling and molecular dynamics simulation studies of these phosphorylation events were carried out. Our models suggest that a positively charged region on CK1δ near the adenosine triphosphate (ATP) binding pocket, which is conserved across species, sequesters the negatively charged pSer15, thereby constraining the positioning of the rest of the peptide, such that the side chain of Thr18 is positioned close to the γ-phosphate of ATP. Furthermore, our studies show that the phosphorylated p53 TAD1 (p53pSer15) peptide binds more strongly to CK1δ than does p53. p53 adopts a helical structure when bound to CK1δ, which is lost upon phosphorylation at Ser15, thus gaining higher flexibility and ability to morph into the binding site. We propose that upon phosphorylation at Ser15 the p53 TAD1 peptide binds to CK1δ through an electrostatically driven induced fit mechanism resulting in a flanking fuzzy complex.

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.

Proteins are a diverse set of biological molecules responsible for numerous functions within cells, such as obtaining energy from food or transport of small molecules, and many processes rely on interactions of specific proteins. Moreover, a single protein may acquire different roles depending on cellular requirements and as a response to changes in the environment. A commonly used way to quickly change protein’s function or activity is by introducing small chemical modifications on specific locations within the protein. These modifications can cause the protein to interact in a more or less stable way with other proteins. We have previously developed a computational pipeline for predicting the effect of modifications on interactions of proteins, and in this work we apply it to all yeast proteins with known structures. We find differences in effects on the binding for different types of modifications. Importantly, we demonstrate that the modifications far from the interaction interface also significantly contribute to binding due to their impact on protein’s shape, which is often neglected by other methods. This work contributes to our understanding of the modulation of protein interactions in yeast due to modifications, while our widely applicable method will allow similar investigations in other organisms.

Explicit Characterization of the Free Energy Landscape of pKID-KIX Coupled Folding and Binding

The most fundamental aspect of the free energy landscape of proteins is that it is globally funneled such that protein folding is energetically biased. Then, what are the distinctive characteristics of the landscape of intrinsically disordered proteins, apparently lacking such energetic bias, that nevertheless fold upon binding? Here, we address this fundamental issue through the explicit characterization of the free energy landscape of the paradigmatic pKID-KIX system (pKID, phosphorylated kinase-inducible domain; KIX, kinase interacting domain). This is done based on unguided, fully atomistic, explicit-water molecular dynamics simulations with an aggregated simulation time of >30 μs and on the computation of the free energy that defines the landscape. We find that, while the landscape of pKID before binding is considerably shallower than the one for a protein that autonomously folds, it becomes progressively more funneled as the binding of pKID with KIX proceeds. This explains why pKID is disordered in a free state, and the binding of pKID with KIX is a prerequisite for pKID's folding. In addition, we observe that the key event in completing the pKID-KIX coupled folding and binding is the directed self-assembly where pKID is docked upon the KIX surface to maximize the surface electrostatic complementarity, which, in turn, require pKID to adopt the correct folded structure. This key process shows up as the free energy barrier in the pKID landscape separating the intermediate nonspecific complex state and the specific complex state. The present work not only provides a detailed molecular picture of the coupled folding and binding of pKID but also expands the funneled landscape perspective to intrinsically disordered proteins.

Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB

Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.

pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions

Understanding the detailed mechanism of interaction of intrinsically disordered proteins with their partners is crucial to comprehend their functions in signaling and transcription. Through its interaction with KIX, the disordered pKID region of CREB protein is central in the transcription of cAMP responsive genes, including those involved in long-term memory. Numerous simulation studies have investigated these interactions. Combined with experimental results, these can provide valuable and comprehensive understanding of the mechanisms involved. Here, we probe the transition state of this interaction experimentally through analyzing the kinetic effect of mutating both interface and solvent exposed residues in pKID. We show that very few specific interactions between pKID and KIX are required in the initial binding process. Only a small number of weak interactions are formed at the transition state, including nonnative interactions, and most of the folding occurs after the initial binding event. These properties are consistent with computational results and also the majority of experimental studies of intrinsically disordered protein coupled folding and binding in other protein systems, suggesting that these may be common features.

Simulation of coupled folding and binding of an intrinsically disordered protein in explicit solvent with metadynamics

The C-terminal domain of measles virus nucleoprotein is an intrinsically disordered protein that could bind to the X domain (XD) of phosphoprotein P to exert its physiological function. Experiments reveal that the minimal binding unit is a 21-residue α-helical molecular recognition element (α-MoRE-MeV), which adopts a fully helical conformation upon binding to XD. Due to currently limited computing power, direct simulation of this coupled folding and binding process with atomic force field in explicit solvent cannot be achieved. In this work, two advanced sampling methods, metadynamics and parallel tempering, are combined to characterize the free energy surface of this process and investigate the underlying mechanism. Starting from an unbound and partially folded state of α-MoRE-MeV, multiple folding and binding events are observed during the simulation and the energy landscape was well estimated. The results demonstrate that the isolated α-MoRE-MeV resembles a molten globule and rapidly interconverts between random coil and multiple partially helical states in solution. The coupled folding and binding process occurs through the induced fit mechanism, with the residual helical conformations providing the initial binding sites. Upon binding, α-MoRE-MeV can easily fold into helical conformation without obvious energy barriers. Two mechanisms, namely, the system tending to adopt the structure in which the free energy of isolated α-MoRE-MeV is the minimum, and the binding energy of α-MoRE-MeV to its partner protein XD tending to the minimum, jointly dominate the coupled folding and binding process. With the advanced sampling approach, more IDP systems could be simulated and common mechanisms concerning the coupled folding and binding process could be investigated in the future.

Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis

Histone modification plays a key role in gene regulation and gene expression. TRIM24 as a histone reader can recognize histone modification. However the specific recognition mechanism between TRIM24 and histone modification is unsolved. Here, systems biology method of dynamics correlation network based on molecular dynamics simulation was used to answer the question. Our network analysis shows that the dynamics correlation network of H3K23ac is distinctly different from that of wild type and other modifications. A hypothesis of “synergistic modification induced recognition” is then proposed to link histone modification and TRIM24 binding. These observations were further confirmed from community analysis of networks with mutation and network perturbation. Finally, a possible recognition pathway is also identified based on the shortest path search for H3K23ac. Significant difference of recognition pathway was found among different systems due to methylation and acetylation modifications. The analysis presented here and other studies show that the dynamic network-based analysis might be a useful general strategy to study the biology of protein post-translational modification and associated recognition.

Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine

Each amino acid has its intrinsic propensity for certain local backbone conformations, which can be further modulated by the physicochemical environment and post-translational modifications. In this work, we study the effects of phosphorylation on the intrinsic propensity for different local backbone conformations of serine/threonine by molecular dynamics simulations. We showed that phosphorylation has very different effects on the intrinsic propensity for certain local backbone conformations for the serine and threonine. The phosphorylation of serine increases the propensity of forming polyproline II, whereas that of threonine has the opposite effect. Detailed analysis showed that such different responses to phosphorylation mainly arise from their different perturbations to the backbone hydration and the geometrical constraints by forming side-chain-backbone hydrogen bonds due to phosphorylation. Such an effect of phosphorylation on backbone conformations can be crucial for understanding the molecular mechanism of phosphorylation-regulated protein structures/dynamics and functions.

Thermal unfolding simulations of NBD1 domain variants reveal structural motifs associated with the impaired folding of F508del-CFTR

The deletion of phenylalanine 508 reshapes the conformational space of the NBD1 domain that populates unique intermediate states that provide insights into the molecular events that underlie the impaired folding of F508del-NBD1.

Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations

A complex of the phosphorylated kinase-inducible domain (pKID) with its interacting domain (KIX) is a model system for studies of mechanisms by which intrinsically unfolded proteins perform their functions. These mechanisms are not fully understood. Using an efficient coarse-grained model, ab initio simulations were performed of the coupled folding and binding of the pKID to the KIX. The simulations start from an unbound, randomly positioned and disordered pKID structure. During the simulations the pKID chain and its position remain completely unrestricted, while the KIX backbone is limited to near-native fluctuations. Ab initio simulations of such large-scale conformational transitions, unaffected by any knowledge about the bound pKID structure, remain inaccessible to classical simulations. Our simulations recover an ensemble of transient encounter complexes in good agreement with experimental results. We find that a key folding and binding step is linked to the formation of weak native interactions between a preformed nativelike fragment of a pKID helix and KIX surface. Once that nucleus forms, the pKID chain may condense from a largely disordered encounter ensemble to a natively bound and ordered conformation. The observed mechanism is reminiscent of a nucleation-condensation model, a common scenario for folding of globular proteins.

Selectivity Mechanism of ATP-Competitive Inhibitors for PKB and PKA

Protein kinase B (PKB) acts as a central node on the PI3K kinase pathway. Constitutive activation and overexpression of PKB have been identified to involve in various cancers. However, protein kinase A (PKA) sharing high homology with PKB is essential for metabolic regulation. Therefore, specific targeting on PKB is crucial strategy in drug design and development for antitumor. Here, we had revealed the selectivity mechanism for PKB inhibitors with molecular dynamics simulation and 3D-QSAR methods. Selective inhibitors of PKB could form more hydrogen bonds and hydrophobic contacts with PKB than those with PKA. This could explain that selective inhibitor M128 is more potent to PKB than to PKA. Then, 3D-QSAR models were constructed for these selective inhibitors and evaluated by test set compounds. 3D-QSAR model comparison of PKB inhibitors and PKA inhibitors reveals possible methods to improve the selectivity of inhibitors. These models can be used to design new chemical entities and make quantitative prediction of the specific selective inhibitors before resorting to in vitro and in vivo experiment.

Kinetic modulation of a disordered protein domain by phosphorylation

Phosphorylation is a major post-translational mechanism of regulation that frequently targets disordered protein domains, but it remains unclear how phosphorylation modulates disordered states of proteins. Here we determine the kinetics and energetics of a disordered protein domain the kinase-inducible domain (KID) of the transcription factor CREB and that of its phosphorylated form pKID, using high-throughput molecular dynamic simulations. We identify the presence of a metastable, partially ordered state with a 60-fold slowdown in conformational kinetics that arises due to phosphorylation, kinetically stabilizing residues known to participate in an early binding intermediate. We show that this effect is only partially reconstituted by mutation to glutamate, indicating that the phosphate is uniquely required for the long-lived state to arise. This mechanism of kinetic modulation could be important for regulation beyond conformational equilibrium shifts.

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

The kink-turn sRNA motif in archaea, whose combination with protein L7Ae initializes the assembly of small ribonucleoprotein particles (sRNPs), plays a key role in ribosome maturation and the translation process. Although many studies have been reported on this motif, the mechanism of sRNA folding coupled with protein binding is still poorly understood. Here, room and high temperature molecular dynamics (MD) simulations were performed on the complex of 25-nt kink-turn sRNA and L7Ae. The average RMSD values between the bound and corresponding apo structures and Kolmogorov-Smirnov P test analysis indicate that sRNA may follow an induced fit mechanism upon binding with L7Ae, both locally and globally. These conclusions are further supported by high-temperature unfolding kinetic analysis. Principal component analysis (PCA) found both closing and opening motions of the kink-turn sRNA. This might play a key role in the sRNP assembly and methylation catalysis. These combined computational methods can be used to study the specific recognition of other sRNAs and proteins.

Frustration-induced protein intrinsic disorder

Spontaneous folding into a specific native structure is the most important property of protein to perform their biological functions within organisms. Spontaneous folding is understood on the basis of an energy landscape picture based on the minimum frustration principle. Therefore, frustration seemingly only leads to protein functional disorder. However, frustration has recently been suggested to have a function in allosteric regulation. Functional frustration has the possibility to be a key to our deeper understanding of protein function. To explore another functional frustration, we theoretically examined structural frustration, which is designed to induce intrinsic disorder of a protein and its function through the coupled folding and binding. We extended the Wako-Saitô-Muñoz-Eaton model to take into account a frustration effect. With the model, we analyzed the binding part of neuron-restrictive silencer factor and showed that designed structural frustration in it induces intrinsic disorder. Furthermore, we showed that the folding and the binding are cooperative in interacting with a target protein. The cooperativity enables an intrinsically disordered protein to exhibit a sharp switch-like folding response to binding chemical potential change. Through this switch-like response, the structural frustration may contribute to the regulation function of interprotein interaction of the intrinsically disordered protein.

Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation

Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And while unstructured in solution, IDPs typically fold into a well-defined three-dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either or both simplified representations and advanced enhanced sampling schemes. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well-suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarise what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package.

Native-based simulations of the binding interaction between RAP74 and the disordered FCP1 peptide

By dephosphorylating the C-terminal domain (CTD) of RNA polymerase II (Pol II), the Transcription Factor IIF (TFIIF)-associating CTD phosphatase (FCP1) performs an essential function in recycling Pol II for subsequent rounds of transcription. The interaction between FCP1 and TFIIF is mediated by the disordered C-terminal tail of FCP1, which folds to form an α-helix upon binding the RAP74 subunit of TFIIF. The present work reports a structure-based simulation study of this interaction between the folded winged-helix domain of RAP74 and the disordered C-terminal tail of FCP1. The comparison of measured and simulated chemical shifts suggests that the FCP1 peptide samples 40-60% of its native helical structure in the unbound disordered ensemble. Free energy calculations suggest that productive binding begins when RAP74 makes hydrophobic contacts with the C-terminal region of the FCP1 peptide. The FCP1 peptide then folds into an amphipathic helix by zipping up the binding interface. The relative plasticity of FCP1 results in a more cooperative binding mechanism, allows for a greater diversity of pathways leading to the bound complex, and may also eliminate the need for "backtracking" from contacts that form out of sequence.

Using simulations to provide the framework for experimental protein folding studies

Molecular dynamics simulations are a powerful theoretical tool to model the protein folding process in atomistic details under realistic conditions. Combined with a number of experimental techniques, simulations provide a detailed picture of how a protein folds or unfolds in the presence of explicit solvent and other molecular species, such as cosolvents, osmolytes, cofactors, active binding partners or inert crowding agents. The denaturing effects of temperature, pressure and external mechanical forces can also be probed. Qualitative and quantitative agreement with experiment contributes to a comprehensive molecular picture of protein states along the folding/unfolding pathway. The variety of systems examined reveals key features of the protein folding process.

Computational studies on the substrate interactions of influenza A virus PB2 subunit

Influenza virus, which spreads around the world in seasonal epidemics and leads to large numbers of deaths every year, has several ribonucleoproteins in the central core of the viral particle. These viral ribonucleoproteins can specifically bind the conserved 3' and 5' caps of the viral RNAs with responsibility for replication and transcription of the viral RNA in the nucleus of infected cells. A fundamental question of most importance is that how the cap-binding proteins in the influenza virus discriminates between capped RNAs and non-capped ones. To get an answer, we performed molecular dynamics simulations and free energy calculations on the influenza A virus PB2 subunit, an important component of the RNP complexes, with a cap analog m7GTP. Our calculations showed that some key residues in the active site, such as Arg355, His357, Glu361 as well as Gln406, could offer significant hydrogen bonding and hydrophobic interactions with the guanine ring of the cap analog m7GTP to form an aromatic sandwich mechanism for the cap recognition and positioning in the active site. Subsequently, we applied this idea to a virtual screening procedure and identified 5 potential candidates that might be inhibitors against the PB2 subunit. Interestingly, 2 candidates Cpd1 and Cpd2 have been already reported to have inhibitory activities to the influenza virus cap-binding proteins. Further calculation also showed that they had comparatively higher binding affinities to the PB2 subunit than that of m7GTP. We believed that our findings could give an atomic insight into the deeper understanding of the cap recognition and binding mechanism, providing useful information for searching or designing novel drugs against influenza viruses.

Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations

MicroRNAs are endogenous 23–25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0) mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2) are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.

Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B

Histone chaperones facilitate assembly and disassembly of nucleosomes. Understanding the process of how histone chaperones associate and dissociate from the histones can help clarify their roles in chromosome metabolism. Some histone chaperones are intrinsically disordered proteins (IDPs). Recent studies of IDPs revealed that the recognition of the biomolecules is realized by the flexibility and dynamics, challenging the century-old structure-function paradigm. Here we investigate the binding between intrinsically disordered chaperone Chz1 and histone variant H2A.Z-H2B by developing a structure-based coarse-grained model, in which Debye-Hückel model is implemented for describing electrostatic interactions due to highly charged characteristic of Chz1 and H2A.Z-H2B. We find that major structural changes of Chz1 only occur after the rate-limiting electrostatic dominant transition state and Chz1 undergoes folding coupled binding through two parallel pathways. Interestingly, although the electrostatic interactions stabilize bound complex and facilitate the recognition at first stage, the rate for formation of the complex is not always accelerated due to slow escape of conformations with non-native electrostatic interactions at low salt concentrations. Our studies provide an ionic-strength-controlled binding/folding mechanism, leading to a cooperative mechanism of “local collapse or trapping” and “fly-casting” together and a new understanding of the roles of electrostatic interactions in IDPs' binding.

Histone chaperones facilitate the assembly and disassembly of nucleosome by interacting with the corresponding histones or histone variants. As the biomolecules in nucleosome are highly charged, electrostatic interactions are particularly important in these processes. The experiments have explored that the histone chaperon Chz1 as an intrinsically disordered protein (IDP) can fold by binding to its histone variants H2A.Z-H2B. Here, we developed a molecular simulation program that treated electrostatic interactions with Debye-Hückel model to study the mechanism of the association. We found that the inter-chain electrostatic interactions facilitate the coupled folding and binding transitions, consistent with the kinetic experiments and microscopic structural perspectives. Furthermore, we show that the intra-chain electrostatic interactions collapse Chz1 and slow the binding rate. The collapsed structure in IDPs caused by intra-chain electrostatic interactions has been widely found in experiments and the effect in binding is well studied in our work. Our theoretical approach shed new light on the role of electrostatics on inter-chain and intra-chain interactions for IDPs' binding and is applicable to the binding/folding of other IDPs to their targets.

Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding

Why doesn't the F19A mutant of p53 bind to MDM2? Binding thermodynamics have suggested that the loss of packing interactions upon mutating Phe into Ala sidechain results in destabilizing the binding free energy between p53 and MDM2. Does this mutation also modulate the initial recognition between p53 and MDM2? We look at atomistic computer simulations of the process of the initial encounter between wild type p53 peptide and its F19A mutant with the N-terminal domain of MDM2. These simulations show that binding is characterized by a complex multistep process. It starts with the capture of F19 of wild type p53 by certain residues in the MDM2 binding pocket. This initial step anchors the peptide onto the surface of MDM2, and with the consequent reduction in the search space of the peptide, the peptide docks into the partially occluded surface of MDM2. This is similar to a crack forming in an otherwise occluded hydrophobic cavity in MDM2, and the peptide, docked through F19, modulates the propagation of this crack, which subsequently results in the stepwise docking of the rest of the peptide through insertions of W23 and L26. The lack of the bulky sidechain of F in the F19A mutant results in the absence of the initial "grasp" complex, and hence the mutant peptide diffuses randomly on the surface of MDM2 without binding. This is the first such demonstration of the possibility that a "kinetic" effect may partly underlie the destabilized thermodynamics of binding of F19A and is a feature that appears to be conserved in evolution. The observations by Wallace et al. (Mol Cell 2006; 23:251-63) that despite the inability of F19A to bind at the N-terminal domain of MDM2, it gets ubiquitinated, can now be partly understood based on a mechanism whereby the occupation of the binding pocket by ligands/peptides induces, via crack propagation and the dynamics of gatekeeper Y100, the ubiquitination signal for interactions between the acidic domain of MDM2 and the DNA binding domain of p53.

Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation

Amyloid fibrils are found in many fatal neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes, and prion disease. The VEALYL short peptide from insulin has been confirmed to aggregate amyloid-like fibrils. However, the aggregation mechanism of amyloid fibril is poorly understood. Here, we utilized molecular dynamics simulation to analyse the stability of VEALYL hexamer. The statistical results indicate that hydrophobic residues play key roles in stabilizing VEALYL hexamer. Single point and two linkage mutants confirmed that Val1, Leu4, and Tyr5 of VEALYL are key residues. The consistency of the results for the VEALYL oligomer suggests that the intermediate states might be trimer (3-0) and pentamer(3-2). These results can help us to obtain an insight into the aggregation mechanism of amyloid fibril. These methods can be used to study the stability of amyloid fibril from other short peptides.

Revealing interaction mode between HIV-1 protease and mannitol analog inhibitor

HIV protease is a key enzyme to play a key role in the HIV-1 replication cycle and control the maturation from HIV viruses to an infectious virion. HIV-1 protease has become an important target for anti-HIV-1 drug development. Here, we used molecular dynamics simulation to study the binding mode between mannitol derivatives and HIV-1 protease. The results suggest that the most active compound (M35) has more stable hydrogen bonds and stable native contacts than the less active one (M17). These mannitol derivatives might have similar interaction mode with HIV-1 protease. Then, 3D-QSAR was used to construct quantitative structure-activity models. The cross-validated q(2) values are found as 0.728 and 0.611 for CoMFA and CoMSIA, respectively. And the non-cross-validated r(2) values are 0.973 and 0.950. Nine test set compounds validate the model. The results show that this model possesses better prediction ability than the previous work. This model can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV-1 protease inhibitors before resorting to in vitro and in vivo experiment.

Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response

Intrinsically disordered proteins (IDPs) are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTα) and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2), with a common binding partner, Kelch-like ECH-associated protein 1(Keap1), are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5-1.0 microsecond atomistic molecular dynamics (MD) simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTα and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTα and Neh2 have propensities to form bound-state-like β-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTα and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs) and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTα bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response.

Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1α with CBP

Intrinsically disordered proteins that acquire their three dimensional structures only upon binding to their targets are very important in cellular signal regulation. While experimental studies have been made on the structures of both bound (structured) and unbound (disordered) states, less is known about the actual folding-binding transition. Coarse grained simulations using native-centric (i.e. Gō) potentials have been particularly useful in addressing this problem, given the large search space for IDP binding, but have well-known deficiencies in reproducing the unfolded state structure and dynamics. Here, we investigate the interaction of HIF1α with CBP using a hierarchy of coarse-grained models, in each case matching the binding affinity at 300 K to the experimental value. Starting from a pure Gō-like model based on the native structure of the complex we go on to consider a more realistic model of helix propensity in the HIF1α, and finally the effect of non-native interactions between binding partners. We find structural disorder (i.e."fuzziness") in the bound state of HIF1α in all models which is supported by the results of atomistic simulations. Correcting the over-stabilized helices in the unbound state gives rise to a more cooperative folding-binding transition (destabilizing partially bound intermediates). Adding non-native contacts lowers the free energy barrier for binding to an almost barrierless scenario, leading to higher binding/unbinding rates relative to the other models, in better agreement with the near diffusion-limited binding rates measured experimentally. Transition state structures for the three models are highly disordered, supporting a fly-casting mechanism for binding.

Intrinsically disordered proteins in a physics-based world

Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins that rely on a lack of stable structure for function. They are highly prevalent in biology, play fundamental roles, and are extensively involved in human diseases. For signaling and regulation, IDPs often fold into stable structures upon binding to specific targets. The mechanisms of these coupled binding and folding processes are of significant importance because they underlie the organization of regulatory networks that dictate various aspects of cellular decision-making. This review first discusses the challenge in detailed experimental characterization of these heterogeneous and dynamics proteins and the unique and exciting opportunity for physics-based modeling to make crucial contributions, and then summarizes key lessons from recent de novo simulations of the structure and interactions of several regulatory IDPs.

Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR

Diaryltriazine inhibitors have highly potent and effective bioactivities for the wild type of HIV-1 reverse transcription. To design new drug of antimutant HIV-1 reverse transcriptase, the mechanism of drug resistance for four types of mutants was revealed. Molecular dynamics simulations suggest that Lys101, Leu100, Lys103, Tyr181, and Tyr188 are key residues. Different mutants of key residues may have different interaction modes and lead to different drug resistances. Then, CoMFA and CoMSIA methods were employed to construct 3D quantitative structure-activity relationship models. These models were evaluated by test set compounds. These models can be used to make quantitative prediction of their bioactivities for lead compounds before resorting to in vitro and in vivo experimentation.

Induced fit or conformational selection for RNA/U1A folding

The hairpin II of U1 snRNA can bind U1A protein with high affinity and specificity. NMR spectra suggest that the loop region of apo-RNA is largely unstructured and undergoes a transition from unstructured to well-folded upon U1Abinding. However, the mechanism that RNA folding coupled protein binding is poorly understood. To get an insight into the mechanism, we have performed explicit-solvent molecular dynamics (MD) to study the folding kinetics of bound RNA and apo-RNA. Room-temperature MD simulations suggest that the conformation of bound RNA has significant adjustment and becomes more stable upon U1A binding. Kinetic analysis of high-temperature MD simulations shows that bound RNA and apo-RNA unfold via a two-state process, respectively. Both kinetics and free energy landscape analyses indicate that bound RNA folds in the order of RNA contracting, U1A binding, and tertiary folding. The predicted Phi-values suggest that A8, C10, A11, and G16 are key bases for bound RNA folding. Mutant Arg52Gln analysis shows that electrostatic interaction and hydrogen bonds between RNA and U1A (Arg52Gln) decrease. These results are in qualitative agreement with experiments. Furthermore, this method could be used in other studies about biomolecule folding upon receptor binding.