Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

Pietrek, Lisa M.; Stelzl, Lukas S.; Hummer, Gerhard

doi:10.1021/acs.jctc.9b00809

Cited by 80 publications

(133 citation statements)

References 81 publications

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“…Next we investigated the conformational properties of A182-S197 with MD simulations. For the simulations, we used the state-of-the art force field/water model that accurately reproduced NMR parameters of the intrinsically disordered protein αsynuclein (Pietrek et al, 2020). In agreement with the NMR analysis, residues next to R189 populate transient α-helical structure ( Figure 3C).…”

Section: Rna-interaction Of the Mutation-prone Sr-regionmentioning

confidence: 80%

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Savastano

Opakua

Ranković

et al. 2020

Preprint

136

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The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription and is essential for viral replication. Here we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.

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Section: Rna-interaction Of the Mutation-prone Sr-regionmentioning

confidence: 80%

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Savastano

Opakua

Ranković

et al. 2020

Preprint

136

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“…Atomistic Molecular Dynamics (MD) simulations can characterize the conformational ensembles of single proteins and protein complexes [ 56 , 57 , 58 ], pinpoint the link between chemical modifications and sequence mutations, and the modulation of protein–protein and protein-DNA interactions [ 59 , 60 , 61 , 62 ], reveal the conformational heterogeneity of IDRs within small aggregates [ 63 ], and guide the development of chemically accurate coarse-grained models for LLPS [ 64 , 65 ]. Furthermore, the predictive and explanatory power of atomistic simulations is constantly being ramped up by the collective efforts to develop even more accurate atomistic force fields for IDRs [ 66 , 67 ].…”

Section: Introductionmentioning

confidence: 99%

Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation

et al. 2020

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Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid–liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, including conformational switching, where they transition between alternate conformational ensembles. Using Molecular Dynamics simulations of a minimal coarse-grained model for IDRs, we show that the role of protein conformation has a non-trivial effect in the liquid–liquid phase behaviour of IDRs. When an IDR transitions to a conformational ensemble enriched in disordered extended states, LLPS is enhanced. In contrast, IDRs that switch to ensembles that preferentially sample more compact and structured states show inhibited LLPS. This occurs because extended and disordered protein conformations facilitate LLPS-stabilising multivalent protein–protein interactions by reducing steric hindrance; thereby, such conformations maximize the molecular connectivity of the condensed liquid network. Extended protein configurations promote phase separation regardless of whether LLPS is driven by homotypic and/or heterotypic protein–protein interactions. This study sheds light on the link between the dynamic conformational plasticity of IDRs and their liquid–liquid phase behaviour.

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“…30 However, the presence of both ordered and disordered domains in these proteins places a strong demand on the model's accuracy. All-atom force fields, with their everimproving accuracy, [31][32][33][34][35][36] can in principle, accurately model protein conformations. They are computational expensive though, and long-timescale simulations needed to study slow conformational rearrangement and aggregation kinetics remain inaccessible for most proteins of interest.…”

Section: Introductionmentioning

confidence: 99%

Consistent Force Field Captures Homolog Resolved HP1 Phase Separation

Latham

Zhang

2021

Preprint

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Many proteins have been shown to function via liquid-liquid phase separation. Computational modeling could offer much needed structural details of protein condensates and reveal the set of molecular interactions that dictate their stability. However, the presence of both ordered and disordered domains in these proteins places a high demand on the model accuracy. Here, we present an algorithm to derive a coarse-grained force field, MOFF, that can model both ordered and disordered proteins with consistent accuracy. It combines maximum entropy biasing, least-squares fitting, and basic principles of energy landscape theory to ensure that MOFF recreates experimental radii of gyration while predicting the folded structures for globular proteins with lower energy. The theta temperature determined from MOFF separates ordered and disordered proteins at 300 K and exhibits a strikingly linear relationship with amino acid sequence composition. We further applied MOFF to study the phase behavior of HP1, an essential protein for posttranslational modification and spatial organization of chromatin. The force field successfully resolved the structural difference of two HP1 homologs, despite their high sequence similarity. We carried out large scale simulations with hundreds of proteins to determine the critical temperature of phase separation and uncover multivalent interactions that stabilize higher-order assemblies. In all, our work makes significant methodological strides to connect theories of ordered and disordered proteins and provides a powerful tool for studying liquid-liquid phase separation with near-atomistic details.

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Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

Cited by 80 publications

References 81 publications

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation

Consistent Force Field Captures Homolog Resolved HP1 Phase Separation

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