Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase

Kim, Tae Hun; Payliss, Brandon J.; Nosella, Michael L; Lee, Ian T W; Toyama, Yoshiyuki; Forman‐Kay, Julie D.; Kay, Lewis E.

doi:10.1073/pnas.2104897118

Cited by 45 publications

(64 citation statements)

References 68 publications

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“… 85 Kim et al combined a specific labeling scheme with edited-filtered nuclear Overhauser effect spectroscopy (NOESY) to probe intermolecular contacts relevant for the LLPS of the C-terminal intrinsically disordered region of RNA-binding CAPRIN1 protein at a residue-specific level. 182 Whereas the importance of the interaction between aromatic side chains for CAPRIN1 LLPS was confirmed, a previously not fully appreciated role of backbone interactions, in particular H α –H N contacts involving aromatic and nonaromatic residues, was established. These contacts were suggested to be stabilized through amide hydrogen bond formation and/or π–π interactions.…”

Section: Dynamics Of Intrinsically Disordered Proteins In Liquid–liqu...mentioning

confidence: 96%

Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry

2022

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Motions in biomolecules are critical for biochemical reactions. In cells, many biochemical reactions are executed inside of biomolecular condensates formed by ultradynamic intrinsically disordered proteins. A deep understanding of the conformational dynamics of intrinsically disordered proteins in biomolecular condensates is therefore of utmost importance but is complicated by diverse obstacles. Here we review emerging data on the motions of intrinsically disordered proteins inside of liquidlike condensates. We discuss how liquid–liquid phase separation modulates internal motions across a wide range of time and length scales. We further highlight the importance of intermolecular interactions that not only drive liquid–liquid phase separation but appear as key determinants for changes in biomolecular motions and the aging of condensates in human diseases. The review provides a framework for future studies to reveal the conformational dynamics of intrinsically disordered proteins in the regulation of biomolecular condensate chemistry.

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Section: Dynamics Of Intrinsically Disordered Proteins In Liquid–liqu...mentioning

confidence: 96%

Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry

2022

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“…IDRs, however, do not adopt the static structures that are depicted in the AFDB (Ruff & Pappu 2021). Instead, IDRs populate an ensemble of interconverting conformations that depends strongly on the primary structure (Das & Pappu 2013), and the properties of these ensembles directly impact on the functions of IDRs (Borcherds et al 2014;Conicella et al 2020;Das et al 2016;Iešmantavičius et al 2014;Kim et al 2021;Maltsev et al 2012;Milles et al 2015;Mittag et al 2008;Sugase et al 2007;Zosel et al 2018). However, experimentally determined structural information for IDR conformational ensembles constitutes only a tiny fraction of the available data for structured proteins (Lazar et al 2021;Varadi et al 2014), and such ensembles are not deposited in the Protein Data Bank (PDB), an online repository that contains more than 150,000 high-resolution structures of biomolecules (Burley & Berman 2021), data which were mined to create AlphaFold2 (Jumper et al 2021a) and RoseTTAFold (Baek et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2

Alderson

Pritišanac

Moses

et al. 2022

Preprint

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Deep learning-based approaches to protein structure prediction, such as AlphaFold2 and RoseTTAFold, can now define many protein structures with atomic-level accuracy. The AlphaFold Protein Structure Database (AFDB) contains a predicted structure for nearly every protein in the human proteome, including proteins that have intrinsically disordered regions (IDRs), which do not adopt a stable structure and rapidly interconvert between conformations. Although it is generally assumed that IDRs have very low AlphaFold2 confidence scores that reflect low-confidence structural predictions, we show here that AlphaFold2 assigns confident structures to nearly 15% of human IDRs. The amino-acid sequences of IDRs with high-confidence structures do not show significant similarity to the Protein Data Bank; instead, these IDR sequences exhibit a higher degree of positional amino-acid sequence conservation and are more enriched in charged and hydrophobic residues than IDRs with low-confidence structures. We compared the AlphaFold2 predictions to experimental NMR data for a subset of IDRs known to fold under specific conditions, finding that AlphaFold2 tends to capture the folded state structure. We note, however, that these AlphaFold2 predictions cannot detect functionally relevant structural plasticity within IDRs and cannot offer an ensemble representation of IDRs. Nevertheless, AlphaFold2 assigns high-confidence scores to about 60% of a set of 350 IDRs that have been reported to conditionally fold, suggesting that AlphaFold2 has learned to identify conditionally folded IDRs, which is unexpected, since IDRs were minimally represented in the training data. Leveraging this ability to discover IDRs that conditionally fold, we find that up to 80% of IDRs in archaea and bacteria are predicted to conditionally fold, but less than 20% of eukaryotic IDRs. Our results suggest that a large majority of IDRs in the proteomes of human and other eukaryotes would be expected to function in the absence of conditional folding.

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“…Finally, we compare aspects of higher-order assembly and LLPS. LLPS depends on highly multi-valent, weak interactions (54), such as transient aromatic side-chain and backbone interactions of disordered chains (55). These can be expected to differ from protein/NA and protein-protein interactions that stabilize the discrete oligomeric co-assemblies observed above (56), including the tetramerization property augmented by the G215C mutation.…”

Section: Resultsmentioning

confidence: 99%

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein

Zhao

Nguyen

et al. 2022

Preprint

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Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by 3-4 different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced co-assembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.

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Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase

Cited by 45 publications

References 68 publications

Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry

Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry

Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein

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