Application of NMR to studies of intrinsically disordered proteins

Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a phenomenon that underlies membraneless compartmentalization of the cell. The underlying molecular interactions that underpin biomolecular LLPS have been of increased interest due to the importance of membraneless organelles in facilitating various biological processes and the disease association of several of the proteins that mediate LLPS. Proteins that are able to undergo LLPS often contain intrinsically disordered regions and remain dynamic in solution. Solution-state NMR spectroscopy has emerged as a leading structural technique to characterize protein LLPS due to the variety and specificity of information that can be obtained about intrinsically disordered sequences. This review discusses practical aspects of studying LLPS by NMR, summarizes recent work on the molecular aspects of LLPS of various protein systems, and discusses future opportunities for characterizing the molecular details of LLPS to modulate phase separation.

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“…However, advances in isotopic labeling and resonance assignment have made studying IDPs easier (reviewed in Ref. 36).…”

Section: Chemical Shiftsmentioning

confidence: 99%

The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy

Murthy

Fawzi

2020

Journal of Biological Chemistry

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“…The conformation of IDPs is sensitive to environmental changes (e.g., pH, temperature, ionic strength, and presence of ligands and/or binding molecules). Environment-induced conformational changes in IDPs can be detected by an NMR chemical shift [ 15 , 16 ]. This chemical shift, a sophisticated reporter of the backbone conformation, also indicates protein dynamics [ 17 ] and binding sites of ligands and/or other proteins.…”

Section: Conformational Study Of Idps Using Experimental Techniquementioning

confidence: 99%

“…This chemical shift, a sophisticated reporter of the backbone conformation, also indicates protein dynamics [ 17 ] and binding sites of ligands and/or other proteins. Compared with NMR of globular proteins, that of IDPs presents narrow line shapes [ 15 , 16 , 18 , 19 , 20 , 21 ] due to the highly dynamic nature of the polypeptide chain. Thanks to these narrow line shapes, the signal-to-noise ratio (S/N ratio) in NMR spectra of IDPs is usually high.…”

Section: Conformational Study Of Idps Using Experimental Techniquementioning

confidence: 99%

How Do We Study the Dynamic Structure of Unstructured Proteins: A Case Study on Nopp140 as an Example of a Large, Intrinsically Disordered Protein

Lee

2018

IJMS

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Intrinsically disordered proteins (IDPs) represent approximately 30% of the human genome and play key roles in cell proliferation and cellular signaling by modulating the function of target proteins via protein–protein interactions. In addition, IDPs are involved in various human disorders, such as cancer, neurodegenerative diseases, and amyloidosis. To understand the underlying molecular mechanism of IDPs, it is important to study their structural features during their interactions with target proteins. However, conventional biochemical and biophysical methods for analyzing proteins, such as X-ray crystallography, have difficulty in characterizing the features of IDPs because they lack an ordered three-dimensional structure. Here, we present biochemical and biophysical studies on nucleolar phosphoprotein 140 (Nopp140), which mostly consists of disordered regions, during its interaction with casein kinase 2 (CK2), which plays a central role in cell growth. Surface plasmon resonance and electron paramagnetic resonance studies were performed to characterize the interaction between Nopp140 and CK2. A single-molecule fluorescence resonance energy transfer study revealed conformational change in Nopp140 during its interaction with CK2. These studies on Nopp140 can provide a good model system for understanding the molecular function of IDPs.

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“…We studied this eIF4G1 region using an eIF4G1 1-249 construct that is stable for days under different pH conditions ( Supplementary Figure 1). We then analyzed eIF4G1 1-249 using NMR, which is a very powerful technique for investigation of IDRs and their interactions at the residue level ( 33,34 and references therein).…”

Section: The N-terminal Eif4g1 Idr Contains Residual Structural Featuresmentioning

confidence: 99%

Multivalent interactions between eIF4G1, Pub1 and Pab1 drive the formation of protein condensates

Chaves‐Arquero

Martínez-Lumbreras

Sibille

et al. 2020

Preprint

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Yeast eIF4G1 interacts with RNA binding proteins (RBPs) like Pab1 and Pub1 affecting its function in translation initiation and stress granules formation. We present an NMR and SAXS study of the intrinsically disordered region of eIF4G1, eIF4G11-249, and its interactions with Pub1 and Pab1. The conformational ensemble of eIF4G11-249 shows an α-helix within the BOX3 conserved element and a dynamic network of fuzzy π-π and π-cation interactions involving arginine and aromatic residues. The Pab1 RRM2 domain interacts with eIF4G1 BOX3, the canonical interaction site, but also with BOX2, a conserved element of unknown function to date. In contrast, the Pub1 RRM3 domain interacts with the RNA1-1 and BOX1 regions of eIF4G1. Mixtures of Pub1, Pab1 and eIF4G1 form micrometer-size protein condensates that require the presence of the eIF4G1 BOX1 element. These homotypic interactions suggest a double key mechanism of eIF4G1 regulation, important for understanding the architecture of stress granule cores.

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Application of NMR to studies of intrinsically disordered proteins

Cited by 95 publications

References 144 publications

The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy

The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy

How Do We Study the Dynamic Structure of Unstructured Proteins: A Case Study on Nopp140 as an Example of a Large, Intrinsically Disordered Protein

Multivalent interactions between eIF4G1, Pub1 and Pab1 drive the formation of protein condensates

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