The molecular basis for cellular function of intrinsically disordered protein regions

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 25(3), P. 187 - 211

Published: Nov. 13, 2023

Language: Английский

---

“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(21), P. 3970 - 3984

Published: Oct. 19, 2022

Language: Английский

---

Liquid–Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins

Journal of the American Chemical Society, Journal Year: 2023, Volume and Issue: 145(19), P. 10548 - 10563

Published: May 5, 2023

Liquid–liquid phase separation of flexible biomolecules has been identified as a ubiquitous phenomenon underlying the formation membraneless organelles that harbor multitude essential cellular processes. We use nuclear magnetic resonance (NMR) spectroscopy to compare dynamic properties an intrinsically disordered protein (measles virus NTAIL) in dilute and dense phases at atomic resolution. By measuring 15N NMR relaxation different field strengths, we are able characterize dynamics crowded conditions amplitude timescale motional modes those present organelle. Although local backbone conformational sampling appears be largely retained, occurring on all detectable timescales, including librational, dihedral angle segmental, chainlike motions, considerably slowed down. Their relative amplitudes also drastically modified, with slower, chain-like motions dominating profile. In order provide additional mechanistic insight, performed extensive molecular simulations under self-crowding concentrations comparable found liquid phase. Simulation broadly reproduces impact condensed both free energy landscape kinetic interconversion between states. particular, experimentally observed reduction fastest component correlates higher levels intermolecular contacts or entanglement simulations, reducing space available this mode strongly conditions.

Language: Английский

---

Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(12), P. 8071 - 8085

Published: March 16, 2024

The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, DNA damage response. Clinically, they are linked to Ewing family tumors neurodegenerative diseases such as amyotrophic lateral sclerosis. fusion EWS::FLI1, the causative mutation of sarcoma, arises from a genomic translocation that fuses portion low-complexity domain (LCD) EWS (EWSLCD) with binding ETS transcription factor FLI1. This modifies programs disrupts native functions, splicing. exact role intrinsically disordered EWSLCD remains topic active investigation, but its ability phase separate form biomolecular condensates is believed be central EWS::FLI1's oncogenic properties. Here, we used paramagnetic relaxation enhancement NMR, microscopy, all-atom molecular dynamics (MD) simulations better understand self-association separation tendencies EWSLCD. Our NMR data mutational analysis suggest higher density proximity tyrosine residues amplify likelihood condensate formation. MD revealed tyrosine-rich termini exhibit compact conformations unique contact networks provided critical input on relationship between contacts formed within single molecule (intramolecular) inside condensed (intermolecular). These findings enhance our understanding proteins' condensate-forming capabilities underline differences TAF15.

Language: Английский

---

Interaction Dynamics of Intrinsically Disordered Proteins from Single-Molecule Spectroscopy

Annual Review of Biophysics, Journal Year: 2023, Volume and Issue: 52(1), P. 433 - 462

Published: Feb. 8, 2023

Many proteins contain large structurally disordered regions or are entirely under physiological conditions. The functions of these intrinsically (IDPs) often involve interactions with other biomolecules. An important emerging effort has thus been to identify the molecular mechanisms IDP and how they differ from textbook notions biomolecular binding for folded proteins. In this review, we summarize versatile tool kit single-molecule fluorescence spectroscopy can aid investigation conformationally heterogeneous highly dynamic systems. We discuss experimental observables that be employed enable complexes probed on timescales nanoseconds hours. Key insights include diverse structural properties bound IDPs kinetic facilitated by disorder, such as fly-casting; disorder-mediated encounter complexes; competitive substitution via ternary complexes, which enables rapid dissociation even high-affinity complexes. also links aggregation, liquid-liquid phase separation, cellular processes, well current technical advances further expand scope spectroscopy.

Language: Английский

---

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(10), P. 6501 - 6542

Published: May 9, 2024

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number UAAs with tailored chemical and/or physical properties have been developed and used wide array biological applications. In particular, specific spectroscopic characteristics can be as external reporters produce additional signals, hence increasing the information content obtainable protein imaging measurements. this Review, we summarize progress past two decades development such their applications spectroscopy microscopy, focus on that vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic (NMR) probes. Wherever applicable, also discuss future directions.

Language: Английский

---

Protein Disorder in Plant Stress Adaptation: From Late Embryogenesis Abundant to Other Intrinsically Disordered Proteins

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(2), P. 1178 - 1178

Published: Jan. 18, 2024

Global climate change has caused severe abiotic and biotic stresses, affecting plant growth food security. The mechanical understanding of stress responses is critical for achieving sustainable agriculture. Intrinsically disordered proteins (IDPs) are a group without unique three-dimensional structures. environmental sensitivity structural flexibility IDPs contribute to the developmental plasticity sessile plants deal with challenges. This article discusses roles various in tolerance resistance, describes current mechanistic insights into unstructured such as disorder-to-order transition adopting secondary structures interact specific partners (i.e., cellular membranes, membrane proteins, metal ions, DNA), elucidates liquid–liquid phase separation driven by protein disorder responses. By comparing IDP studies animal systems, this provides conceptual principles adaptation, reveals research gaps, advises on future direction. highlighting relevant unanswered questions aims encourage more these emerging topics understand mechanisms action behind their resistance phenotypes.

Language: Английский

---

Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(6)

Published: Jan. 31, 2024

A central challenge in the study of intrinsically disordered proteins is characterization mechanisms by which they bind their physiological interaction partners. Here, we utilize a deep learning–based Markov state modeling approach to characterize folding-upon-binding pathways observed long timescale molecular dynamics simulation region measles virus nucleoprotein N TAIL reversibly binding X domain phosphoprotein complex. We find that predominantly occurs via two distinct encounter complexes are differentiated orientation, helical content, and conformational heterogeneity . observe proceeds through multi-step induced fit mechanism with several intermediates do not evidence for existence canonical selection pathways. four kinetically separated native-like bound states interconvert on timescales eighty five hundred nanoseconds. These share core set native intermolecular contacts stable helices sequential formation non-native additional turns. Our analyses provide an atomic resolution structural description intermediate pathway elucidate nature kinetic barriers between metastable dynamic heterogenous, or “fuzzy”, protein

Language: Английский

---

Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology

JACS Au, Journal Year: 2024, Volume and Issue: 4(2), P. 369 - 383

Published: Feb. 5, 2024

The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains be examined. Moreover, understanding the changes interactions response stimuli within cells, both normal disease conditions, is key grasping proteins' functionality cellular processes. Nevertheless, achieving high-resolution identification these presents a technical challenge. In this Perspective, we summarize recent advancements in-cell nuclear magnetic resonance (NMR) vivo cross-linking mass spectrometry (XL-MS) for studying context. Additionally, discuss challenges, opportunities, potential benefits integrating NMR XL-MS future research offer an exhaustive approach proteins their natural habitat.

Language: Английский

---

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies

Structural Dynamics, Journal Year: 2024, Volume and Issue: 11(3)

Published: May 1, 2024

Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems treating disease. Despite the deposition of over 215 000 macromolecular structures in Protein Data Bank advent AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, ESMFold, static representations are typically produced, which fail to fully capture motion. Here, we discuss importance integrating experimental with computational clustering explore landscapes that manifest function. We describe method developed by Europe - Knowledge Base identify distinct states, demonstrate resource's primary use cases, through examples, need further efforts annotate conformations functional information. Such initiatives will be unlocking potential data, expediting drug discovery research, deepening our mechanisms.

Language: Английский

---