Disordered Proteins Enable Histone Chaperoning on the Nucleosome

SUMMARYProteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.

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Regulation of KIF1A motility via polyglutamylation of tubulin C-terminal tails

10.1101/410860 ◽

2018 ◽

Author(s):

Dominique V. Lessard ◽

Oraya J. Zinder ◽

Takashi Hotta ◽

Kristen J. Verhey ◽

Ryoma Ohi ◽

...

Keyword(s):

Axonal Transport ◽

Single Molecule ◽

Posttranslational Modifications ◽

Molecular Motors ◽

Regulatory Mechanism ◽

Traffic Signals ◽

Cargo Delivery ◽

Motility Regulation ◽

Initial Interaction ◽

Positively Charged

ABSTRACTAxonal transport is a highly regulated cellular process responsible for site-specific neuronal cargo delivery. This process is mediated in part by KIF1A, a member of the kinesin-3 family of molecular motors. It is imperative that KIF1A’s highly efficient, superprocessive motility along microtubules is tightly regulated as misregulation of KIF1A cargo delivery is observed in many neurodegenerative diseases. However, the regulatory mechanisms responsible for KIF1A’s motility, and subsequent proper spatiotemporal cargo delivery, are largely unknown. One potential regulatory mechanism of KIF1A motility is through the posttranslational modifications (PTMs) of axonal microtubules. These PTMs, often occurring on the C-terminal tails of the microtubule tracks, act as molecular “traffic signals” helping to direct kinesin motor cargo delivery. Occurring on neuronal microtubules, C-terminal tail polygutamylation is known to be important for KIF1A cargo transport. KIF1A’s initial interaction with microtubule C-terminal tails is facilitated by the K-loop, a positively charged surface loop of the KIF1A motor domain. However, the K-loop’s role in KIF1A motility and response to perturbations in C-terminal tail polyglutamylation is underexplored. Using single-molecule imaging, we present evidence of KIF1A’s previously unreported pausing behavior on multiple microtubule structures. Further analysis revealed that these pauses link multiple processive segments together, contributing to KIF1A’s characteristic superprocessive run length. We further demonstrate that KIF1A pausing is mediated by a K-loop/polyglutamylated C-terminal tail interaction and is a regulatory mechanism of KIF1A motility. In summary, we introduce a new mechanism of KIF1A motility regulation, providing further insight into KIF1A’s role in axonal transport.

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Faculty Opinions recommendation of Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717991572.793473403 ◽

2013 ◽

Author(s):

Devarajan Thirumalai

Keyword(s):

Single Molecule ◽

Scaling Laws ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Single Molecule Spectroscopy ◽

Intrinsically Disordered

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Mechanical single-molecule potentiometers with large switching factors from ortho-pentaphenylene foldamers

Nature Communications ◽

10.1038/s41467-020-20311-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jinshi Li ◽

Pingchuan Shen ◽

Shijie Zhen ◽

Chun Tang ◽

Yiling Ye ◽

...

Keyword(s):

Charge Transport ◽

Single Molecule ◽

Scanning Tunneling ◽

Tunneling Microscopy ◽

Helical Structures ◽

Anchoring Groups ◽

Molecular Conductance ◽

And Control ◽

Helical Molecules ◽

Shed Light

AbstractMolecular potentiometers that can indicate displacement-conductance relationship, and predict and control molecular conductance are of significant importance but rarely developed. Herein, single-molecule potentiometers are designed based on ortho-pentaphenylene. The ortho-pentaphenylene derivatives with anchoring groups adopt multiple folded conformers and undergo conformational interconversion in solutions. Solvent-sensitive multiple conductance originating from different conformers is recorded by scanning tunneling microscopy break junction technique. These pseudo-elastic folded molecules can be stretched and compressed by mechanical force along with a variable conductance by up to two orders of magnitude, providing an impressively higher switching factor (114) than the reported values (ca. 1~25). The multichannel conductance governed by through-space and through-bond conducting pathways is rationalized as the charge transport mechanism for the folded ortho-pentaphenylene derivatives. These findings shed light on exploring robust single-molecule potentiometers based on helical structures, and are conducive to fundamental understanding of charge transport in higher-order helical molecules.

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Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER

Science Advances ◽

10.1126/sciadv.abg0942 ◽

2021 ◽

Vol 7 (21) ◽

pp. eabg0942

Author(s):

Jae Ho Lee ◽

Ahmad Jomaa ◽

SangYoon Chung ◽

Yu-Hsien Hwang Fu ◽

Ruilin Qian ◽

...

Keyword(s):

Single Molecule ◽

Protein Translocation ◽

Molecular Model ◽

Genetic Diseases ◽

Signal Recognition Particle ◽

Biological Regulation ◽

Single Molecule Studies ◽

Guanosine Triphosphatase ◽

Gtpase Cycle

The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)–driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.

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Planar Boronic Graphene and Nitrogenized Graphene Heterostructure for Protein Stretch and Confinement

Biomolecules ◽

10.3390/biom11121756 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1756

Author(s):

Xuchang Su ◽

Zhi He ◽

Lijun Meng ◽

Hong Liang ◽

Ruhong Zhou

Keyword(s):

Single Molecule ◽

Intrinsically Disordered Proteins ◽

Electron Tunneling ◽

Amyloid Β ◽

Protein Sequencing ◽

Disordered Proteins ◽

Force Microscopy ◽

Intrinsically Disordered ◽

Atomic Force ◽

Dynamics Simulations

Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that a planar heterostructure comprising boronic graphene (BC3) and nitrogenized graphene (C3N) sandwiched stripe (BC3/C3N/BC3) is capable of the effective stretching and confinement of three types of intrinsically disordered proteins (IDPs), including amyloid-β (1–42), polyglutamine (Q42), and α-Synuclein (61–95). Our molecular dynamics simulations demonstrate that the protein molecules interact more strongly with the C3N stripe than the BC3 one, which leads to their capture, elongation, and confinement along the center C3N stripe of the heterostructure. The conformational fluctuations of IDPs are substantially reduced after being stretched. This design may serve as a platform for single-molecule protein analysis with reduced thermal noise.

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Intrinsically disordered proteins identified in the aggregate proteome serve as biomarkers of neurodegeneration

Metabolic Brain Disease ◽

10.1007/s11011-021-00791-8 ◽

2021 ◽

Author(s):

Srinivas Ayyadevara ◽

Akshatha Ganne ◽

Meenakshisundaram Balasubramaniam ◽

Robert J. Shmookler Reis

Keyword(s):

Intrinsically Disordered Proteins ◽

Protein Complexes ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Physiological Processes ◽

Protein Partners ◽

And Function ◽

Computational Analyses ◽

Disordered Regions

AbstractA protein’s structure is determined by its amino acid sequence and post-translational modifications, and provides the basis for its physiological functions. Across all organisms, roughly a third of the proteome comprises proteins that contain highly unstructured or intrinsically disordered regions. Proteins comprising or containing extensive unstructured regions are referred to as intrinsically disordered proteins (IDPs). IDPs are believed to participate in complex physiological processes through refolding of IDP regions, dependent on their binding to a diverse array of potential protein partners. They thus play critical roles in the assembly and function of protein complexes. Recent advances in experimental and computational analyses predicted multiple interacting partners for the disordered regions of proteins, implying critical roles in signal transduction and regulation of biological processes. Numerous disordered proteins are sequestered into aggregates in neurodegenerative diseases such as Alzheimer’s disease (AD) where they are enriched even in serum, making them good candidates for serum biomarkers to enable early detection of AD.

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The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance

International Journal of Molecular Sciences ◽

10.3390/ijms221910677 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10677

Author(s):

Huqiang Wang ◽

Haolin Zhong ◽

Chao Gao ◽

Jiayin Zang ◽

Dong Yang

Keyword(s):

Intrinsically Disordered Proteins ◽

Protein Domains ◽

Comprehensive Analysis ◽

Disordered Proteins ◽

Functional Constraints ◽

Biological Functions ◽

Post Translational Modification ◽

Intrinsically Disordered ◽

And Function ◽

Disordered Regions

The consecutive disordered regions (CDRs) are the basis for the formation of intrinsically disordered proteins, which contribute to various biological functions and increasing organism complexity. Previous studies have revealed that CDRs may be present inside or outside protein domains, but a comprehensive analysis of the property differences between these two types of CDRs and the proteins containing them is lacking. In this study, we investigated this issue from three viewpoints. Firstly, we found that in-domain CDRs are more hydrophilic and stable but have less stickiness and fewer post-translational modification sites compared with out-domain CDRs. Secondly, at the protein level, we found that proteins with only in-domain CDRs originated late, evolved rapidly, and had weak functional constraints, compared with the other two types of CDR-containing proteins. Proteins with only in-domain CDRs tend to be expressed spatiotemporal specifically, but they tend to have higher abundance and are more stable. Thirdly, we screened the CDR-containing protein domains that have a strong correlation with organism complexity. The CDR-containing domains tend to be evolutionarily young, or they changed from a domain without CDR to a CDR-containing domain during evolution. These results provide valuable new insights about the evolution and function of CDRs and protein domains.

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From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers

Essays in Biochemistry ◽

10.1042/ebc20200024 ◽

2021 ◽

Author(s):

Pétur O. Heidarsson ◽

Ciro Cecconi

Keyword(s):

Optical Tweezers ◽

Single Molecule ◽

Structural Changes ◽

Intrinsically Disordered Proteins ◽

Conformational Dynamics ◽

Disordered Proteins ◽

Kinase Activation ◽

Intrinsically Disordered ◽

Complex Protein ◽

Methodological Principles

Abstract Single-molecule manipulation with optical tweezers has uncovered macromolecular behaviour hidden to other experimental techniques. Recent instrumental improvements have made it possible to expand the range of systems accessible to optical tweezers. Beyond focusing on the folding and structural changes of isolated single molecules, optical tweezers studies have evolved into unraveling the basic principles of complex molecular processes such as co-translational folding on the ribosome, kinase activation dynamics, ligand–receptor binding, chaperone-assisted protein folding, and even dynamics of intrinsically disordered proteins (IDPs). In this mini-review, we illustrate the methodological principles of optical tweezers before highlighting recent advances in studying complex protein conformational dynamics – from protein synthesis to physiological function – as well as emerging future issues that are beginning to be addressed with novel approaches.

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