1
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Usher ET, Fossat MJ, Holehouse AS. Phosphorylation of disordered proteins tunes local and global intramolecular interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598315. [PMID: 38915510 PMCID: PMC11195077 DOI: 10.1101/2024.06.10.598315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.
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Affiliation(s)
- Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Martin J. Fossat
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
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2
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Ding EA, Kumar S. Neurofilament Biophysics: From Structure to Biomechanics. Mol Biol Cell 2024; 35:re1. [PMID: 38598299 PMCID: PMC11151108 DOI: 10.1091/mbc.e23-11-0438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
Neurofilaments (NFs) are multisubunit, neuron-specific intermediate filaments consisting of a 10-nm diameter filament "core" surrounded by a layer of long intrinsically disordered protein (IDP) "tails." NFs are thought to regulate axonal caliber during development and then stabilize the mature axon, with NF subunit misregulation, mutation, and aggregation featuring prominently in multiple neurological diseases. The field's understanding of NF structure, mechanics, and function has been deeply informed by a rich variety of biochemical, cell biological, and mouse genetic studies spanning more than four decades. These studies have contributed much to our collective understanding of NF function in axonal physiology and disease. In recent years, however, there has been a resurgence of interest in NF subunit proteins in two new contexts: as potential blood- and cerebrospinal fluid-based biomarkers of neuronal damage, and as model IDPs with intriguing properties. Here, we review established principles and more recent discoveries in NF structure and function. Where possible, we place these findings in the context of biophysics of NF assembly, interaction, and contributions to axonal mechanics.
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Affiliation(s)
- Erika A. Ding
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720
| | - Sanjay Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158
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3
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Kravikass M, Koren G, Saleh OA, Beck R. From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:13. [PMID: 38358563 PMCID: PMC10869404 DOI: 10.1140/epje/s10189-024-00409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.
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Affiliation(s)
- Mathar Kravikass
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Gil Koren
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, USA
- Physics Department, University of California, Santa Barbara, USA
| | - Roy Beck
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.
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4
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Krieg JL, Leonard AV, Turner RJ, Corrigan F. Identifying the Phenotypes of Diffuse Axonal Injury Following Traumatic Brain Injury. Brain Sci 2023; 13:1607. [PMID: 38002566 PMCID: PMC10670443 DOI: 10.3390/brainsci13111607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Diffuse axonal injury (DAI) is a significant feature of traumatic brain injury (TBI) across all injury severities and is driven by the primary mechanical insult and secondary biochemical injury phases. Axons comprise an outer cell membrane, the axolemma which is anchored to the cytoskeletal network with spectrin tetramers and actin rings. Neurofilaments act as space-filling structural polymers that surround the central core of microtubules, which facilitate axonal transport. TBI has differential effects on these cytoskeletal components, with axons in the same white matter tract showing a range of different cytoskeletal and axolemma alterations with different patterns of temporal evolution. These require different antibodies for detection in post-mortem tissue. Here, a comprehensive discussion of the evolution of axonal injury within different cytoskeletal elements is provided, alongside the most appropriate methods of detection and their temporal profiles. Accumulation of amyloid precursor protein (APP) as a result of disruption of axonal transport due to microtubule failure remains the most sensitive marker of axonal injury, both acutely and chronically. However, a subset of injured axons demonstrate different pathology, which cannot be detected via APP immunoreactivity, including degradation of spectrin and alterations in neurofilaments. Furthermore, recent work has highlighted the node of Ranvier and the axon initial segment as particularly vulnerable sites to axonal injury, with loss of sodium channels persisting beyond the acute phase post-injury in axons without APP pathology. Given the heterogenous response of axons to TBI, further characterization is required in the chronic phase to understand how axonal injury evolves temporally, which may help inform pharmacological interventions.
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Affiliation(s)
- Justin L Krieg
- Translational Neuropathology Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide 5000, Australia
| | - Anna V Leonard
- Translational Neuropathology Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide 5000, Australia
| | - Renée J Turner
- Translational Neuropathology Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide 5000, Australia
| | - Frances Corrigan
- Translational Neuropathology Laboratory, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide 5000, Australia
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5
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Koren G, Meir S, Holschuh L, Mertens HDT, Ehm T, Yahalom N, Golombek A, Schwartz T, Svergun DI, Saleh OA, Dzubiella J, Beck R. Intramolecular structural heterogeneity altered by long-range contacts in an intrinsically disordered protein. Proc Natl Acad Sci U S A 2023; 120:e2220180120. [PMID: 37459524 PMCID: PMC10372579 DOI: 10.1073/pnas.2220180120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 06/02/2023] [Indexed: 07/20/2023] Open
Abstract
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs' amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments' structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function.
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Affiliation(s)
- Gil Koren
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Sagi Meir
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Lennard Holschuh
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | | | - Tamara Ehm
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany
| | - Nadav Yahalom
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Adina Golombek
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tal Schwartz
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg22607, Germany
| | - Omar A. Saleh
- BMSE Program, University of California, Santa Barbara, CA93110
- Materials Department, University of California, Santa Barbara, CA93110
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | - Roy Beck
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
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6
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Lefebvre-Omar C, Liu E, Dalle C, d'Incamps BL, Bigou S, Daube C, Karpf L, Davenne M, Robil N, Jost Mousseau C, Blanchard S, Tournaire G, Nicaise C, Salachas F, Lacomblez L, Seilhean D, Lobsiger CS, Millecamps S, Boillée S, Bohl D. Neurofilament accumulations in amyotrophic lateral sclerosis patients' motor neurons impair axonal initial segment integrity. Cell Mol Life Sci 2023; 80:150. [PMID: 37184603 DOI: 10.1007/s00018-023-04797-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/24/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common motor neuron (MN) disease in adults with no curative treatment. Neurofilament (NF) level in patient' fluids have recently emerged as the prime biomarker of ALS disease progression, while NF accumulation in MNs of patients is the oldest and one of the best pathological hallmarks. However, the way NF accumulations could lead to MN degeneration remains unknown. To assess NF accumulations and study the impact on MNs, we compared MNs derived from induced pluripotent stem cells (iPSC) of patients carrying mutations in C9orf72, SOD1 and TARDBP genes, the three main ALS genetic causes. We show that in all mutant MNs, light NF (NF-L) chains rapidly accumulate in MN soma, while the phosphorylated heavy/medium NF (pNF-M/H) chains pile up in axonal proximal regions of only C9orf72 and SOD1 MNs. Excitability abnormalities were also only observed in these latter MNs. We demonstrate that the integrity of the MN axonal initial segment (AIS), the region of action potential initiation and responsible for maintaining axonal integrity, is impaired in the presence of pNF-M/H accumulations in C9orf72 and SOD1 MNs. We establish a strong correlation between these pNF-M/H accumulations, an AIS distal shift, increased axonal calibers and modified repartition of sodium channels. The results expand our understanding of how NF accumulation could dysregulate components of the axonal cytoskeleton and disrupt MN homeostasis. With recent cumulative evidence that AIS alterations are implicated in different brain diseases, preserving AIS integrity could have important therapeutic implications for ALS.
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Affiliation(s)
- Cynthia Lefebvre-Omar
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Elise Liu
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Carine Dalle
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Boris Lamotte d'Incamps
- Université Paris-Cité, CNRS, Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Stéphanie Bigou
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Clément Daube
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Léa Karpf
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Marc Davenne
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | | | - Coline Jost Mousseau
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Stéphane Blanchard
- Institut Pasteur, INSERM U1115, Unité Biothérapies pour les Maladies Neurodégénératives, Paris, France
| | - Guillaume Tournaire
- Institut Pasteur, INSERM U1115, Unité Biothérapies pour les Maladies Neurodégénératives, Paris, France
| | | | - François Salachas
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de Référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Lucette Lacomblez
- Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de Référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Danielle Seilhean
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Département de Neuropathologie, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Christian S Lobsiger
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Stéphanie Millecamps
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Séverine Boillée
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France.
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7
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Abu-Rumeileh S, Abdelhak A, Foschi M, D'Anna L, Russo M, Steinacker P, Kuhle J, Tumani H, Blennow K, Otto M. The multifaceted role of neurofilament light chain protein in non-primary neurological diseases. Brain 2023; 146:421-437. [PMID: 36083979 PMCID: PMC9494370 DOI: 10.1093/brain/awac328] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The advancing validation and exploitation of CSF and blood neurofilament light chain protein as a biomarker of neuroaxonal damage has deeply changed the current diagnostic and prognostic approach to neurological diseases. Further, recent studies have provided evidence of potential new applications of this biomarker also in non-primary neurological diseases. In the present review we summarize the state of the art, future perspectives, but also limitations, of neurofilament light chain protein as a CSF and blood biomarker in several medical fields, including intensive care medicine, surgery, internal medicine and psychiatry. In particular, neurofilament light chain protein is associated with the degree of neurological impairment and outcome in patients admitted to intensive care units or in the perioperative phase and it seems to be highly interconnected with cardiovascular risk factors. Beyond that, interesting diagnostic and prognostic insights have been provided by the investigation of neurofilament light chain protein in psychiatric disorders as well as in the current coronavirus disease-19 pandemic and in normal ageing. Altogether, current data outline a multifaceted applicability of CSF and blood neurofilament light chain protein ranging from the critical clinical setting to the development of precision medicine models suggesting a strict interplay between the nervous system pathophysiology and the health-illness continuum.
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Affiliation(s)
- Samir Abu-Rumeileh
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Ahmed Abdelhak
- Department of Neurology, University of California San Francisco (UCSF), San Francisco, USA
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Matteo Foschi
- Department of Neuroscience, Neurology Unit – S. Maria delle Croci Hospital of Ravenna, AUSL Romagna, Ravenna, Italy
| | - Lucio D'Anna
- Department of Stroke and Neuroscience, Charing Cross Hospital, Imperial College London, NHS Healthcare Trust, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Michele Russo
- Department of Cardiology, S. Maria dei Battuti Hospital, AULSS 2 Veneto, Conegliano, Italy
| | - Petra Steinacker
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Jens Kuhle
- Neurologic Clinic and Policlinic, MS Center and Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), Departments of Biomedicine and Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Markus Otto
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
- Department of Neurology, Ulm University Hospital, Ulm, Germany
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8
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Ehm T, Shinar H, Jacoby G, Meir S, Koren G, Segal Asher M, Korpanty J, Thompson MP, Gianneschi NC, Kozlov MM, Azoulay-Ginsburg S, Amir RJ, Rädler JO, Beck R. Self-Assembly of Tunable Intrinsically Disordered Peptide Amphiphiles. Biomacromolecules 2023; 24:98-108. [PMID: 36469950 PMCID: PMC9832477 DOI: 10.1021/acs.biomac.2c00866] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered peptide amphiphiles (IDPAs) present a novel class of synthetic conjugates that consist of short hydrophilic polypeptides anchored to hydrocarbon chains. These hybrid polymer-lipid block constructs spontaneously self-assemble into dispersed nanoscopic aggregates or ordered mesophases in aqueous solution due to hydrophobic interactions. Yet, the possible sequence variations and their influence on the self-assembly structures are vast and have hardly been explored. Here, we measure the nanoscopic self-assembled structures of four IDPA systems that differ by their amino acid sequence. We show that permutations in the charge pattern along the sequence remarkably alter the headgroup conformation and consequently alter the pH-triggered phase transitions between spherical, cylindrical micelles and hexagonal condensed phases. We demonstrate that even a single amino acid mutation is sufficient to tune structural transitions in the condensed IDPA mesophases, while peptide conformations remain unfolded and disordered. Furthermore, alteration of the peptide sequence can render IDPAs to become susceptible to enzymatic cleavage and induce enzymatically activated phase transitions. These results hold great potential for embedding multiple functionalities into lipid nanoparticle delivery systems by incorporating IDPAs with the desired properties.
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Affiliation(s)
- Tamara Ehm
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,Faculty
of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Shinar
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Guy Jacoby
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sagi Meir
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gil Koren
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Merav Segal Asher
- The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel,Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Joanna Korpanty
- Department
of Chemistry, International Institute for Nanotechnology, Chemistry
of Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew P. Thompson
- Department
of Chemistry, International Institute for Nanotechnology, Chemistry
of Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry, International Institute for Nanotechnology, Chemistry
of Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States,Department
of Materials Science & Engineering, Department of Biomedical Engineering
and Department of Pharmacology, Northwestern
University, Evanston, Illinois 60208, United States
| | - Michael M. Kozlov
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,Raymond
& Beverly Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Salome Azoulay-Ginsburg
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roey J. Amir
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel,Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel,The
ADAMA Center for Novel Delivery Systems in Crop Protection, Tel Aviv University, Tel Aviv 6997801, Israel,Email
| | - Joachim O. Rädler
- Faculty
of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany,
| | - Roy Beck
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel,The
Center for NanoTechnology & NanoScience, Tel Aviv University, Tel Aviv 6997801, Israel,
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9
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Foschi M, Padroni M, Abu-Rumeileh S, Abdelhak A, Russo M, D'Anna L, Guarino M. Diagnostic and Prognostic Blood Biomarkers in Transient Ischemic Attack and Minor Ischemic Stroke: An Up-To-Date Narrative Review. J Stroke Cerebrovasc Dis 2022; 31:106292. [PMID: 35026496 DOI: 10.1016/j.jstrokecerebrovasdis.2021.106292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Early diagnosis and correct risk stratification in patients with transient ischemic attack (TIA) and minor ischemic stroke (MIS) is crucial for the high rate of subsequent disabling stroke. Although highly improved, diagnosis and prognostication of TIA/MIS patients remain still based on clinical and neuroimaging findings, with some inter-rater variability even among trained neurologists. OBJECTIVES To provide an up-to-date overview of diagnostic and prognostic blood biomarkers in TIA and MIS patients. MATERIAL AND METHODS We performed a bibliographic search on PubMed database with last access on July 10th 2021. More than 680 articles were screened and we finally included only primary studies on blood biomarkers. RESULTS In a narrative fashion, we discussed about blood biomarkers investigated in TIA/MIS patients, including inflammatory, thrombosis, neuronal injury and cardiac analytes, antibodies and microRNAs. Other soluble molecules have been demonstrated to predict the risk of recurrent cerebrovascular events or treatment response in these patients. A rapid point of care assay, combining the determination of different biomarkers, has been developed to improve triage recognition of acute cerebrovascular accidents. CONCLUSIONS The implementation of blood biomarkers in the clinical management of TIA/MIS could ameliorate urgent identification, risk stratification and individual treatment choice. Large prospective and longitudinal studies, adopting standardized sampling and analytic procedures, are needed to clarify blood biomarkers kinetic and their relationship with TIA and minor stroke etiology.
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Affiliation(s)
- Matteo Foschi
- Department of Neuroscience, Neurology Unit, S. Maria delle Croci Hospital of Ravenna, AUSL Romagna, Ravenna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Marina Padroni
- Neurology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona, Ferrara, Italy
| | - Samir Abu-Rumeileh
- Department of Neurology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ahmed Abdelhak
- Department of Neurology, University of California San Francisco (UCSF), San Francisco, USA; Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Michele Russo
- Department of Cardiovascular Diseases, Division of Cardiology - S. Maria delle Croci Hospital, AUSL Romagna, Ravenna, Italy
| | - Lucio D'Anna
- Department of Stroke and Neuroscience, Charing Cross Hospital, Imperial College London, NHS Healthcare Trust, London, United Kingdom; Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Maria Guarino
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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10
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Hoffmann PC, Giandomenico SL, Ganeva I, Wozny MR, Sutcliffe M, Lancaster MA, Kukulski W. Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoids. eLife 2021; 10:e70269. [PMID: 34698018 PMCID: PMC8547956 DOI: 10.7554/elife.70269] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/08/2021] [Indexed: 12/17/2022] Open
Abstract
During brain development, axons must extend over great distances in a relatively short amount of time. How the subcellular architecture of the growing axon sustains the requirements for such rapid build-up of cellular constituents has remained elusive. Human axons have been particularly poorly accessible to imaging at high resolution in a near-native context. Here, we present a method that combines cryo-correlative light microscopy and electron tomography with human cerebral organoid technology to visualize growing axon tracts. Our data reveal a wealth of structural details on the arrangement of macromolecules, cytoskeletal components, and organelles in elongating axon shafts. In particular, the intricate shape of the endoplasmic reticulum is consistent with its role in fulfilling the high demand for lipid biosynthesis to support growth. Furthermore, the scarcity of ribosomes within the growing shaft suggests limited translational competence during expansion of this compartment. These findings establish our approach as a powerful resource for investigating the ultrastructure of defined neuronal compartments.
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Affiliation(s)
- Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
| | | | - Iva Ganeva
- MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
| | - Michael R Wozny
- MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
| | - Magdalena Sutcliffe
- MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Francis Crick AvenueCambridgeUnited Kingdom
- Institute of Biochemistry and Molecular Medicine, University of BernBernSwitzerland
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11
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Jacoby G, Segal Asher M, Ehm T, Abutbul Ionita I, Shinar H, Azoulay-Ginsburg S, Zemach I, Koren G, Danino D, Kozlov MM, Amir RJ, Beck R. Order from Disorder with Intrinsically Disordered Peptide Amphiphiles. J Am Chem Soc 2021; 143:11879-11888. [PMID: 34310121 PMCID: PMC8397319 DOI: 10.1021/jacs.1c06133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 01/02/2023]
Abstract
Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing demands for functional complexity have been met with challenges in biochemical engineering, driving researchers to innovate in the design of new amphiphiles. An emerging class of molecules, namely, peptide amphiphiles, combines key advantages and circumvents some of the disadvantages of conventional phospholipids and block copolymers. Herein, we present new peptide amphiphiles composed of an intrinsically disordered peptide conjugated to two variants of hydrophobic dendritic domains. These molecules, termed intrinsically disordered peptide amphiphiles (IDPA), exhibit a sharp pH-induced micellar phase-transition from low-dispersity spheres to extremely elongated worm-like micelles. We present an experimental characterization of the transition and propose a theoretical model to describe the pH-response. We also present the potential of the shape transition to serve as a mechanism for the design of a cargo hold-and-release application. Such amphiphilic systems demonstrate the power of tailoring the interactions between disordered peptides for various stimuli-responsive biomedical applications.
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Affiliation(s)
- Guy Jacoby
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Merav Segal Asher
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamara Ehm
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
- Faculty
of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, München D-80539, Germany
| | - Inbal Abutbul Ionita
- CryoEM
Laboratory of Soft Matter, Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Hila Shinar
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Salome Azoulay-Ginsburg
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ido Zemach
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Gil Koren
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Dganit Danino
- CryoEM
Laboratory of Soft Matter, Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Guangdong-Technion
Israel Institute of Technology, Shantou, Guangdong Province 515063, China
| | - Michael M. Kozlov
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Sackler School
of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roey J. Amir
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roy Beck
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
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12
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Bailey S, Sroga GE, Hoac B, Katsamenis OL, Wang Z, Bouropoulos N, McKee MD, Sørensen ES, Thurner PJ, Vashishth D. The role of extracellular matrix phosphorylation on energy dissipation in bone. eLife 2020; 9:58184. [PMID: 33295868 PMCID: PMC7746230 DOI: 10.7554/elife.58184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/07/2020] [Indexed: 01/22/2023] Open
Abstract
Protein phosphorylation, critical for cellular regulatory mechanisms, is implicated in various diseases. However, it remains unknown whether heterogeneity in phosphorylation of key structural proteins alters tissue integrity and organ function. Here, osteopontin phosphorylation level declined in hypo- and hyper- phosphatemia mouse models exhibiting skeletal deformities. Phosphorylation increased cohesion between osteopontin polymers, and adhesion of osteopontin to hydroxyapatite, enhancing energy dissipation. Fracture toughness, a measure of bone’s mechanical competence, increased with ex-vivo phosphorylation of wildtype mouse bones and declined with ex-vivo dephosphorylation. In osteopontin-deficient mice, global matrix phosphorylation level was not associated with toughness. Our findings suggest that phosphorylated osteopontin promotes fracture toughness in a dose-dependent manner through increased interfacial bond formation. In the absence of osteopontin, phosphorylation increases electrostatic repulsion, and likely protein alignment and interfilament distance leading to decreased fracture resistance. These mechanisms may be of importance in other connective tissues, and the key to unraveling cell–matrix interactions in diseases.
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Affiliation(s)
- Stacyann Bailey
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, United States
| | - Grazyna E Sroga
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, United States
| | - Betty Hoac
- Faculty of Dentistry, McGill University, Montreal, Canada
| | - Orestis L Katsamenis
- Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
| | - Zehai Wang
- Department of Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, United States
| | | | - Marc D McKee
- Faculty of Dentistry, McGill University, Montreal, Canada.,Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, Montreal, Canada
| | - Esben S Sørensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philipp J Thurner
- Institute of Lightweight Design and Structural Biomechanics, Vienna University of Technology, Vienna, Austria
| | - Deepak Vashishth
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, United States
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13
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Morgan IL, Avinery R, Rahamim G, Beck R, Saleh OA. Glassy Dynamics and Memory Effects in an Intrinsically Disordered Protein Construct. PHYSICAL REVIEW LETTERS 2020; 125:058001. [PMID: 32794838 DOI: 10.1103/physrevlett.125.058001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Glassy, nonexponential relaxations in globular proteins are typically attributed to conformational behaviors that are missing from intrinsically disordered proteins. Yet, we show that single molecules of a disordered-protein construct display two signatures of glassy dynamics, logarithmic relaxations and a Kovacs memory effect, in response to changes in applied tension. We attribute this to the presence of multiple independent local structures in the chain, which we corroborate with a model that correctly predicts the force dependence of the relaxation. The mechanism established here likely applies to other disordered proteins.
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Affiliation(s)
- Ian L Morgan
- BMSE Program, University of California, Santa Barbara, California 93106, USA
| | - Ram Avinery
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gil Rahamim
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roy Beck
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Omar A Saleh
- BMSE Program, University of California, Santa Barbara, California 93106, USA
- Materials Department, University of California, Santa Barbara, California 93106, USA
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14
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Chakraborty I, Rahamim G, Avinery R, Roichman Y, Beck R. Nanoparticle Mobility over a Surface as a Probe for Weak Transient Disordered Peptide-Peptide Interactions. NANO LETTERS 2019; 19:6524-6534. [PMID: 31456409 DOI: 10.1021/acs.nanolett.9b02764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Weak interactions form the core basis of a vast number of biological processes, in particular, those involving intrinsically disordered proteins. Here, we establish a new technique capable of probing these weak interactions between synthetic unfolded polypeptides using a convenient yet efficient, quantitative method based on single particle tracking of peptide-coated gold nanoparticles over peptide-coated surfaces. We demonstrate that our technique is sensitive enough to observe the influence of a single amino acid mutation on the transient peptide-peptide interactions. Furthermore, the effects of buffer salinity, which are expected to alter weak electrostatic interactions, are also readily detected and examined in detail. The method presented here has the potential to evaluate, in a high-throughput manner, weak interactions for a wide range of disordered proteins, polypeptides, and other biomolecules.
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Affiliation(s)
| | - Gil Rahamim
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Ram Avinery
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Yael Roichman
- School of Chemistry , Tel Aviv University , Tel Aviv 6997801 , Israel
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Roy Beck
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
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15
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Smith DW, Lee CJ, Morgan W, Gardiner BS. Estimating three-dimensional outflow and pressure gradients within the human eye. PLoS One 2019; 14:e0214961. [PMID: 30964894 PMCID: PMC6456205 DOI: 10.1371/journal.pone.0214961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/23/2019] [Indexed: 12/22/2022] Open
Abstract
In this paper we set the previously reported pressure-dependent, ordinary differential equation outflow model by Smith and Gardiner for the human eye, into a new three-dimensional (3D) porous media outflow model of the eye, and calibrate model parameters using data reported in the literature. Assuming normal outflow through anterior pathways, we test the ability of 3D flow model to predict the pressure elevation with a silicone oil tamponade. Then assuming outflow across the retinal pigment epithelium is normal, we test the ability of the 3D model to predict the pressure elevation in Schwartz-Matsuo syndrome. For the first time we find the flow model can successfully model both conditions, which helps to build confidence in the validity and accuracy of the 3D pressure-dependent outflow model proposed here. We employ this flow model to estimate the translaminar pressure gradient within the optic nerve head of a normal eye in both the upright and supine postures, and during the day and at night. Based on a ratio of estimated and measured pressure gradients, we define a factor of safety against acute interruption of axonal transport at the laminar cribrosa. Using a completely independent method, based on the behaviour of dynein molecular motors, we compute the factor of safety against stalling the dynein molecule motors, and so compromising retrograde axonal transport. We show these two independent methods for estimating factors of safety agree reasonably well and appear to be consistent. Taken together, the new 3D pressure-dependent outflow model proves itself to capable of providing a useful modeling platform for analyzing eye behaviour in a variety of physiological and clinically useful contexts, including IOP elevation in Schwartz-Matsuo syndrome and with silicone oil tamponade, and potentially for risk assessment for optic glaucomatous neuropathy.
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Affiliation(s)
- David W. Smith
- Faculty of Engineering and Mathematical Sciences, The University of Western Australia, Perth, Australia
- * E-mail:
| | - Chang-Joon Lee
- Faculty of Engineering and Mathematical Sciences, The University of Western Australia, Perth, Australia
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - William Morgan
- Lions Eye Institute, The University of Western Australia, Perth, Australia
| | - Bruce S. Gardiner
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
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16
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Lei R, Lee JP, Francis MB, Kumar S. Structural Regulation of a Neurofilament-Inspired Intrinsically Disordered Protein Brush by Multisite Phosphorylation. Biochemistry 2018; 57:4019-4028. [PMID: 29557644 DOI: 10.1021/acs.biochem.8b00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intrinsically disordered proteins (IDPs) play central roles in numerous cellular processes. While IDP structure and function are often regulated by multisite phosphorylation, the biophysical mechanisms linking these post-translational modifications to IDP structure remain elusive. For example, the intrinsically disordered C-terminal sidearm domain of the neurofilament heavy subunit (NFH-SA) forms a dense brush along axonal NF backbones and is subject to extensive serine phosphorylation. Yet, biophysical insight into the relationship between phosphorylation and structure has been limited by the lack of paradigms in which NF brush conformational responses can be measured in the setting of controlled phosphorylation. Here, we approach this question by immobilizing a recombinant NFH-SA (rNFH-SA) as IDP brushes onto glass, and controllably phosphorylating the sequence in situ with mitogen-activated protein kinase 1 (ERK2) preactivated by mitogen-activated protein kinase kinase (MKK). We then monitor brush height changes using atomic force microscopy, which shows that phosphorylation induces significant brush swelling to an extent that strongly depends upon pH and ionic strength, consistent with a mechanism in which phosphorylation regulates brush structure through local electrostatic interactions. Further consistent with this mechanism, the phosphorylated rNFH-SA brush may be dramatically condensed with micromolar concentrations of divalent cations. Phosphorylation-induced height changes are qualitatively reversible via alkaline phosphatase-mediated dephosphorylation. Our study demonstrates that multisite phosphorylation controls NFH-SA structure through modulation of chain electrostatics and points to a general strategy for engineering IDP-based interfaces that can be reversibly and dynamically modulated by enzymes.
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Affiliation(s)
| | | | - Matthew B Francis
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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17
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Uversky VN. Paradoxes and wonders of intrinsic disorder: Stability of instability. INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1327757. [PMID: 30250771 DOI: 10.1080/21690707.2017.1327757] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 01/03/2023]
Abstract
This article continues a series of short comments on the paradoxes and wonders of the protein intrinsic disorder phenomenon by introducing the "stability of instability" paradox. Intrinsically disordered proteins (IDPs) are characterized by the lack of stable 3D-structure, and, as a result, have an exceptional ability to sustain exposure to extremely harsh environmental conditions (an illustration of the "you cannot break what is already broken" principle). Extended IDPs are known to possess extreme thermal and acid stability and are able either to keep their functionality under these extreme conditions or to rapidly regain their functionality after returning to the normal conditions. Furthermore, sturdiness of intrinsic disorder and its capability to "ignore" harsh conditions provides some interesting and important advantages to its carriers, at the molecular (e.g., the cell wall-anchored accumulation-associated protein playing a crucial role in intercellular adhesion within the biofilm of Staphylococcus epidermidis), supramolecular (e.g., protein complexes, biologic liquid-liquid phase transitions, and proteinaceous membrane-less organelles), and organismal levels (e.g., the recently popularized case of the microscopic animals, tardigrades, or water bears, that use intrinsically disordered proteins to survive desiccation).
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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18
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Vohnoutka RB, Boumil EF, Liu Y, Uchida A, Pant HC, Shea TB. Influence of a GSK3β phosphorylation site within the proximal C-terminus of Neurofilament-H on neurofilament dynamics. Biol Open 2017; 6:1516-1527. [PMID: 28882840 PMCID: PMC5665472 DOI: 10.1242/bio.028522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation of the C-terminal tail of the heavy neurofilament subunit (NF-H) impacts neurofilament (NF) axonal transport and residence within axons by fostering NF-NF associations that compete with transport. We tested the role of phosphorylation of a GSK-3β consensus site (S493) located in the proximal portion of the NF-H tail in NF dynamics by transfection of NB2a/d1 cells with NF-H, where S493 was mutated to aspartic acid (S493D) or to alanine (S493A) to mimic constitutive phosphorylation and non-phosphorylation. S493D underwent increased transport into axonal neurites, while S493A displayed increased perikaryal NF aggregates that were decorated by anti-kinesin. Increased levels of S493A co-precipitated with anti-kinesin indicating that reduced transport of S493A was not due to reduced kinesin association but due to premature NF-NF interactions within perikarya. S493D displayed increased phospho-immunoreactivity within axonal neurites at downstream C-terminal sites attributable to mitogen-activated protein kinase and cyclin-dependent kinase 5. However, S493D was more prone to proteolysis following kinase inhibition, suggesting that S493 phosphorylation is an early event that alters sidearm configuration in a manner that promotes appropriate NF distribution. We propose a novel model for sidearm configuration. Summary: We demonstrate that phosphorylation of a critical site regulates neurofilament transport, proteolysis and interaction with other axonal cytoskeletal elements, and present evidence that it does so by altering protein conformation. This article has an associated First Person interview with the first author of the paper as part of the supplementary information.
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Affiliation(s)
| | - Edward F Boumil
- Laboratory for Neuroscience, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Yuguan Liu
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Atsuko Uchida
- Department of Neuroscience, Ohio State University, Columbus, OH 43210, USA
| | - Harish C Pant
- Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas B Shea
- Laboratory for Neuroscience, University of Massachusetts Lowell, Lowell, MA 01854, USA
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