1
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Le TP, Cavalcanti L, Tellam JP, Malo de Molina P. Effect of the Protein Chain Conformation on the Collapse into Nanoparticles. Biomacromolecules 2024. [PMID: 39228081 DOI: 10.1021/acs.biomac.4c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Protein single-chain nanoparticles can outperform synthetic nanoparticles in biomedical applications due to enhanced biocompatibility. Compared to synthetic (co)polymers, the chemical complexity of proteins challenges chain conformation control. Here, we investigate the impact of the precursor chain conformation of bovine serum albumin (BSA) on the nanoparticle structure after intramolecular cross-linking. We explore the urea concentration (denaturant), pH, salt, cross-linker length, and concentration. Small-angle neutron scattering and dynamic light scattering experiments reveal a shrinking chain conformation upon cross-linking. However, the ability to collapse depends on solvent conditions: more expanded chains collapse more, whereas proteins that are already compact barely change in size upon cross-linking. Static light scattering measurements demonstrate that binding is primarily intramolecular. The use of a shorter cross-linker does not lead to collapse of extended chains. Overall, BSA exhibits a similar behavior to that of polymer nanoparticles, which then allows to harness the precursor conformation for morphological control.
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Affiliation(s)
- Thu Phuong Le
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 Donostia, Spain
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología, University of the Basque Country (UPV/EHU), Paseo Manuel Lardizabal 3, E-20018 Donostia, Spain
| | - Leide Cavalcanti
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, U.K
| | - James P Tellam
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, U.K
| | - Paula Malo de Molina
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 Donostia, Spain
- IKERBASQUE─Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
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2
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Folimonova V, Chen X, Negi H, Schwieters CD, Li J, Byrd RA, Taylor N, Youkharibache P, Walters KJ. CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder. Commun Biol 2024; 7:1072. [PMID: 39217198 PMCID: PMC11365992 DOI: 10.1038/s42003-024-06770-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
T-cell therapies based on chimeric antigen receptor (CAR) targeting of a tumor-specific antigen offer hope for patients with relapsed or refractory cancers. CAR hinge and transmembrane regions link antigen recognition domains to intracellular signal transduction domains. Here, we apply biophysical methods to characterize the structure and dynamic properties of the CD28 CAR hinge (CD28H) used in an FDA-approved CD19 CAR for the treatment of B-lineage leukemia/lymphoma. By using nuclear Overhauser effect spectroscopy (NOESY), which detects even transiently occupied structural motifs, we observed otherwise elusive local structural elements amidst overall disorder in CD28H, including a conformational switch from a native β-strand to a 310-helix and polyproline II helix-like structure. These local structural motifs contribute to an overall loosely formed extended geometry that could be captured by NOESY data. All FDA-approved CARs use prolines in the hinge region, which we find in CD28, and previously in CD8α, isomerize to promote structural plasticity and dynamics. These local structural elements may function in recognition and signaling events and constrain the spacing between the transmembrane and antigen recognition domains. Our study thus demonstrates a method for detecting local and transient structure within intrinsically disordered systems and moreover, our CD28H findings may inform future CAR design.
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Affiliation(s)
- Varvara Folimonova
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Hitendra Negi
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jess Li
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - R Andrew Byrd
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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3
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Hu G, Song H, Chen X, Li J. Wet Conformation of Prion-Like Domain and Intimate Correlation of Hydration and Conformational Fluctuations. J Phys Chem Lett 2024; 15:8315-8325. [PMID: 39109535 DOI: 10.1021/acs.jpclett.4c01476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Proteins with prion-like domains (PLDs) are involved in neurodegeneration-associated aggregation and are prevalent in liquid-like membrane-less organelles. These PLDs contain amyloidogenic stretches but can maintain dynamic disordered conformations, even in the condensed phase. However, the molecular mechanism underlying such intricate conformational properties of PLDs remains elusive. Here we employed molecular dynamics simulations to investigate the conformational properties of a prototypical PLD system (i.e., FUS PLD). According to our simulation results, PLD adopts a wet collapsed conformation, wherein most residues maintain sufficient hydration with the abundance of internal water. These internal water molecules can rapidly exchange between the protein interior and the bulk, enabling intensive coupling of the entire protein with its hydration environment. The dynamic exchange of water molecules is intimately correlated to the overall conformational fluctuations of PLD. Furthermore, the abundance of dynamic internal water suppresses the formation of aggregation-prone ordered structures. These results collectively elucidate the crucial role of internal water in sustaining the dynamic disordered conformation of the PLD and inhibiting its aggregation propensity.
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Affiliation(s)
- Guorong Hu
- School of Physics, Zhejiang University, Hangzhou 310058, China
| | - Haoyu Song
- School of Physics, Zhejiang University, Hangzhou 310058, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jingyuan Li
- School of Physics, Zhejiang University, Hangzhou 310058, China
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4
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Boushehri S, Holey H, Brosz M, Gumbsch P, Pastewka L, Aponte-Santamaría C, Gräter F. O-glycans Expand Lubricin and Attenuate Its Viscosity and Shear Thinning. Biomacromolecules 2024; 25:3893-3908. [PMID: 38815979 PMCID: PMC11238335 DOI: 10.1021/acs.biomac.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/01/2024]
Abstract
Lubricin, an intrinsically disordered glycoprotein, plays a pivotal role in facilitating smooth movement and ensuring the enduring functionality of synovial joints. The central domain of this protein serves as a source of this excellent lubrication and is characterized by its highly glycosylated, negatively charged, and disordered structure. However, the influence of O-glycans on the viscosity of lubricin remains unclear. In this study, we employ molecular dynamics simulations in the absence and presence of shear, along with continuum simulations, to elucidate the intricate interplay between O-glycans and lubricin and the impact of O-glycans on lubricin's conformational properties and viscosity. We found the presence of O-glycans to induce a more extended conformation in fragments of the disordered region of lubricin. These O-glycans contribute to a reduction in solution viscosity but at the same time weaken shear thinning at high shear rates, compared to nonglycosylated systems with the same density. This effect is attributed to the steric and electrostatic repulsion between the fragments, which prevents their conglomeration and structuring. Our computational study yields a mechanistic mechanism underlying previous experimental observations of lubricin and paves the way to a more rational understanding of its function in the synovial fluid.
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Affiliation(s)
- Saber Boushehri
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Hannes Holey
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
- Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, Freiburg 79110, Germany
| | - Matthias Brosz
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
| | - Peter Gumbsch
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
- Fraunhofer IWM, Wöhlerstraße 11, Freiburg 79108, Germany
| | - Lars Pastewka
- Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, Freiburg 79110, Germany
| | - Camilo Aponte-Santamaría
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
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5
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Korkola NC, Stillman MJ. Human apo-metallothionein 1a is not a random coil: Evidence from guanidinium chloride, high temperature, and acidic pH unfolding studies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141010. [PMID: 38490456 DOI: 10.1016/j.bbapap.2024.141010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
The structures of apo-metallothioneins (apo-MTs) have been relatively elusive due to their fluxional, disordered state which has been difficult to characterize. However, intrinsically disordered protein (IDP) structures are rather diverse, which raises questions about where the structure of apo-MTs fit into the protein structural spectrum. In this paper, the unfolding transitions of apo-MT1a are discussed with respect to the effect of the chemical denaturant GdmCl, temperature conditions, and pH environment. Cysteine modification in combination with electrospray ionization mass spectrometry was used to probe the unfolding transition of apo-MT1a in terms of cysteine exposure. Circular dichroism spectroscopy was also used to monitor the change in secondary structure as a function of GdmCl concentration. For both of these techniques, cooperative unfolding was observed, suggesting that apo-MT1a is not a random coil. More GdmCl was required to unfold the protein backbone than to expose the cysteines, indicating that cysteine exposure is likely an early step in the unfolding of apo-MT1a. MD simulations complement the experimental results, suggesting that apo-MT1a adopts a more compact structure than expected for a random coil. Overall, these results provide further insight into the intrinsically disordered structure of apo-MT.
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Affiliation(s)
- Natalie C Korkola
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada.
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6
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Somarathne RP, Amarasekara DL, Kariyawasam CS, Robertson HA, Mayatt R, Gwaltney SR, Fitzkee NC. Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305684. [PMID: 38247186 PMCID: PMC11209821 DOI: 10.1002/smll.202305684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/03/2024] [Indexed: 01/23/2024]
Abstract
Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle's interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, a model is developed for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, it is found that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, supports a highly solvated, disordered protein corona anchored at a small number of attachment sites. The scaling of the stoichiometry versus nanoparticle size is consistent with disordered polymer dimensions. Moreover, it is found that proteins are destabilized less in the presence of larger nanoparticles, and hydrophobic exposure decreases at lower curvatures. The observations hold for proteins on flat polystyrene surfaces, which have the lowest hydrophobic exposure. The model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Dhanush L Amarasekara
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Harley A Robertson
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Railey Mayatt
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Steven R Gwaltney
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
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7
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Janson G, Feig M. Transferable deep generative modeling of intrinsically disordered protein conformations. PLoS Comput Biol 2024; 20:e1012144. [PMID: 38781245 PMCID: PMC11152266 DOI: 10.1371/journal.pcbi.1012144] [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: 02/08/2024] [Revised: 06/05/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. Molecular simulations are a valuable computational strategy for constructing structural ensembles of disordered proteins but are highly resource-intensive. Recently, machine learning approaches based on deep generative models that learn from simulation data have emerged as an efficient alternative for generating structural ensembles. However, such methods currently suffer from limited transferability when modeling sequences and conformations absent in the training data. Here, we develop a novel generative model that achieves high levels of transferability for intrinsically disordered protein ensembles. The approach, named idpSAM, is a latent diffusion model based on transformer neural networks. It combines an autoencoder to learn a representation of protein geometry and a diffusion model to sample novel conformations in the encoded space. IdpSAM was trained on a large dataset of simulations of disordered protein regions performed with the ABSINTH implicit solvent model. Thanks to the expressiveness of its neural networks and its training stability, idpSAM faithfully captures 3D structural ensembles of test sequences with no similarity in the training set. Our study also demonstrates the potential for generating full conformational ensembles from datasets with limited sampling and underscores the importance of training set size for generalization. We believe that idpSAM represents a significant progress in transferable protein ensemble modeling through machine learning.
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Affiliation(s)
- Giacomo Janson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
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8
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Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR. How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Sci 2024; 33:e4986. [PMID: 38607226 PMCID: PMC11010952 DOI: 10.1002/pro.4986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
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Affiliation(s)
- Michael C. Baxa
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Xiaoxuan Lin
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Cedrick D. Mukinay
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team (BioCAT), Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical SciencesIllinois Institute of TechnologyChicagoIllinoisUSA
- Present address:
Cytiva, Fast TrakMarlboroughMAUSA
| | | | - Sarah Antilla
- Department of Materials Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Nina Hartrampf
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
Department of ChemistryUniversity of ZurichSwitzerland
| | - Joshua A. Riback
- Graduate Program in Biophysical ScienceUniversity of ChicagoChicagoIllinoisUSA
- Present address:
Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
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9
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Singleton MD, Eisen MB. Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation. PLoS Comput Biol 2024; 20:e1012028. [PMID: 38662765 PMCID: PMC11075841 DOI: 10.1371/journal.pcbi.1012028] [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: 01/08/2024] [Revised: 05/07/2024] [Accepted: 03/28/2024] [Indexed: 05/08/2024] Open
Abstract
Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite the prevalence and importance of IDRs in eukaryotic proteomes and various biological processes, associating them with specific molecular functions remains a significant challenge due to their high rates of sequence evolution. However, by comparing the observed values of various IDR-associated properties against those generated under a simulated model of evolution, a recent study found most IDRs across the entire yeast proteome contain conserved features. Furthermore, it showed clusters of IDRs with common "evolutionary signatures," i.e. patterns of conserved features, were associated with specific biological functions. To determine if similar patterns of conservation are found in the IDRs of other systems, in this work we applied a series of phylogenetic models to over 7,500 orthologous IDRs identified in the Drosophila genome to dissect the forces driving their evolution. By comparing models of constrained and unconstrained continuous trait evolution using the Brownian motion and Ornstein-Uhlenbeck models, respectively, we identified signals of widespread constraint, indicating conservation of distributed features is mechanism of IDR evolution common to multiple biological systems. In contrast to the previous study in yeast, however, we observed limited evidence of IDR clusters with specific biological functions, which suggests a more complex relationship between evolutionary constraints and function in the IDRs of multicellular organisms.
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Affiliation(s)
- Marc D. Singleton
- Howard Hughes Medical Institute, UC Berkeley, Berkeley, California, United States of America
| | - Michael B. Eisen
- Howard Hughes Medical Institute, UC Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, California, United States of America
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10
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The Molecular Architecture of the Nuclear Basket. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587068. [PMID: 38586009 PMCID: PMC10996695 DOI: 10.1101/2024.03.27.587068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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11
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Kohl PA, Song C, Fletcher BJ, Best RL, Tchounwou C, Garcia Arceo X, Chung PJ, Miller HP, Wilson L, Choi MC, Li Y, Feinstein SC, Safinya CR. Complexes of tubulin oligomers and tau form a viscoelastic intervening network cross-bridging microtubules into bundles. Nat Commun 2024; 15:2362. [PMID: 38491006 PMCID: PMC10943092 DOI: 10.1038/s41467-024-46438-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
The axon-initial-segment (AIS) of mature neurons contains microtubule (MT) fascicles (linear bundles) implicated as retrograde diffusion barriers in the retention of MT-associated protein (MAP) tau inside axons. Tau dysfunction and leakage outside of the axon is associated with neurodegeneration. We report on the structure of steady-state MT bundles in varying concentrations of Mg2+ or Ca2+ divalent cations in mixtures containing αβ-tubulin, full-length tau, and GTP at 37 °C in a physiological buffer. A concentration-time kinetic phase diagram generated by synchrotron SAXS reveals a wide-spacing MT bundle phase (Bws), a transient intermediate MT bundle phase (Bint), and a tubulin ring phase. SAXS with TEM of plastic-embedded samples provides evidence of a viscoelastic intervening network (IN) of complexes of tubulin oligomers and tau stabilizing MT bundles. In this model, αβ-tubulin oligomers in the IN are crosslinked by tau's MT binding repeats, which also link αβ-tubulin oligomers to αβ-tubulin within the MT lattice. The model challenges whether the cross-bridging of MTs is attributed entirely to MAPs. Tubulin-tau complexes in the IN or bound to isolated MTs are potential sites for enzymatic modification of tau, promoting nucleation and growth of tau fibrils in tauopathies.
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Affiliation(s)
- Phillip A Kohl
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Chaeyeon Song
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Amorepacific R&I Center, Yongin, 17074, Republic of Korea
| | - Bretton J Fletcher
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Rebecca L Best
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
| | - Christine Tchounwou
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Ximena Garcia Arceo
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, 93106, USA
| | - Peter J Chung
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Herbert P Miller
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Leslie Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon, 34141, Korea
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
| | - Stuart C Feinstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Cyrus R Safinya
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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12
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Pasani S, Menon KS, Viswanath S. The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.13.544884. [PMID: 37398295 PMCID: PMC10312763 DOI: 10.1101/2023.06.13.544884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Desmosomes mediate cell-cell adhesion and are prevalent in tissues under mechanical stress. However, their detailed structural characterization is not available. Here, we characterized the molecular architecture of the desmosomal outer dense plaque (ODP) using Bayesian integrative structural modeling via the Integrative Modeling Platform. Starting principally from the structural interpretation of an electron cryo-tomogram, we integrated information from X-ray crystallography, an immuno-electron microscopy study, biochemical assays, in-silico predictions of transmembrane and disordered regions, homology modeling, and stereochemistry information. The integrative structure was validated by information from imaging, tomography, and biochemical studies that were not used in modeling. The ODP resembles a densely packed cylinder with a PKP layer and a PG layer; the desmosomal cadherins and PKP span these two layers. Our integrative approach allowed us to localize disordered regions, such as N-PKP and PG-C. We refined previous protein-protein interactions between desmosomal proteins and provided possible structural hypotheses for defective cell-cell adhesion in several diseases by mapping disease-related mutations on the structure. Finally, we point to features of the structure that could confer resilience to mechanical stress. Our model provides a basis for generating experimentally verifiable hypotheses on the structure and function of desmosomal proteins in normal and disease states.
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Affiliation(s)
- Satwik Pasani
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Kavya S Menon
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shruthi Viswanath
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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13
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Janson G, Feig M. Transferable deep generative modeling of intrinsically disordered protein conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579522. [PMID: 38370653 PMCID: PMC10871340 DOI: 10.1101/2024.02.08.579522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. Molecular simulations are a valuable computational strategy for constructing structural ensembles of disordered proteins but are highly resource-intensive. Recently, machine learning approaches based on deep generative models that learn from simulation data have emerged as an efficient alternative for generating structural ensembles. However, such methods currently suffer from limited transferability when modeling sequences and conformations absent in the training data. Here, we develop a novel generative model that achieves high levels of transferability for intrinsically disordered protein ensembles. The approach, named idpSAM, is a latent diffusion model based on transformer neural networks. It combines an autoencoder to learn a representation of protein geometry and a diffusion model to sample novel conformations in the encoded space. IdpSAM was trained on a large dataset of simulations of disordered protein regions performed with the ABSINTH implicit solvent model. Thanks to the expressiveness of its neural networks and its training stability, idpSAM faithfully captures 3D structural ensembles of test sequences with no similarity in the training set. Our study also demonstrates the potential for generating full conformational ensembles from datasets with limited sampling and underscores the importance of training set size for generalization. We believe that idpSAM represents a significant progress in transferable protein ensemble modeling through machine learning.
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Affiliation(s)
- Giacomo Janson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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14
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Sauciuc A, Whittaker J, Tadema M, Tych K, Guskov A, Maglia G. Unravelled proteins form blobs during translocation across nanopores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576815. [PMID: 38328101 PMCID: PMC10849628 DOI: 10.1101/2024.01.23.576815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The electroosmotic-driven transport of unravelled proteins across nanopores is an important biological process that is now under investigation for the rapid analysis and sequencing of proteins. For this approach to work, however, it is crucial that the polymer is threaded in single file. Here we found that, contrary to the electrophoretic transport of charged polymers such as DNA, during polypeptide translocation blob-like structures typically form inside nanopores. Comparisons between different nanopore sizes, shapes and surface chemistries showed that under electroosmotic-dominated regimes single-file transport of polypeptides can be achieved using nanopores that simultaneously have an entry and an internal diameter that is smaller than the persistence length of the polymer, have a uniform non-sticky ( i . e . non-aromatic) nanopore inner surface, and using moderate translocation velocities.
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15
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Sheng Q, Intoy BF, Halley JW. Effects of Activation Barriers on Quenching to Stabilize Prebiotic Chemical Systems. Life (Basel) 2024; 14:116. [PMID: 38255731 PMCID: PMC11232558 DOI: 10.3390/life14010116] [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: 12/04/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries with some lifelike properties. We suggested that such quenching processes might have occurred at very high rates on early Earth, giving an efficient mechanism for natural sorting through enormous numbers of nonequilibrium chemistries from which the most lifelike ones could be naturally selected. However, the model used for these studies did not take account of activation barriers to polymer scission (peptide bond hydrolysis in the case of proteins). Such barriers are known to exist and are expected to enhance the quenching effect. Here, we introduce a modified model which takes activation barriers into account and we compare the results to data from experiments on quenched systems of amino acids. We find that the model results turn out to be sensitive to the width of the distribution of barrier heights but quite insensitive to its average value. The results of the new model are in significantly better agreement with the experiments than those found using our previous model. The new parametrization of the model only requires one new parameter and the parametrization is more physical than the previous one, providing a chemical interpretation of the parameter p in our previous models. Within the model, a characteristic temperature Tc emerges such that if the temperature of the hot stage is above Tc and the temperature of the cold stage is below it, then the 'freezing out', in a quench, of a disequilibrium ensemble of long polymers is expected. We discuss the possible relevance of this to models of the origin of life in emissions from deep ocean rifts.
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Affiliation(s)
| | | | - J. W. Halley
- School of Physics and Astronomy, University of Minnesota-Twin
Cities, Minneapolis, MN 55455, USA (B.F.I.)
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16
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Martinez-Yamout MA, Nasir I, Shnitkind S, Ellis JP, Berlow RB, Kroon G, Deniz AA, Dyson HJ, Wright PE. Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2313835120. [PMID: 37971402 PMCID: PMC10666024 DOI: 10.1073/pnas.2313835120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREBTAD) construct. The CREBTAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. Our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.
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Affiliation(s)
- Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Irem Nasir
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jamie P. Ellis
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Rebecca B. Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard Kroon
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
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17
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Rusbjerg-Weberskov C, Johansen ML, Nowak JS, Otzen DE, Pedersen JS, Enghild JJ, Nielsen NS. Periostin C-Terminal Is Intrinsically Disordered and Interacts with 143 Proteins in an In Vitro Epidermal Model of Atopic Dermatitis. Biochemistry 2023; 62:2803-2815. [PMID: 37704583 PMCID: PMC10552548 DOI: 10.1021/acs.biochem.3c00176] [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: 03/31/2023] [Revised: 07/18/2023] [Indexed: 09/15/2023]
Abstract
Human periostin is a 78-91 kDa matricellular protein implicated in extracellular matrix remodeling, tumor development, metastasis, and inflammatory diseases like atopic dermatitis, psoriasis, and asthma. The protein consists of six domains, including an N-terminal Cys-rich CROPT domain, four fasciclin-1 domains, and a C-terminal domain. The exons encoding the C-terminal domain may be alternatively spliced by shuffling four exons, generating ten variants of unknown function. Here, we investigate the structure and interactome of the full-length variant of the C-terminal domain with no exons spliced out. The structural analysis showed that the C-terminal domain lacked a tertiary structure and was intrinsically disordered. In addition, we show that the motif responsible for heparin-binding is in the conserved very C-terminal part of periostin. Pull-down confirmed three known interaction partners and identified an additional 140 proteins, among which nine previously have been implicated in atopic dermatitis. Based on our findings, we suggest that the C-terminal domain of periostin facilitates interactions between connective tissue components in concert with the four fasciclin domains.
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Affiliation(s)
| | - Mette Liere Johansen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
| | - Jan S. Nowak
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Daniel E. Otzen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Jan Skov Pedersen
- Department
of Chemistry, Aarhus University, Aarhus C 8000, Denmark
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus C 8000, Denmark
| | - Jan J. Enghild
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
| | - Nadia Sukusu Nielsen
- Department
of Molecular Biology and Genetics, Aarhus
University, Aarhus
C 8000, Denmark
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18
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Ramans-Harborough S, Kalverda AP, Manfield IW, Thompson GS, Kieffer M, Uzunova V, Quareshy M, Prusinska JM, Roychoudhry S, Hayashi KI, Napier R, del Genio C, Kepinski S. Intrinsic disorder and conformational coexistence in auxin coreceptors. Proc Natl Acad Sci U S A 2023; 120:e2221286120. [PMID: 37756337 PMCID: PMC10556615 DOI: 10.1073/pnas.2221286120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/17/2023] [Indexed: 09/29/2023] Open
Abstract
AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) transcriptional repressor proteins and the TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB) proteins to which they bind act as auxin coreceptors. While the structure of TIR1 has been solved, structural characterization of the regions of the Aux/IAA protein responsible for auxin perception has been complicated by their predicted disorder. Here, we use NMR, CD and molecular dynamics simulation to investigate the N-terminal domains of the Aux/IAA protein IAA17/AXR3. We show that despite the conformational flexibility of the region, a critical W-P bond in the core of the Aux/IAA degron motif occurs at a strikingly high (1:1) ratio of cis to trans isomers, consistent with the requirement of the cis conformer for the formation of the fully-docked receptor complex. We show that the N-terminal half of AXR3 is a mixture of multiple transiently structured conformations with a propensity for two predominant and distinct conformational subpopulations within the overall ensemble. These two states were modeled together with the C-terminal PB1 domain to provide the first complete simulation of an Aux/IAA. Using MD to recreate the assembly of each complex in the presence of auxin, both structural arrangements were shown to engage with the TIR1 receptor, and contact maps from the simulations match closely observations of NMR signal-decreases. Together, our results and approach provide a platform for exploring the functional significance of variation in the Aux/IAA coreceptor family and for understanding the role of intrinsic disorder in auxin signal transduction and other signaling systems.
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Affiliation(s)
- Sigurd Ramans-Harborough
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Arnout P. Kalverda
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Iain W. Manfield
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Gary S. Thompson
- Wellcome Biological Nuclear Magnetic Resonance Facility, Division of Natural Sciences, University of Kent, CanterburyCT2 7NJ, United Kingdom
| | - Martin Kieffer
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Veselina Uzunova
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | | | - Suruchi Roychoudhry
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Ken-ichiro Hayashi
- Department of Bioscience, Okayama University of Science, Okayama700-0005, Japan
| | - Richard Napier
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Charo del Genio
- Centre for Fluid and Complex Systems, Coventry University, CoventryCV1 5FB, United Kingdom
| | - Stefan Kepinski
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
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19
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Wilson C, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level. Protein Sci 2023; 32:e4756. [PMID: 37574757 PMCID: PMC10464302 DOI: 10.1002/pro.4756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We have developed an algorithm, ParSe, which accurately identifies from the primary sequence those protein regions likely to exhibit physiological phase separation behavior. Originally, ParSe was designed to test the hypothesis that, for flexible proteins, phase separation potential is correlated to hydrodynamic size. While our results were consistent with that idea, we also found that many different descriptors could successfully differentiate between three classes of protein regions: folded, intrinsically disordered, and phase-separating intrinsically disordered. Consequently, numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. Built from that finding, ParSe 2.0 uses an optimal set of property scales to predict domain-level organization and compute a sequence-based prediction of phase separation potential. The algorithm is fast enough to scan the whole of the human proteome in minutes on a single computer and is equally or more accurate than other published predictors in identifying proteins and regions within proteins that drive phase separation. Here, we describe a web application for ParSe 2.0 that may be accessed through a browser by visiting https://stevewhitten.github.io/Parse_v2_FASTA to quickly identify phase-separating proteins within large sequence sets, or by visiting https://stevewhitten.github.io/Parse_v2_web to evaluate individual protein sequences.
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Affiliation(s)
- Colorado Wilson
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
- Present address:
Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular BiophysicsUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Karen A. Lewis
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
| | - Nicholas C. Fitzkee
- Department of ChemistryMississippi State UniversityMississippi StateMississippiUSA
| | - Loren E. Hough
- Department of PhysicsUniversity of Colorado BoulderBoulderColoradoUSA
- BioFrontiers InstituteUniversity of Colorado BoulderBoulderColoradoUSA
| | - Steven T. Whitten
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
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20
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Rasmussen HØ, Nielsen J, de Poli A, Otzen DE, Pedersen JS. Tau Fibrillation Induced by Heparin or a Lysophospholipid Show Different Initial Oligomer Formation. J Mol Biol 2023; 435:168194. [PMID: 37437877 DOI: 10.1016/j.jmb.2023.168194] [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: 04/18/2023] [Revised: 06/18/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
The protein tau is involved in several neurogenerative diseases such as Alzheimer's Disease, where tau content and fibrillation have been linked to disease progression. Tau colocalizes with phospholipids and glycosaminoglycans in vivo. We investigated if and how tau fibrillation can be induced by two lysophospholipids, namely the zwitterionic 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC) and the anionic 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) (LPG) as well as the glycosaminoglycan heparin. We used a range of biophysical techniques including small-angle X-ray scattering, Thioflavin T fluorescence, and SDS-PAGE, collecting data at various time points to obtain structural information on each phase of the fibrillation. We find that LPC does not induce fibrillation or interact with tau. Low concentrations of LPG induce fibrillation by formation of small hydrophobic clusters with monomeric tau. At higher LPG concentrations, a core-shell complex is formed where tau wraps around LPG micelles with regions extending away from the micelles. For heparin, loosely associated oligomers are formed rapidly with around ten tau molecules. Fibrils formed with either LPG or heparin show similar final cross-section dimensions. Furthermore, SDS-resistant oligomers are observed for both LPG and heparin. Our study demonstrates that tau fibrillation can be induced by two different biologically relevant cofactors leading to structurally different initial states but similar cross-sectional dimensions for the fibrils. Structural information about initial states prior to fibril formation is important both to gain a better understanding of the onset of fibrillation in vivo, and for the development of targeted drugs that can reduce or abolish tau fibrillation.
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Affiliation(s)
- Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Angela de Poli
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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21
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Cho H, Lee J, Nho H, Lee K, Gim B, Lee J, Lee J, Ewert KK, Li Y, Feinstein SC, Safinya CR, Jin KS, Choi MC. Synchrotron X-ray study of intrinsically disordered and polyampholytic Tau 4RS and 4RL under controlled ionic strength. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:73. [PMID: 37653246 DOI: 10.1140/epje/s10189-023-00328-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Aggregated and hyperphosphorylated Tau is one of the pathological hallmarks of Alzheimer's disease. Tau is a polyampholytic and intrinsically disordered protein (IDP). In this paper, we present for the first time experimental results on the ionic strength dependence of the radius of gyration (Rg) of human Tau 4RS and 4RL isoforms. Synchrotron X-ray scattering revealed that 4RS Rg is regulated from 65.4 to 58.5 Å and 4RL Rg is regulated from 70.9 to 57.9 Å by varying ionic strength from 0.01 to 0.592 M. The Rg of 4RL Tau is larger than 4RS at lower ionic strength. This result provides an insight into the ion-responsive nature of intrinsically disordered and polyampholytic Tau, and can be implicated to the further study of Tau-Tau and Tau-tubulin intermolecular structure in ionic environments.
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Affiliation(s)
- Hasaeam Cho
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Jimin Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Hanjoon Nho
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Keunmin Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Bopil Gim
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Juncheol Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Jaehee Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Kai K Ewert
- Materials Department, Molecular, Cellular, and Developmental Biology Department, Physics Department, and Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA, 93106, USA
| | - Stuart C Feinstein
- Molecular, Cellular, and Developmental Biology Department, College of Creative Studies Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Cyrus R Safinya
- Materials Department, Molecular, Cellular, and Developmental Biology Department, Physics Department, and Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106, USA
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
- Division of Advanced Nuclear Engineering, POSTECH, Pohang, 37673, Korea
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea.
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22
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [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: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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23
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Carlsson A, Olsson U, Linse S. On the micelle formation of DNAJB6b. QRB DISCOVERY 2023; 4:e6. [PMID: 37593255 PMCID: PMC10427797 DOI: 10.1017/qrd.2023.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 08/19/2023] Open
Abstract
The human chaperone DNAJB6b increases the solubility of proteins involved in protein aggregation diseases and suppresses the nucleation of amyloid structures. Due to such favourable properties, DNAJB6b has gained increasing attention over the past decade. The understanding of how DNAJB6b operates on a molecular level may aid the design of inhibitors against amyloid formation. In this work, fundamental aspects of DNAJB6b self-assembly have been examined, providing a basis for future experimental designs and conclusions. The results imply the formation of large chaperone clusters in a concentration-dependent manner. Microfluidic diffusional sizing (MDS) was used to evaluate how DNAJB6b average hydrodynamic radius varies with concentration. We found that, in 20 mM sodium phosphate buffer, 0.2 mM EDTA, at pH 8.0 and room temperature, DNAJB6b displays a micellar behaviour, with a critical micelle concentration (CMC) of around 120 nM. The average hydrodynamic radius appears to be concentration independent between ∼10 μM and 100 μM, with a mean radius of about 12 nm. The CMC found by MDS is supported by native agarose gel electrophoresis and the size distribution appears bimodal in the DNAJB6b concentration range ∼100 nM to 4 μM.
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Affiliation(s)
- Andreas Carlsson
- Biochemistry and Structural Biology, Chemical Centre, Lund University, Lund, Sweden
| | - Ulf Olsson
- Physical Chemistry, Chemical Centre, Lund University, Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Chemical Centre, Lund University, Lund, Sweden
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24
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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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25
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Somarathne RP, Amarasekara DL, Kariyawasam CS, Robertson HA, Mayatt R, Fitzkee NC. Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548033. [PMID: 37461509 PMCID: PMC10350082 DOI: 10.1101/2023.07.06.548033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle's interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, using a comprehensive thermodynamic approach, along with supporting spectroscopic experiments, we develop a model for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, we find that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, support a highly solvated, disordered protein corona anchored at a small number of enthalpically-driven attachment sites. The scaling of the stoichiometry vs. nanoparticle size is consistent disordered polymer dimensions. Moreover, we find that proteins are destabilized less severely in the presence of larger nanoparticles, and this is supported by measurements of hydrophobic exposure, which becomes less pronounced at lower curvatures. Our observations hold for flat polystyrene surfaces, which, when controlled for total surface area, have the lowest hydrophobic exposure of all systems. Our model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.
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Affiliation(s)
- Radha P. Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | | | | | - Harley A. Robertson
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | - Railey Mayatt
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
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26
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins. J Phys Chem B 2023; 127:4746-4760. [PMID: 37200094 PMCID: PMC10875986 DOI: 10.1021/acs.jpcb.3c01619] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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27
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Paladino A, Vitagliano L, Graziano G. The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins. BIOLOGY 2023; 12:biology12050754. [PMID: 37237566 DOI: 10.3390/biology12050754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.
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Affiliation(s)
- Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, 82100 Benevento, Italy
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28
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Yu M, Heidari M, Mikhaleva S, Tan PS, Mingu S, Ruan H, Reinkemeier CD, Obarska-Kosinska A, Siggel M, Beck M, Hummer G, Lemke EA. Visualizing the disordered nuclear transport machinery in situ. Nature 2023; 617:162-169. [PMID: 37100914 PMCID: PMC10156602 DOI: 10.1038/s41586-023-05990-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
The approximately 120 MDa mammalian nuclear pore complex (NPC) acts as a gatekeeper for the transport between the nucleus and cytosol1. The central channel of the NPC is filled with hundreds of intrinsically disordered proteins (IDPs) called FG-nucleoporins (FG-NUPs)2,3. Although the structure of the NPC scaffold has been resolved in remarkable detail, the actual transport machinery built up by FG-NUPs-about 50 MDa-is depicted as an approximately 60-nm hole in even highly resolved tomograms and/or structures computed with artificial intelligence4-11. Here we directly probed conformations of the vital FG-NUP98 inside NPCs in live cells and in permeabilized cells with an intact transport machinery by using a synthetic biology-enabled site-specific small-molecule labelling approach paired with highly time-resolved fluorescence microscopy. Single permeabilized cell measurements of the distance distribution of FG-NUP98 segments combined with coarse-grained molecular simulations of the NPC allowed us to map the uncharted molecular environment inside the nanosized transport channel. We determined that the channel provides-in the terminology of the Flory polymer theory12-a 'good solvent' environment. This enables the FG domain to adopt expanded conformations and thus control transport between the nucleus and cytoplasm. With more than 30% of the proteome being formed from IDPs, our study opens a window into resolving disorder-function relationships of IDPs in situ, which are important in various processes, such as cellular signalling, phase separation, ageing and viral entry.
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Affiliation(s)
- Miao Yu
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maziar Heidari
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Sofya Mikhaleva
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Piau Siong Tan
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sara Mingu
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
| | - Hao Ruan
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
| | - Christopher D Reinkemeier
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology Mainz, Mainz, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Marc Siggel
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Molecular Biology Mainz, Mainz, Germany.
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29
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Eickhoff L, Keßler M, Stubbs C, Derksen J, Viefhues M, Anselmetti D, Gibson MI, Hoge B, Koop T. Ice nucleation in aqueous solutions of short- and long-chain poly(vinyl alcohol) studied with a droplet microfluidics setup. J Chem Phys 2023; 158:2882248. [PMID: 37093996 DOI: 10.1063/5.0136192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/22/2023] [Indexed: 04/26/2023] Open
Abstract
Poly(vinyl alcohol) (PVA) has ice binding and ice nucleating properties. Here, we explore the dependence of the molecular size of PVA on its ice nucleation activity. For this purpose, we studied ice nucleation in aqueous solutions of PVA samples with molar masses ranging from 370 to 145 000 g mol-1, with a particular focus on oligomer samples with low molar mass. The experiments employed a novel microfluidic setup that is a follow-up on the previous WeIzmann Supercooled Droplets Observation on a Microarray (WISDOM) design by Reicher et al. The modified setup introduced and characterized here, termed nanoliter Bielefeld Ice Nucleation ARraY (nanoBINARY), uses droplet microfluidics with droplets (96 ± 4) µm in diameter and a fluorinated continuous oil phase and surfactant. A comparison of homogeneous and heterogeneous ice nucleation data obtained with nanoBINARY to those obtained with WISDOM shows very good agreement, underpinning its ability to study low-temperature ice nucleators as well as homogeneous ice nucleation due to the low background of impurities. The experiments on aqueous PVA solutions revealed that the ice nucleation activity of shorter PVA chains strongly decreases with a decrease in molar mass. While the cumulative number of ice nucleating sites per mass nm of polymers with different molar masses is the same, it becomes smaller for oligomers and completely vanishes for dimer and monomer representatives such as 1,3-butanediol, propan-2-ol, and ethanol, most likely because these molecules become too small to effectively stabilize the critical ice embryo. Overall, our results are consistent with PVA polymers and oligomers acting as heterogeneous ice nucleators.
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Affiliation(s)
- Lukas Eickhoff
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Mira Keßler
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Christopher Stubbs
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jakob Derksen
- Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Martina Viefhues
- Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Dario Anselmetti
- Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Berthold Hoge
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Thomas Koop
- Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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30
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Li J, Jiang B, Chang X, Yu H, Han Y, Zhang F. Bi-terminal fusion of intrinsically-disordered mussel foot protein fragments boosts mechanical strength for protein fibers. Nat Commun 2023; 14:2127. [PMID: 37059716 PMCID: PMC10104820 DOI: 10.1038/s41467-023-37563-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/22/2023] [Indexed: 04/16/2023] Open
Abstract
Microbially-synthesized protein-based materials are attractive replacements for petroleum-derived synthetic polymers. However, the high molecular weight, high repetitiveness, and highly-biased amino acid composition of high-performance protein-based materials have restricted their production and widespread use. Here we present a general strategy for enhancing both strength and toughness of low-molecular-weight protein-based materials by fusing intrinsically-disordered mussel foot protein fragments to their termini, thereby promoting end-to-end protein-protein interactions. We demonstrate that fibers of a ~60 kDa bi-terminally fused amyloid-silk protein exhibit ultimate tensile strength up to 481 ± 31 MPa and toughness of 179 ± 39 MJ*m-3, while achieving a high titer of 8.0 ± 0.70 g/L by bioreactor production. We show that bi-terminal fusion of Mfp5 fragments significantly enhances the alignment of β-nanocrystals, and intermolecular interactions are promoted by cation-π and π-π interactions between terminal fragments. Our approach highlights the advantage of self-interacting intrinsically-disordered proteins in enhancing material mechanical properties and can be applied to a wide range of protein-based materials.
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Affiliation(s)
- Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Bojing Jiang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Xinyuan Chang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Han Yu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Yichao Han
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA.
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31
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [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: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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32
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.531990. [PMID: 36993592 PMCID: PMC10054940 DOI: 10.1101/2023.03.12.531990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory Random Coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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33
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Gurumoorthy V, Shrestha UR, Zhang Q, Pingali SV, Boder ET, Urban VS, Smith JC, Petridis L, O'Neill H. Disordered Domain Shifts the Conformational Ensemble of the Folded Regulatory Domain of the Multidomain Oncoprotein c-Src. Biomacromolecules 2023; 24:714-723. [PMID: 36692364 DOI: 10.1021/acs.biomac.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
c-Src kinase is a multidomain non-receptor tyrosine kinase that aberrantly phosphorylates several signaling proteins in cancers. Although the structural properties of the regulatory domains (SH3-SH2) and the catalytic kinase domain have been extensively characterized, there is less knowledge about the N-terminal disordered region (SH4UD) and its interactions with the other c-Src domains. Here, we used domain-selective isotopic labeling combined with the small-angle neutron scattering contrast matching technique to study SH4UD interactions with SH3-SH2. Our results show that in the presence of SH4UD, the radius of gyration (Rg) of SH3-SH2 increases, indicating that it has a more extended conformation. Hamiltonian replica exchange molecular dynamics simulations provide a detailed molecular description of the structural changes in SH4UD-SH3-SH2 and show that the regulatory loops of SH3 undergo significant conformational changes in the presence of SH4UD, while SH2 remains largely unchanged. Overall, this study highlights how a disordered region can drive a folded region of a multidomain protein to become flexible, which may be important for allosteric interactions with binding partners. This may help in the design of therapeutic interventions that target the regulatory domains of this important family of kinases.
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Affiliation(s)
- Viswanathan Gurumoorthy
- UT/ORNL Graduate School of Genome and Science Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Utsab R Shrestha
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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34
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Rasmussen HØ, Kumar A, Shin B, Stylianou F, Sewell L, Xu Y, Otzen DE, Pedersen JS, Matthews SJ. FapA is an Intrinsically Disordered Chaperone for Pseudomonas Functional Amyloid FapC. J Mol Biol 2023; 435:167878. [PMID: 36368411 DOI: 10.1016/j.jmb.2022.167878] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Bacterial functional amyloids contribute to biofilm development by bacteria and provide protection from the immune system and prevent antibiotic treatment. Strategies to target amyloid formation and interrupt biofilm formation have attracted recent interest due to their antimicrobial potential. Functional amyloid in Pseudomonas (Fap) includes FapC as the major component of the fibril while FapB is a minor component suggested to function as a nucleator of FapC. The system also includes the small periplasmic protein FapA, which has been shown to regulate fibril composition and morphology. The interplay between these three components is central in Fap fibril biogenesis. Here we present a comprehensive biophysical and spectroscopy analysis of FapA, FapB and FapC and provide insight into their molecular interactions. We show that all three proteins are primarily disordered with some regions with structural propensities for α-helix and β-sheet. FapA inhibits FapC fibrillation by targeting the nucleation step, whereas for FapB the elongation step is modulated. Furthermore, FapA alters the morphology of FapC (more than FapB) fibrils. Complex formation is observed between FapA and FapC, but not between FapA and FapB, and likely involves the N-terminus of FapA. We conclude that FapA is an intrinsically disordered chaperone for FapC that guards against fibrillation within the periplasm. This new understanding of a natural protective mechanism of Pseudomonas against amyloid formations can serve as inspiration for strategies blocking biofilm formation in infections.
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Affiliation(s)
- Helena Ø Rasmussen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Amit Kumar
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Ben Shin
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Lee Sewell
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Steve J Matthews
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom.
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35
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Pastore A, Temussi PA. The Protein Unfolded State: One, No One and One Hundred Thousand. J Am Chem Soc 2022; 144:22352-22357. [PMID: 36450361 DOI: 10.1021/jacs.2c07696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Many in vitro studies, in which proteins have been unfolded by the action of a variety of physical or chemical agents, have led to the definition of a folded versus an unfolded state and to the question of what is the nature of the unfolded state. The unstructured nature of this state could suggest that "the" unfolded state is a unique entity which holds true for all kinds of unfolding processes. This assumption has to be questioned because the unfolding processes under different stress conditions are dictated by entirely different mechanisms. As a consequence, it can be easily understood that the final state, generically referred to as "the unfolded state", can be completely different for each of the unfolding processes. The present review examines recent data on the characteristics of the unfolded states emerging from experiments under different conditions, focusing specific attention to the level of compaction of the unfolded species.
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Affiliation(s)
- Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, United Kingdom
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, United Kingdom
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36
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Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
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37
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The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy. Essays Biochem 2022; 66:875-890. [PMID: 36416865 PMCID: PMC9760427 DOI: 10.1042/ebc20220065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) have emerged as key players across many biological functions and diseases. Differently from structured proteins, disordered proteins lack stable structure and are particularly sensitive to changes in the surrounding environment. Investigation of disordered ensembles requires new approaches and concepts for quantifying conformations, dynamics, and interactions. Here, we provide a short description of the fundamental biophysical properties of disordered proteins as understood through the lens of single-molecule fluorescence observations. Single-molecule Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) provides an extensive and versatile toolbox for quantifying the characteristics of conformational distributions and the dynamics of disordered proteins across many different solution conditions, both in vitro and in living cells.
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38
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González-Delgado J, Bernadó P, Neuvial P, Cortés J. Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations. J Struct Biol 2022; 214:107907. [PMID: 36272694 DOI: 10.1016/j.jsb.2022.107907] [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: 03/30/2022] [Revised: 10/03/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
Abstract
Backbone dihedral angles ϕ and ψ are the main structural descriptors of proteins and peptides. The distribution of these angles has been investigated over decades as they are essential for the validation and refinement of experimental measurements, as well as for structure prediction and design methods. The dependence of these distributions, not only on the nature of each amino acid but also on that of the closest neighbors, has been the subject of numerous studies. Although neighbor-dependent distributions are nowadays generally accepted as a good model, there is still some controversy about the combined effects of left and right neighbors. We have investigated this question using rigorous methods based on recently-developed statistical techniques. Our results unambiguously demonstrate that the influence of left and right neighbors cannot be considered independently. Consequently, three-residue fragments should be considered as the minimal building blocks to investigate polypeptide sequence-structure relationships.
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Affiliation(s)
- Javier González-Delgado
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France; Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, France
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, France
| | - Pierre Neuvial
- Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
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39
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Baidya L, Reddy G. pH Induced Switch in the Conformational Ensemble of Intrinsically Disordered Protein Prothymosin-α and Its Implications for Amyloid Fibril Formation. J Phys Chem Lett 2022; 13:9589-9598. [PMID: 36206480 DOI: 10.1021/acs.jpclett.2c01972] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aggregation of intrinsically disordered proteins (IDPs) can lead to neurodegenerative diseases. Although there is experimental evidence that acidic pH promotes IDP monomer compaction leading to aggregation, the general mechanism is unclear. We studied the pH effect on the conformational ensemble of prothymosin-α (proTα), which is involved in multiple essential functions, and probed its role in aggregation using computer simulations. We show that compaction in the proTα dimension at low pH is due to the protein's collapse in the intermediate region (E41-D80) rich in glutamic acid residues, enhancing its β-sheet content. We observed by performing dimer simulations that the conformations with high β-sheet content could act as aggregation-prone (N*) states and nucleate the aggregation process. The simulations initiated using N* states form dimers within a microsecond time scale, whereas the non-N* states do not form dimers within this time scale. This study contributes to understanding the general principles of pH-induced IDP aggregation.
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Affiliation(s)
- Lipika Baidya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka560012, India
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40
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Lasker K, Boeynaems S, Lam V, Scholl D, Stainton E, Briner A, Jacquemyn M, Daelemans D, Deniz A, Villa E, Holehouse AS, Gitler AD, Shapiro L. The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems. Nat Commun 2022; 13:5643. [PMID: 36163138 PMCID: PMC9512792 DOI: 10.1038/s41467-022-33221-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. It remains incompletely resolved how biological function is encoded in these assemblies and whether this depends on their material state. The conserved intrinsically disordered protein PopZ forms condensates at the poles of the bacterium Caulobacter crescentus, which in turn orchestrate cell-cycle regulating signaling cascades. Here we show that the material properties of these condensates are determined by a balance between attractive and repulsive forces mediated by a helical oligomerization domain and an expanded disordered region, respectively. A series of PopZ mutants disrupting this balance results in condensates that span the material properties spectrum, from liquid to solid. A narrow range of condensate material properties supports proper cell division, linking emergent properties to organismal fitness. We use these insights to repurpose PopZ as a modular platform for generating tunable synthetic condensates in human cells.
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Affiliation(s)
- Keren Lasker
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinson Lam
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emma Stainton
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam Briner
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, QLD, Australia
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ashok Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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41
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Yu L, Brüschweiler R. Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins. PLoS Comput Biol 2022; 18:e1010036. [PMID: 36084124 PMCID: PMC9491582 DOI: 10.1371/journal.pcbi.1010036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/21/2022] [Accepted: 08/03/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup, which are two IDPs that fold upon binding to their targets, how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. Further inspection revealed that 10-20% of the individual MD trajectories display the formation of secondary structures not observed in the experimental NMR data. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.
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Affiliation(s)
- Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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42
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Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks. iScience 2022; 25:104892. [PMID: 36060052 PMCID: PMC9436757 DOI: 10.1016/j.isci.2022.104892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/03/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
PPM1D is a p53-regulated protein phosphatase that modulates the DNA damage response (DDR) and is frequently altered in cancer. Here, we employed chemical inhibition of PPM1D and quantitative mass spectrometry-based phosphoproteomics to identify the substrates of PPM1D upon induction of DNA double-strand breaks (DSBs) by etoposide. We identified 73 putative PPM1D substrates that are involved in DNA repair, regulation of transcription, and RNA processing. One-third of DSB-induced S/TQ phosphorylation sites are dephosphorylated by PPM1D, demonstrating that PPM1D only partially counteracts ATM/ATR/DNA-PK signaling. PPM1D-targeted phosphorylation sites are found in a specific amino acid sequence motif that is characterized by glutamic acid residues, high intrinsic disorder, and poor evolutionary conservation. We identified a functionally uncharacterized protein Kanadaptin as ATM and PPM1D substrate upon DSB induction. We propose that PPM1D plays a role during the response to DSBs by regulating the phosphorylation of DNA- and RNA-binding proteins in intrinsically disordered regions. MS-based phosphoproteomic profiling of PPM1D substrates in U2OS and HCT116 cells PPM1D counteracts ATM in the cellular response to DNA double-strand breaks PPM1D target sites localize to glutamic acid-rich regions with high intrinsic disorder Kanadaptin is a putative DNA damage response factor regulated by ATM and PPM1D
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43
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Halley JW. Some Factors from Theory, Simulation, Experiment and Proteomes in the Current Biosphere Supporting Deep Oceans as the Location of the Origin of Terrestrial Life. Life (Basel) 2022; 12:1330. [PMID: 36143367 PMCID: PMC9503746 DOI: 10.3390/life12091330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Some standard arguments are reviewed supporting deep ocean trenches as a likely location for the origin of terrestrial life. An analysis of proteomes of contemporary prokaryotes carried out by this group is cited as supporting evidence, indicating that the original proteins were formed by quenching from temperatures close to the boiling point of water. Coarse-grained simulations of the network formation process which agree quite well with experiments of such quenches both in drying and rapid fluid emission from a hot to a cold fluid are also described and cited as support for such a scenario. We suggest further experiments, observations and theoretical and simulation work to explore this hypothesis.
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Affiliation(s)
- J W Halley
- School of Physics and Astronomy, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
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44
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Sahin C, Østerlund EC, Österlund N, Costeira-Paulo J, Pedersen JN, Christiansen G, Nielsen J, Grønnemose AL, Amstrup SK, Tiwari MK, Rao RSP, Bjerrum MJ, Ilag LL, Davies MJ, Marklund EG, Pedersen JS, Landreh M, Møller IM, Jørgensen TJD, Otzen DE. Structural Basis for Dityrosine-Mediated Inhibition of α-Synuclein Fibrillization. J Am Chem Soc 2022; 144:11949-11954. [PMID: 35749730 PMCID: PMC9284551 DOI: 10.1021/jacs.2c03607] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
α-Synuclein
(α-Syn) is an intrinsically disordered
protein which self-assembles into highly organized β-sheet structures
that accumulate in plaques in brains of Parkinson’s disease
patients. Oxidative stress influences α-Syn structure and self-assembly;
however, the basis for this remains unclear. Here we characterize
the chemical and physical effects of mild oxidation on monomeric α-Syn
and its aggregation. Using a combination of biophysical methods, small-angle
X-ray scattering, and native ion mobility mass spectrometry, we find
that oxidation leads to formation of intramolecular dityrosine cross-linkages
and a compaction of the α-Syn monomer by a factor of √2.
Oxidation-induced compaction is shown to inhibit ordered self-assembly
and amyloid formation by steric hindrance, suggesting an important
role of mild oxidation in preventing amyloid formation.
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Affiliation(s)
- Cagla Sahin
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Eva Christina Østerlund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Joana Costeira-Paulo
- Department of Chemistry - BMC, BMC - Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Gunna Christiansen
- Department of Health Science and Technology, Medical Microbiology and Immunology, Aalborg University, Fredrik Bajers Vej 3b, DK-9220 Aalborg Ø, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Anne Louise Grønnemose
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Søren Kirk Amstrup
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Manish K Tiwari
- Department Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangaluru-575018, Karnataka, India
| | - Morten Jannik Bjerrum
- Department Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Leopold L Ilag
- Department of Materials and Environmental Chemistry, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Erik G Marklund
- Department of Chemistry - BMC, BMC - Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
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45
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Sarkar A, Gasic AG, Cheung MS, Morrison G. Effects of Protein Crowders and Charge on the Folding of Superoxide Dismutase 1 Variants: A Computational Study. J Phys Chem B 2022; 126:4458-4471. [PMID: 35686856 DOI: 10.1021/acs.jpcb.2c00819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The neurodegenerative disease amyotrophic lateral sclerosis (ALS) is associated with the misfolding and aggregation of the metalloenzyme protein superoxide dismutase 1 (SOD1) via mutations that destabilize the monomer-dimer interface. In a cellular environment, crowding and electrostatic screening play essential roles in the folding and aggregation of the SOD1 monomers. Despite numerous studies on the effects of mutations on SOD1 folding, a clear understanding of the interplay between crowding, folding, and aggregation in vivo remains lacking. Using a structure-based minimal model for molecular dynamics simulations, we investigate the role of self-crowding and charge on the folding stability of SOD1 and the G41D mutant where experimentalists were intrigued by an alteration of the folding mechanism by a single point mutation from glycine to charged aspartic acid. We show that unfolded SOD1 configurations are significantly affected by charge and crowding, a finding that would be extremely costly to achieve with all-atom simulations, while the native state is not significantly altered. The mutation at residue 41 alters the interactions between proteins in the unfolded states instead of those within a protein. This paper suggests electrostatics may play an important role in the folding pathway of SOD1 and modifying the charge via mutation and ion concentration may change the dominant interactions between proteins, with potential impacts for aggregation of the mutants. This work provides a plausible reason for the alteration of the unfolded states to address why the mutant G41D causes the changes to the folding mechanism of SOD1 that have intrigued experimentalists.
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Affiliation(s)
- Atrayee Sarkar
- Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Andrei G Gasic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Pacific Northwest National Laboratory, Seattle Research Center, Seattle, Washington 98109, United States
| | - Greg Morrison
- Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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46
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Haris L, Biehl R, Dulle M, Radulescu A, Holderer O, Hoffmann I, Stadler AM. Variation of Structural and Dynamical Flexibility of Myelin Basic Protein in Response to Guanidinium Chloride. Int J Mol Sci 2022; 23:6969. [PMID: 35805997 PMCID: PMC9266411 DOI: 10.3390/ijms23136969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Myelin basic protein (MBP) is intrinsically disordered in solution and is considered as a conformationally flexible biomacromolecule. Here, we present a study on perturbation of MBP structure and dynamics by the denaturant guanidinium chloride (GndCl) using small-angle scattering and neutron spin-echo spectroscopy (NSE). A concentration of 0.2 M GndCl causes charge screening in MBP resulting in a compact, but still disordered protein conformation, while GndCl concentrations above 1 M lead to structural expansion and swelling of MBP. NSE data of MBP were analyzed using the Zimm model with internal friction (ZIF) and normal mode (NM) analysis. A significant contribution of internal friction was found in compact states of MBP that approaches a non-vanishing internal friction relaxation time of approximately 40 ns at high GndCl concentrations. NM analysis demonstrates that the relaxation rates of internal modes of MBP remain unaffected by GndCl, while structural expansion due to GndCl results in increased amplitudes of internal motions. Within the model of the Brownian oscillator our observations can be rationalized by a loss of friction within the protein due to structural expansion. Our study highlights the intimate coupling of structural and dynamical plasticity of MBP, and its fundamental difference to the behavior of ideal polymers in solution.
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Affiliation(s)
- Luman Haris
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
| | - Martin Dulle
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
| | - Aurel Radulescu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungzentrum Jülich GmbH, 85747 Garching, Germany; (A.R.); (O.H.)
| | - Olaf Holderer
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungzentrum Jülich GmbH, 85747 Garching, Germany; (A.R.); (O.H.)
| | - Ingo Hoffmann
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, CEDEX 9, 38042 Grenoble, France;
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
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47
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Bazmi S, Wallin S. Crowding-induced protein destabilization in the absence of soft attractions. Biophys J 2022; 121:2503-2513. [PMID: 35672949 DOI: 10.1016/j.bpj.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, φc. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with φc. Hence, for all φc>0, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, Tm, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-φc conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at T<Tm, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at φc=0, but increasing monotonically with φc. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.
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Affiliation(s)
- Saman Bazmi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada.
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48
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Ghosh K, Huihui J, Phillips M, Haider A. Rules of Physical Mathematics Govern Intrinsically Disordered Proteins. Annu Rev Biophys 2022; 51:355-376. [PMID: 35119946 PMCID: PMC9190209 DOI: 10.1146/annurev-biophys-120221-095357] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In stark contrast to foldable proteins with a unique folded state, intrinsically disordered proteins and regions (IDPs) persist in perpetually disordered ensembles. Yet an IDP ensemble has conformational features-even when averaged-that are specific to its sequence. In fact, subtle changes in an IDP sequence can modulate its conformational features and its function. Recent advances in theoretical physics reveal a set of elegant mathematical expressions that describe the intricate relationships among IDP sequences, their ensemble conformations, and the regulation of their biological functions. These equations also describe the molecular properties of IDP sequences that predict similarities and dissimilarities in their functions and facilitate classification of sequences by function, an unmet challenge to traditional bioinformatics. These physical sequence-patterning metrics offer a promising new avenue for advancing synthetic biology at a time when multiple novel functional modes mediated by IDPs are emerging.
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Affiliation(s)
- Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, USA,Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, USA
| | - Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, USA
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Colorado, USA
| | - Austin Haider
- Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, USA
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49
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Tashiro D, Suetaka S, Sato N, Ooka K, Kunihara T, Kudo H, Inatomi J, Hayashi Y, Arai M. Intron-Encoded Domain of Herstatin, An Autoinhibitor of Human Epidermal Growth Factor Receptors, Is Intrinsically Disordered. Front Mol Biosci 2022; 9:862910. [PMID: 35573740 PMCID: PMC9100580 DOI: 10.3389/fmolb.2022.862910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Human epidermal growth factor receptors (HER/ERBB) form dimers that promote cell proliferation, migration, and differentiation, but overexpression of HER proteins results in cancer. Consequently, inhibitors of HER dimerization may function as effective antitumor drugs. An alternatively spliced variant of HER2, called herstatin, is an autoinhibitor of HER proteins, and the intron 8-encoded 79-residue domain of herstatin, called Int8, binds HER family receptors even in isolation. However, the structure of Int8 remains poorly understood. Here, we revealed by circular dichroism, NMR, small-angle X-ray scattering, and structure prediction that isolated Int8 is largely disordered but has a residual helical structure. The radius of gyration of Int8 was almost the same as that of fully unfolded states, although the conformational ensemble of Int8 was less flexible than random coils. These results demonstrate that Int8 is intrinsically disordered. Thus, Int8 is an interesting example of an intrinsically disordered region with tumor-suppressive activity encoded by an intron. Furthermore, we show that the R371I mutant of Int8, which is defective in binding to HER2, is prone to aggregation, providing a rationale for the loss of function.
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Affiliation(s)
- Daisuke Tashiro
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Koji Ooka
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kunihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Junichi Inatomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- *Correspondence: Munehito Arai,
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50
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Whitehead RD, Teschke CM, Alexandrescu AT. Pulse-field gradient nuclear magnetic resonance of protein translational diffusion from native to non-native states. Protein Sci 2022; 31:e4321. [PMID: 35481638 PMCID: PMC9047038 DOI: 10.1002/pro.4321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/31/2022] [Accepted: 04/12/2022] [Indexed: 01/31/2023]
Abstract
Hydrodynamic radii (Rh -values) calculated from diffusion coefficients measured by pulse-field-gradient nuclear magnetic resonance are compared for folded and unfolded proteins. For native globular proteins, the Rh -values increase as a power of 0.35 with molecular size, close to the scaling factor of 0.33 predicted from polymer theory. Unfolded proteins were studied under four sets of conditions: in the absence of denaturants, in the presence of 6 M urea, in 95% dimethyl sulfoxide (DMSO), and in 40% hexafluoroisopropanol (HFIP). Scaling factors under all four unfolding conditions are similar (0.49-0.53) approaching the theoretical value of 0.60 for a fully unfolded random coil. Persistence lengths are also similar, except smaller in 95% DMSO, suggesting that the polypeptides are more disordered on a local scale with this solvent. Three of the proteins in our unfolded set have an asymmetric sequence-distribution of charged residues. While these proteins behave normally in water and 6 M urea, they give atypically low Rh -values in 40% HFIP and 95% DMSO suggesting they are forming electrostatic hairpins, favored by their asymmetric sequence charge distribution and the low dielectric constants of DMSO and HFIP. While diffusion-ordered NMR spectroscopy can separate small molecules, we show a number of factors combine to make protein-sized molecules much more difficult to resolve in mixtures. Finally, we look at the temperature dependence of apparent diffusion coefficients. Small molecules show a linear temperature response, while large proteins show abnormally large apparent diffusion coefficients at high temperatures due to convection, suggesting diffusion reference standards are only useful near 25°C.
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Affiliation(s)
- Richard D Whitehead
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.,Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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