1
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Bakker MJ, Gaffour A, Juhás M, Zapletal V, Stošek J, Bratholm LA, Pavlíková Přecechtělová J. Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering. J Chem Inf Model 2024; 64:6542-6556. [PMID: 39099394 DOI: 10.1021/acs.jcim.4c00809] [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: 08/06/2024]
Abstract
By merging advanced dimensionality reduction (DR) and clustering algorithm (CA) techniques, our study advances the sampling procedure for predicting NMR chemical shifts (CS) in intrinsically disordered proteins (IDPs), making a significant leap forward in the field of protein analysis/modeling. We enhance NMR CS sampling by generating clustered ensembles that accurately reflect the different properties and phenomena encapsulated by the IDP trajectories. This investigation critically assessed different rapid CS predictors, both neural network (e.g., Sparta+ and ShiftX2) and database-driven (ProCS-15), and highlighted the need for more advanced quantum calculations and the subsequent need for more tractable-sized conformational ensembles. Although neural network CS predictors outperformed ProCS-15 for all atoms, all tools showed poor agreement with HN CSs, and the neural network CS predictors were unable to capture the influence of phosphorylated residues, highly relevant for IDPs. This study also addressed the limitations of using direct clustering with collective variables, such as the widespread implementation of the GROMOS algorithm. Clustered ensembles (CEs) produced by this algorithm showed poor performance with chemical shifts compared to sequential ensembles (SEs) of similar size. Instead, we implement a multiscale DR and CA approach and explore the challenges and limitations of applying these algorithms to obtain more robust and tractable CEs. The novel feature of this investigation is the use of solvent-accessible surface area (SASA) as one of the fingerprints for DR alongside previously investigated α carbon distance/angles or ϕ/ψ dihedral angles. The ensembles produced with SASA tSNE DR produced CEs better aligned with the experimental CS of between 0.17 and 0.36 r2 (0.18-0.26 ppm) depending on the system and replicate. Furthermore, this technique produced CEs with better agreement than traditional SEs in 85.7% of all ensemble sizes. This study investigates the quality of ensembles produced based on different input features, comparing latent spaces produced by linear vs nonlinear DR techniques and a novel integrated silhouette score scanning protocol for tSNE DR.
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Affiliation(s)
- Michael J Bakker
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Amina Gaffour
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Martin Juhás
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Rokitanského 62, 500 03 Hradec Králové, Czech Republic
| | - Vojtěch Zapletal
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Jakub Stošek
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lars A Bratholm
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS Bristol, U.K
| | - Jana Pavlíková Přecechtělová
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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2
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Melnikova D, Ranjan VV, Nesmelov YE, Skirda VD, Nesmelova IV. Translational Diffusion and Self-Association of an Intrinsically Disordered Protein κ-Casein Using NMR with Ultra-High Pulsed-Field Gradient and Time-Resolved FRET. J Phys Chem B 2024; 128:7781-7791. [PMID: 39106061 PMCID: PMC11331516 DOI: 10.1021/acs.jpcb.4c03625] [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: 06/01/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024]
Abstract
Much attention has been given to studying the translational diffusion of globular proteins, whereas the translational diffusion of intrinsically disordered proteins (IDPs) is less studied. In this study, we investigate the translational diffusion and how it is affected by the self-association of an IDP, κ-casein, using pulsed-field gradient nuclear magnetic resonance and time-resolved Förster resonance energy transfer. Using the analysis of the shape of diffusion attenuation and the concentration dependence of κ-casein diffusion coefficients and intermolecular interactions, we demonstrate that κ-casein exhibits continuous self-association. When the volume fraction of κ-casein is below 0.08, we observe that κ-casein self-association results in a macroscopic phase separation upon storage at 4 °C. At κ-casein volume fractions above 0.08, self-association leads to the formation of labile gel-like networks without subsequent macroscopic phase separation. Unlike α-casein, which shows a strong concentration dependence and extensive gel-like network formation, only one-third of κ-casein molecules participate in the gel network at a time, resulting in a more dynamic and less extensive structure. These findings highlight the unique association properties of κ-casein, contributing to a better understanding of its behavior under various conditions and its potential role in casein micelle formation.
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Affiliation(s)
- Daria
L. Melnikova
- Department
of Physics of Molecular Systems, Kazan Federal
University, Kazan 420011, Russia
| | - Venkatesh V. Ranjan
- Department
of Chemistry, University of North Carolina, Charlotte, North Carolina 28223, United States
- Department
of Physics and Optical Sciences, University
of North Carolina, Charlotte, North Carolina 28223, United States
| | - Yuri E. Nesmelov
- Department
of Physics and Optical Sciences, University
of North Carolina, Charlotte, North Carolina 28223, United States
| | - Vladimir D. Skirda
- Department
of Physics of Molecular Systems, Kazan Federal
University, Kazan 420011, Russia
| | - Irina V. Nesmelova
- Department
of Physics and Optical Sciences, University
of North Carolina, Charlotte, North Carolina 28223, United States
- School
of Data Science, University of North Carolina, Charlotte, North Carolina 28223, United States
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3
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Rekhi S, Garcia CG, Barai M, Rizuan A, Schuster BS, Kiick KL, Mittal J. Expanding the molecular language of protein liquid-liquid phase separation. Nat Chem 2024; 16:1113-1124. [PMID: 38553587 PMCID: PMC11230844 DOI: 10.1038/s41557-024-01489-x] [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: 03/20/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024]
Abstract
Understanding the relationship between a polypeptide sequence and its phase separation has important implications for analysing cellular function, treating disease and designing novel biomaterials. Several sequence features have been identified as drivers for protein liquid-liquid phase separation (LLPS), schematized as a 'molecular grammar' for LLPS. Here we further probe how sequence modulates phase separation and the material properties of the resulting condensates, targeting sequence features previously overlooked in the literature. We generate sequence variants of a repeat polypeptide with either no charged residues, high net charge, no glycine residues or devoid of aromatic or arginine residues. All but one of 12 variants exhibited LLPS, albeit to different extents, despite substantial differences in composition. Furthermore, we find that all the condensates formed behaved like viscous fluids, despite large differences in their viscosities. Our results support the model of multiple interactions between diverse residue pairs-not just a handful of residues-working in tandem to drive the phase separation and dynamics of condensates.
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Affiliation(s)
- Shiv Rekhi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Mayur Barai
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA.
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4
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Hurieva B, Kumar DK, Morag R, Lupo O, Carmi M, Barkai N, Jonas F. Disordered sequences of transcription factors regulate genomic binding by integrating diverse sequence grammars and interaction types. Nucleic Acids Res 2024:gkae521. [PMID: 38908024 DOI: 10.1093/nar/gkae521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/25/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024] Open
Abstract
Intrinsically disordered regions (IDRs) guide transcription factors (TFs) to their genomic binding sites, raising the question of how structure-lacking regions encode for complex binding patterns. We investigated this using the TF Gln3, revealing sets of IDR-embedded determinants that direct Gln3 binding to respective groups of functionally related promoters, and enable tuning binding preferences between environmental conditions, phospho-mimicking mutations, and orthologs. Through targeted mutations, we defined the role of short linear motifs (SLiMs) and co-binding TFs (Hap2) in stabilizing Gln3 at respiration-chain promoters, while providing evidence that Gln3 binding at nitrogen-associated promoters is encoded by the IDR amino-acid composition, independent of SLiMs or co-binding TFs. Therefore, despite their apparent simplicity, TF IDRs can direct and regulate complex genomic binding patterns through a combination of SLiM-mediated and composition-encoded interactions.
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Affiliation(s)
- Bohdana Hurieva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Divya Krishna Kumar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Morag
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Offir Lupo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- School of Science, Constructor University, 28759 Bremen, Germany
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5
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Guo HB, Huntington B, Perminov A, Smith K, Hastings N, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein. PLoS One 2024; 19:e0301866. [PMID: 38739602 PMCID: PMC11090348 DOI: 10.1371/journal.pone.0301866] [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: 12/05/2023] [Accepted: 03/23/2024] [Indexed: 05/16/2024] Open
Abstract
We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP), Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures of Nvjp-1 when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions in Nvjp-1 are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.
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Affiliation(s)
- Hao-Bo Guo
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- UES Inc., Dayton, OH, United States of America
| | - Baxter Huntington
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- Miami University, Oxford, OH, United States of America
| | - Alexander Perminov
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- Miami University, Oxford, OH, United States of America
| | - Kenya Smith
- United States Air Force Academy, Colorado Springs, CO, United States of America
| | - Nicholas Hastings
- United States Air Force Academy, Colorado Springs, CO, United States of America
| | - Patrick Dennis
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| | - Nancy Kelley-Loughnane
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| | - Rajiv Berry
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
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6
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Marchese D, Guislain F, Pringels T, Bridoux L, Rezsohazy R. A poly-histidine motif of HOXA1 is involved in regulatory interactions with cysteine-rich proteins. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:194993. [PMID: 37952572 DOI: 10.1016/j.bbagrm.2023.194993] [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: 06/05/2023] [Revised: 10/05/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Homopolymeric amino acid repeats are found in about 24 % of human proteins and are over-represented in transcriptions factors and kinases. Although relatively rare, homopolymeric histidine repeats (polyH) are more significantly found in proteins involved in the regulation of embryonic development. To gain a better understanding of the role of polyH in these proteins, we used a bioinformatic approach to search for shared features in the interactomes of polyH-containing proteins in human. Our analysis revealed that polyH protein interactomes are enriched in cysteine-rich proteins and in proteins containing (a) cysteine repeat(s). Focusing on HOXA1, a HOX transcription factor displaying one long polyH motif, we identified that the polyH motif is required for the HOXA1 interaction with such cysteine-rich proteins. We observed a correlation between the length of the polyH repeat and the strength of the HOXA1 interaction with one Cys-rich protein, MDFI. We also found that metal ion chelators disrupt the HOXA1-MDFI interaction supporting that such metal ions are required for the interaction. Furthermore, we identified three polyH interactors which down-regulate the transcriptional activity of HOXA1. Taken together, our data point towards the involvement of polyH and cysteines in regulatory interactions between proteins, notably transcription factors like HOXA1.
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Affiliation(s)
- Damien Marchese
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - Florent Guislain
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium.
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7
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Ghosh C, Nagpal S, Muñoz V. Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins. Curr Opin Struct Biol 2024; 84:102756. [PMID: 38118365 PMCID: PMC11242915 DOI: 10.1016/j.sbi.2023.102756] [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: 10/08/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
Intrinsically disordered proteins (IDPs) exploit their plasticity to deploy a rich panoply of soft interactions and binding phenomena. Advances in tailoring molecular simulations for IDPs combined with experimental cross-validation offer an atomistic view of the mechanisms that control IDP binding, function, and dysfunction. The emerging theme is that unbound IDPs autonomously form transient local structures and self-interactions that determine their binding behavior. Recent results have shed light on whether and how IDPs fold, stay disordered or drive condensation upon binding; how they achieve binding specificity and select among competing partners. The disorder-binding paradigm is now being proactively used by researchers to target IDPs for rational drug design and engineer molecular responsive elements for biosensing applications.
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Affiliation(s)
- Catherine Ghosh
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA. https://twitter.com/cat_ghosh
| | - Suhani Nagpal
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA; OpenEye, Cadence Molecular Sciences, Boston, 02114 MA, USA
| | - Victor Muñoz
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA.
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8
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Hsiao AS. Protein Disorder in Plant Stress Adaptation: From Late Embryogenesis Abundant to Other Intrinsically Disordered Proteins. Int J Mol Sci 2024; 25:1178. [PMID: 38256256 PMCID: PMC10816898 DOI: 10.3390/ijms25021178] [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: 10/29/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Global climate change has caused severe abiotic and biotic stresses, affecting plant growth and food security. The mechanical understanding of plant stress responses is critical for achieving sustainable agriculture. Intrinsically disordered proteins (IDPs) are a group of proteins without unique three-dimensional structures. The environmental sensitivity and structural flexibility of IDPs contribute to the growth and developmental plasticity for sessile plants to deal with environmental challenges. This article discusses the roles of various disordered proteins in plant stress tolerance and resistance, describes the current mechanistic insights into unstructured proteins such as the disorder-to-order transition for adopting secondary structures to interact with specific partners (i.e., cellular membranes, membrane proteins, metal ions, and DNA), and elucidates the roles of liquid-liquid phase separation driven by protein disorder in stress responses. By comparing IDP studies in animal systems, this article provides conceptual principles of plant protein disorder in stress adaptation, reveals the current research gaps, and advises on the future research direction. The highlighting of relevant unanswered questions in plant protein disorder research aims to encourage more studies on these emerging topics to understand the mechanisms of action behind their stress resistance phenotypes.
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Affiliation(s)
- An-Shan Hsiao
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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9
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Jiao X, Di Sante G, Casimiro MC, Tantos A, Ashton AW, Li Z, Quach Y, Bhargava D, Di Rocco A, Pupo C, Crosariol M, Lazar T, Tompa P, Wang C, Yu Z, Zhang Z, Aldaaysi K, Vadlamudi R, Mann M, Skordalakes E, Kossenkov A, Du Y, Pestell RG. A cyclin D1 intrinsically disordered domain accesses modified histone motifs to govern gene transcription. Oncogenesis 2024; 13:4. [PMID: 38191593 PMCID: PMC10774418 DOI: 10.1038/s41389-023-00502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
The essential G1-cyclin, CCND1, is frequently overexpressed in cancer, contributing to tumorigenesis by driving cell-cycle progression. D-type cyclins are rate-limiting regulators of G1-S progression in mammalian cells via their ability to bind and activate CDK4 and CDK6. In addition, cyclin D1 conveys kinase-independent transcriptional functions of cyclin D1. Here we report that cyclin D1 associates with H2BS14 via an intrinsically disordered domain (IDD). The same region of cyclin D1 was necessary for the induction of aneuploidy, induction of the DNA damage response, cyclin D1-mediated recruitment into chromatin, and CIN gene transcription. In response to DNA damage H2BS14 phosphorylation occurs, resulting in co-localization with γH2AX in DNA damage foci. Cyclin D1 ChIP seq and γH2AX ChIP seq revealed ~14% overlap. As the cyclin D1 IDD functioned independently of the CDK activity to drive CIN, the IDD domain may provide a rationale new target to complement CDK-extinction strategies.
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Affiliation(s)
- Xuanmao Jiao
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | - Mathew C Casimiro
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Department of Science and Mathematics, Abraham Baldwin Agricultural College, Tifton, GA, 31794, USA
| | - Agnes Tantos
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
| | - Anthony W Ashton
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Division of Cardiovascular Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, 19003, USA
| | - Zhiping Li
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Yen Quach
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | | | | | - Claudia Pupo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Marco Crosariol
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Peter Tompa
- Institute of Enzymology, Hun-Ren Research Centre for Natural Sciences, Budapest, Hungary
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhao Zhang
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Kawthar Aldaaysi
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Ratna Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | - Monica Mann
- Department of Obstetrics and Gynecology, University of Texas Health Sciences Center, San Antonio, TX, 78229, USA
| | | | | | - Yanming Du
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA
| | - Richard G Pestell
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba.
- The Wistar Institute, Philadelphia, PA, 19107, USA.
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10
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Kumar P, Bhardwaj A, Mukherjee B, Joshi R, Giri R. Coronaviruses spike glycoprotein endodomains: The sequence and structure-based comprehensive study. Protein Sci 2023; 32:e4804. [PMID: 37833239 PMCID: PMC10599102 DOI: 10.1002/pro.4804] [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: 08/25/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
Any protein's flexibility or region makes it available to interact with many biomolecules in the cell. Specifically, such interactions in viruses help them to perform more functions despite having a smaller genome. Therefore, these flexible regions can be exciting and essential targets to be explored for their role in pathogenicity and therapeutic developments as they achieve essential interactions. In the continuation with our previous study on disordered analysis of SARS-CoV-2 spike protein's cytoplasmic tail (CTR), or endodomain, here we have explored the endodomain's disordered potential of six other coronaviruses using multiple bioinformatics approaches and molecular dynamics simulations. Based on the comprehensive analysis of its sequence and structural composition, we report the varying disorder propensity in endodomains of spike proteins of coronaviruses. The observations of this study may help to understand the importance of spike glycoprotein endodomain and creating therapeutic interventions against them.
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Affiliation(s)
- Prateek Kumar
- School of Biosciences and BioengineeringIndian Institute of Technology MandiMandiHimachal PradeshIndia
| | - Aparna Bhardwaj
- School of Biosciences and BioengineeringIndian Institute of Technology MandiMandiHimachal PradeshIndia
| | - Bodhidipra Mukherjee
- School of Biosciences and BioengineeringIndian Institute of Technology MandiMandiHimachal PradeshIndia
| | - Richa Joshi
- School of Biosciences and BioengineeringIndian Institute of Technology MandiMandiHimachal PradeshIndia
| | - Rajanish Giri
- School of Biosciences and BioengineeringIndian Institute of Technology MandiMandiHimachal PradeshIndia
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11
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Schweitzer-Stenner R, Kurbaj R, O'Neill N, Andrews B, Shah R, Urbanc B. Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2023; 62:2571-2586. [PMID: 37595285 DOI: 10.1021/acs.biochem.3c00212] [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: 08/20/2023]
Abstract
Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.
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Affiliation(s)
| | - Raghed Kurbaj
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Riya Shah
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
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12
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Upadhyay A, Ekenna C. A New Tool to Study the Binding Behavior of Intrinsically Disordered Proteins. Int J Mol Sci 2023; 24:11785. [PMID: 37511544 PMCID: PMC10380747 DOI: 10.3390/ijms241411785] [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: 06/12/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Understanding the binding behavior and conformational dynamics of intrinsically disordered proteins (IDPs) is crucial for unraveling their regulatory roles in biological processes. However, their lack of stable 3D structures poses challenges for analysis. To address this, we propose an algorithm that explores IDP binding behavior with protein complexes by extracting topological and geometric features from the protein surface model. Our algorithm identifies a geometrically favorable binding pose for the IDP and plans a feasible trajectory to evaluate its transition to the docking position. We focus on IDPs from Homo sapiens and Mus-musculus, investigating their interaction with the Plasmodium falciparum (PF) pathogen associated with malaria-related deaths. We compare our algorithm with HawkDock and HDOCK docking tools for quantitative (computation time) and qualitative (binding affinity) measures. Our results indicated that our method outperformed the compared methods in computation performance and binding affinity in experimental conformations.
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Affiliation(s)
- Aakriti Upadhyay
- Department of Computer Science, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Chinwe Ekenna
- Department of Computer Science, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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13
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Jevtic Z, Allram M, Grebien F, Schwaller J. Biomolecular Condensates in Myeloid Leukemia: What Do They Tell Us? Hemasphere 2023; 7:e923. [PMID: 37388925 PMCID: PMC10306439 DOI: 10.1097/hs9.0000000000000923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Recent studies have suggested that several oncogenic and tumor-suppressive proteins carry out their functions in the context of specific membrane-less cellular compartments. As these compartments, generally referred to as onco-condensates, are specific to tumor cells and are tightly linked to disease development, the mechanisms of their formation and maintenance have been intensively studied. Here we review the proposed leukemogenic and tumor-suppressive activities of nuclear biomolecular condensates in acute myeloid leukemia (AML). We focus on condensates formed by oncogenic fusion proteins including nucleoporin 98 (NUP98), mixed-lineage leukemia 1 (MLL1, also known as KMT2A), mutated nucleophosmin (NPM1c) and others. We also discuss how altered condensate formation contributes to malignant transformation of hematopoietic cells, as described for promyelocytic leukemia protein (PML) in PML::RARA-driven acute promyelocytic leukemia (APL) and other myeloid malignancies. Finally, we discuss potential strategies for interfering with the molecular mechanisms related to AML-associated biomolecular condensates, as well as current limitations of the field.
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Affiliation(s)
- Zivojin Jevtic
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
| | - Melanie Allram
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Juerg Schwaller
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
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14
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Cermakova K, Hodges HC. Interaction modules that impart specificity to disordered protein. Trends Biochem Sci 2023; 48:477-490. [PMID: 36754681 PMCID: PMC10106370 DOI: 10.1016/j.tibs.2023.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
Intrinsically disordered regions (IDRs) are especially enriched among proteins that regulate chromatin and transcription. As a result, mechanisms that influence specificity of IDR-driven interactions have emerged as exciting unresolved issues for understanding gene regulation. We review the molecular elements frequently found within IDRs that confer regulatory specificity. In particular, we summarize the differing roles of disordered low-complexity regions (LCRs) and short linear motifs (SLiMs) towards selective nuclear regulation. Examination of IDR-driven interactions highlights SLiMs as organizers of selectivity, with widespread roles in gene regulation and integration of cellular signals. Analysis of recurrent interactions between SLiMs and folded domains suggests diverse avenues for SLiMs to influence phase-separated condensates and highlights opportunities to manipulate these interactions for control of biological activity.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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15
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Hsiao AS, Huang JY. Microtubule Regulation in Plants: From Morphological Development to Stress Adaptation. Biomolecules 2023; 13:biom13040627. [PMID: 37189374 DOI: 10.3390/biom13040627] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/09/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
Microtubules (MTs) are essential elements of the eukaryotic cytoskeleton and are critical for various cell functions. During cell division, plant MTs form highly ordered structures, and cortical MTs guide the cell wall cellulose patterns and thus control cell size and shape. Both are important for morphological development and for adjusting plant growth and plasticity under environmental challenges for stress adaptation. Various MT regulators control the dynamics and organization of MTs in diverse cellular processes and response to developmental and environmental cues. This article summarizes the recent progress in plant MT studies from morphological development to stress responses, discusses the latest techniques applied, and encourages more research into plant MT regulation.
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16
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Functional Characterization of the N-Terminal Disordered Region of the piggyBac Transposase. Int J Mol Sci 2022; 23:ijms231810317. [PMID: 36142241 PMCID: PMC9499001 DOI: 10.3390/ijms231810317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 09/03/2022] [Indexed: 01/15/2023] Open
Abstract
The piggyBac DNA transposon is an active element initially isolated from the cabbage looper moth, but members of this superfamily are also present in most eukaryotic evolutionary lineages. The functionally important regions of the transposase are well described. There is an RNase H-like fold containing the DDD motif responsible for the catalytic DNA cleavage and joining reactions and a C-terminal cysteine-rich domain important for interaction with the transposon DNA. However, the protein also contains a ~100 amino acid long N-terminal disordered region (NTDR) whose function is currently unknown. Here we show that deletion of the NTDR significantly impairs piggyBac transposition, although the extent of decrease is strongly cell-type specific. Moreover, replacing the NTDR with scrambled but similarly disordered sequences did not rescue transposase activity, indicating the importance of sequence conservation. Cell-based transposon excision and integration assays reveal that the excision step is more severely affected by NTDR deletion. Finally, bioinformatic analyses indicated that the NTDR is specific for the piggyBac superfamily and is also present in domesticated, transposase-derived proteins incapable of catalyzing transposition. Our results indicate an essential role of the NTDR in the “fine-tuning” of transposition and its significance in the functions of piggyBac-originated co-opted genes.
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17
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Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered. Biomolecules 2022; 12:biom12081098. [PMID: 36008992 PMCID: PMC9405754 DOI: 10.3390/biom12081098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 01/02/2023] Open
Abstract
There is increasing evidence that many intrinsically disordered regions (IDRs) in proteins play key functional roles through interactions with other proteins or nucleic acids. These interactions often exhibit a context-dependent structural behavior. We hypothesize that low complexity regions (LCRs), often found within IDRs, could have a role in inducing local structure in IDRs. To test this, we predicted IDRs in the human proteome and analyzed their structures or those of homologous sequences in the Protein Data Bank (PDB). We then identified two types of simple LCRs within IDRs: regions with only one (polyX or homorepeats) or with only two types of amino acids (polyXY). We were able to assign structural information from the PDB more often to these LCRs than to the surrounding IDRs (polyX 61.8% > polyXY 50.5% > IDRs 39.7%). The most frequently observed polyX and polyXY within IDRs contained E (Glu) or G (Gly). Structural analyses of these sequences and of homologs indicate that polyEK regions induce helical conformations, while the other most frequent LCRs induce coil structures. Our work proposes bioinformatics methods to help in the study of the structural behavior of IDRs and provides a solid basis suggesting a structuring role of LCRs within them.
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18
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Structural and Functional Insights into CP2c Transcription Factor Complexes. Int J Mol Sci 2022; 23:ijms23126369. [PMID: 35742810 PMCID: PMC9223585 DOI: 10.3390/ijms23126369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
CP2c, also known as TFCP2, α-CP2, LSF, and LBP-1c, is a prototypic member of the transcription factor (TF) CP2 subfamily involved in diverse ubiquitous and tissue/stage-specific cellular processes and in human malignancies including cancer. Despite its importance, many fundamental regulatory mechanisms of CP2c are still unclear. Here, we uncover unprecedented structural and functional aspects of CP2c using DSP crosslinking and Western blot in addition to conventional methods. We found that a monomeric form of a CP2c homotetramer (tCP2c; [C4]) binds to the known CP2c-binding DNA motif (CNRG-N(5~6)-CNRG), whereas a dimeric form of a CP2c, CP2b, and PIAS1 heterohexamer ([C2B2P2]2) binds to the three consecutive CP2c half-sites or two staggered CP2c binding motifs, where the [C4] exerts a pioneering function for recruiting the [C2B2P2]2 to the target. All CP2c exists as a [C4], or as a [C2B2P2]2 or [C2B2P2]4 in the nucleus. Importantly, one additional cytosolic heterotetrameric CP2c and CP2a complex, ([C2A2]), exerts some homeostatic regulation of the nuclear complexes. These data indicate that these findings are essential for the transcriptional regulation of CP2c in cells within relevant timescales, providing clues not only for the transcriptional regulation mechanism by CP2c but also for future therapeutics targeting CP2c function.
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19
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Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein. Int J Mol Sci 2022; 23:6352. [PMID: 35683031 PMCID: PMC9181416 DOI: 10.3390/ijms23116352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 02/01/2023] Open
Abstract
Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.
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Affiliation(s)
- Veronika Bilanovičová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (V.B.); (N.R.); (L.K.); (M.H.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Nikola Rýdza
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (V.B.); (N.R.); (L.K.); (M.H.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Lilla Koczka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (V.B.); (N.R.); (L.K.); (M.H.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Martin Hess
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (V.B.); (N.R.); (L.K.); (M.H.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Elena Feraru
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; (E.F.); (J.F.)
- VIB-UGent Center for Plant Systems, Technologiepark 71, 9052 Ghent, Belgium
- Department of Applied Genetics and Cell Biology (DAGZ), Institute of Molecular Plant Biology (IMPB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Jiří Friml
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; (E.F.); (J.F.)
- VIB-UGent Center for Plant Systems, Technologiepark 71, 9052 Ghent, Belgium
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
| | - Tomasz Nodzyński
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (V.B.); (N.R.); (L.K.); (M.H.)
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20
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Sheikhhassani V, Scalvini B, Ng J, Heling LWHJ, Ayache Y, Evers TMJ, Estébanez‐Perpiñá E, McEwan IJ, Mashaghi A. Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor. Protein Sci 2022; 31:e4334. [PMID: 35634773 PMCID: PMC9134807 DOI: 10.1002/pro.4334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 12/28/2022]
Abstract
Human androgen receptor contains a large N‐terminal domain (AR‐NTD) that is highly dynamic and this poses a major challenge for experimental and computational analysis to decipher its conformation. Misfolding of the AR‐NTD is implicated in prostate cancer and Kennedy's disease, yet our knowledge of its structure is limited to primary sequence information of the chain and a few functionally important secondary structure motifs. Here, we employed an innovative combination of molecular dynamics simulations and circuit topology (CT) analysis to identify the tertiary structure of AR‐NTD. We found that the AR‐NTD adopts highly dynamic loopy conformations with two identifiable regions with distinct topological make‐up and dynamics. This consists of a N‐terminal region (NR, residues 1–224) and a C‐terminal region (CR, residues 225–538), which carries a dense core. Topological mapping of the dynamics reveals a traceable time‐scale dependent topological evolution. NR adopts different positioning with respect to the CR and forms a cleft that can partly enclose the hormone‐bound ligand‐binding domain (LBD) of the androgen receptor. Furthermore, our data suggest a model in which dynamic NR and CR compete for binding to the DNA‐binding domain of the receptor, thereby regulating the accessibility of its DNA‐binding site. Our approach allowed for the identification of a previously unknown regulatory binding site within the CR core, revealing the structural mechanisms of action of AR inhibitor EPI‐001, and paving the way for other drug discovery applications.
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Affiliation(s)
- Vahid Sheikhhassani
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
| | - Barbara Scalvini
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
| | - Julian Ng
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
| | - Laurens W. H. J. Heling
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
| | - Yosri Ayache
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
| | - Tom M. J. Evers
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
| | - Eva Estébanez‐Perpiñá
- Department of Biochemistry and Molecular Biomedicine Institute of Biomedicine (IBUB) of the University of Barcelona (UB) Barcelona Spain
| | - Iain J. McEwan
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen Scotland UK
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science Leiden University Leiden The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science Leiden University Leiden The Netherlands
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21
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Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction. Biomolecules 2022; 12:biom12050617. [PMID: 35625550 PMCID: PMC9138321 DOI: 10.3390/biom12050617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Arrestin-dependent pathways are a central component of G protein-coupled receptor (GPCRs) signaling. However, the molecular processes regulating arrestin binding are to be further illuminated, in particular with regard to the structural impact of GPCR C-terminal disordered regions. Here, we used an integrated biophysical strategy to describe the basal conformations of the C-terminal domains of three class A GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR) and the β2-adernergic receptor (β2AR). By doing so, we revealed the presence of transient secondary structures in these regions that are potentially involved in the interaction with arrestin. These secondary structure elements differ from those described in the literature in interaction with arrestin. This suggests a mechanism where the secondary structure conformational preferences in the C-terminal regions of GPCRs could be a central feature for optimizing arrestins recognition.
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22
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Camacho-Zarco AR, Schnapka V, Guseva S, Abyzov A, Adamski W, Milles S, Jensen MR, Zidek L, Salvi N, Blackledge M. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. Chem Rev 2022; 122:9331-9356. [PMID: 35446534 PMCID: PMC9136928 DOI: 10.1021/acs.chemrev.1c01023] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Intrinsically disordered
proteins are ubiquitous throughout all
known proteomes, playing essential roles in all aspects of cellular
and extracellular biochemistry. To understand their function, it is
necessary to determine their structural and dynamic behavior and to
describe the physical chemistry of their interaction trajectories.
Nuclear magnetic resonance is perfectly adapted to this task, providing
ensemble averaged structural and dynamic parameters that report on
each assigned resonance in the molecule, unveiling otherwise inaccessible
insight into the reaction kinetics and thermodynamics that are essential
for function. In this review, we describe recent applications of NMR-based
approaches to understanding the conformational energy landscape, the
nature and time scales of local and long-range dynamics and how they
depend on the environment, even in the cell. Finally, we illustrate
the ability of NMR to uncover the mechanistic basis of functional
disordered molecular assemblies that are important for human health.
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Affiliation(s)
| | - Vincent Schnapka
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Serafima Guseva
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Anton Abyzov
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Wiktor Adamski
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Lukas Zidek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic
| | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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23
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Zeke A, Schád É, Horváth T, Abukhairan R, Szabó B, Tantos A. Deep structural insights into RNA-binding disordered protein regions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1714. [PMID: 35098694 PMCID: PMC9539567 DOI: 10.1002/wrna.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
Abstract
Recent efforts to identify RNA binding proteins in various organisms and cellular contexts have yielded a large collection of proteins that are capable of RNA binding in the absence of conventional RNA recognition domains. Many of the recently identified RNA interaction motifs fall into intrinsically disordered protein regions (IDRs). While the recognition mode and specificity of globular RNA binding elements have been thoroughly investigated and described, much less is known about the way IDRs can recognize their RNA partners. Our aim was to summarize the current state of structural knowledge on the RNA binding modes of disordered protein regions and to propose a classification system based on their sequential and structural properties. Through a detailed structural analysis of the complexes that contain disordered protein regions binding to RNA, we found two major binding modes that represent different recognition strategies and, most likely, functions. We compared these examples with DNA binding disordered proteins and found key differences stemming from the nucleic acids as well as similar binding strategies, implying a broader substrate acceptance by these proteins. Due to the very limited number of known structures, we integrated molecular dynamics simulations in our study, whose results support the proposed structural preferences of specific RNA‐binding IDRs. To broaden the scope of our review, we included a brief analysis of RNA‐binding small molecules and compared their structural characteristics and RNA recognition strategies to the RNA‐binding IDRs. This article is categorized under:RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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24
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Gao M, Li P, Su Z, Huang Y. Topological frustration leading to backtracking in a coupled folding-binding process. Phys Chem Chem Phys 2022; 24:2630-2637. [PMID: 35029261 DOI: 10.1039/d1cp04927e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in all species. Their discovery challenges the traditional "sequence-structure-function" paradigm of protein science because IDPs play important roles in various biological processes without preformed folded structures. Bioinformatic analysis reveals that the intrinsically conformational disorder of IDPs as well as their conformational transition upon binding to their targets is encoded by their amino acid sequences. The rRNase domain of colicin E3 and the immunity protein Im3 are a pair of proteins involved in bacterial survival. While the N-terminal segment and the central segment of E3 make comparable intermolecular contacts with Im3 in the bound state, binding of E3 with Im3 is dominantly triggered by the central segment of E3. In this work, to further investigate the binding mechanism of disordered E3 with Im3, we performed systematic free energy and transition path analysis through coarse-grained molecular dynamics simulations. We observed backtracking of the N-terminal segment of E3 in the binding process, whose occurrence depends on salt concentration. Conformational analysis revealed that initial binding of the N-terminal segment of E3 to Im3 usually leads to misorientation of a central hairpin of E3 on Im3, which generates topological frustration and results in backtracking of the N-terminal segment. Our results not only provide deeper mechanistic insights into the coupled folding-binding process of the E3/Im3 complex, but also suggest that topological frustration could be present in the coupled folding-binding process of IDPs and play an important role in regulating the binding transition pathways.
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Affiliation(s)
- Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Ping Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
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25
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Salem A, Wilson CJ, Rutledge BS, Dilliott A, Farhan S, Choy WY, Duennwald ML. Matrin3: Disorder and ALS Pathogenesis. Front Mol Biosci 2022; 8:794646. [PMID: 35083279 PMCID: PMC8784776 DOI: 10.3389/fmolb.2021.794646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.
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Affiliation(s)
- Ahmed Salem
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Carter J. Wilson
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Benjamin S. Rutledge
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison Dilliott
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
| | - Sali Farhan
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
- Department of Human Genetics, McGill Universty, Montreal, QC, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin L. Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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Hsiao AS. Plant Protein Disorder: Spatial Regulation, Broad Specificity, Switch of Signaling and Physiological Status. FRONTIERS IN PLANT SCIENCE 2022; 13:904446. [PMID: 35685011 PMCID: PMC9171514 DOI: 10.3389/fpls.2022.904446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/10/2022] [Indexed: 05/14/2023]
Affiliation(s)
- An-Shan Hsiao
- *Correspondence: An-Shan Hsiao ; orcid.org/0000-0002-2485-9034
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27
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Lewkowicz E, Gursky O. Dynamic protein structures in normal function and pathologic misfolding in systemic amyloidosis. Biophys Chem 2022; 280:106699. [PMID: 34773861 PMCID: PMC9416430 DOI: 10.1016/j.bpc.2021.106699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 02/08/2023]
Abstract
Dynamic and disordered regions in native proteins are often critical for their function, particularly in ligand binding and signaling. In certain proteins, however, such regions can contribute to misfolding and pathologic deposition as amyloid fibrils in vivo. For example, dynamic and disordered regions can promote amyloid formation by destabilizing the native structure, by directly triggering the aggregation, by promoting protein condensation, or by acting as sites of early proteolytic cleavage that favor a release of aggregation-prone fragments or facilitate fibril maturation. At the same time, enhanced dynamics in the native protein state accelerates proteolytic degradation that counteracts amyloid accumulation in vivo. Therefore, the functional need for dynamic protein regions must be balanced against their inherently labile nature. How exactly this balance is achieved and how is it shifted upon amyloidogenic mutations or post-translational modifications? To illustrate possible scenarios, here we review the beneficial and pathologic roles of dynamic and disordered regions in the native states of three families of human plasma proteins that form amyloid precursors in systemic amyloidoses: immunoglobulin light chain, apolipoproteins, and serum amyloid A. Analysis of structure, stability and local dynamics of these diverse proteins and their amyloidogenic variants exemplifies how disordered/dynamic regions can provide a functional advantage as well as an Achilles heel in pathologic amyloid formation.
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Athar HUR, Zulfiqar F, Moosa A, Ashraf M, Zafar ZU, Zhang L, Ahmed N, Kalaji HM, Nafees M, Hossain MA, Islam MS, El Sabagh A, Siddique KHM. Salt stress proteins in plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:999058. [PMID: 36589054 PMCID: PMC9800898 DOI: 10.3389/fpls.2022.999058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.
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Affiliation(s)
- Habib-ur-Rehman Athar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
| | - Anam Moosa
- Department of Plant Pathology, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Zafar Ullah Zafar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Lixin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nadeem Ahmed
- College of Life Sciences, Northwest A&F University, Yangling, China
- Department of Botany, Mohy-ud-Din Islamic University, Nerian Sharif, Pakistan
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, Warsaw, Poland
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Sohidul Islam
- Department of Agronomy, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Ayman El Sabagh
- Faculty of Agriculture, Department of Field Crops, Siirt University, Siirt, Türkiye
- Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Petrth WA, Australia
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
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29
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Risør MW, Jansma AL, Medici N, Thomas B, Dyson HJ, Wright PE. Characterization of the High-Affinity Fuzzy Complex between the Disordered Domain of the E7 Oncoprotein from High-Risk HPV and the TAZ2 Domain of CBP. Biochemistry 2021; 60:3887-3898. [PMID: 34905914 PMCID: PMC8865373 DOI: 10.1021/acs.biochem.1c00669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The intrinsically disordered N-terminal region of the E7 protein from high-risk human papillomavirus (HPV) strains is responsible for oncogenic transformation of host cells through its interaction with a number of cellular factors, including the TAZ2 domain of the transcriptional coactivator CREB-binding protein. Using a variety of spectroscopic and biochemical tools, we find that despite its nanomolar affinity, the HPV16 E7 complex with TAZ2 is disordered and highly dynamic. The disordered domain of HPV16 E7 protein does not adopt a single conformation on the surface of TAZ2 but engages promiscuously with its target through multiple interactions involving two conserved motifs, termed CR1 and CR2, that occupy an extensive binding surface on TAZ2. The fuzzy nature of the complex is a reflection of the promiscuous binding repertoire of viral proteins, which must efficiently dysregulate host cell processes by binding to a variety of host factors in the cellular environment.
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Affiliation(s)
- Michael W. Risør
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, U.S.A.,Joint first author
| | - Ariane L. Jansma
- Department of Chemistry, Point Loma Nazarene University, San Diego, California, 92106, U.S.A.,Joint first author
| | - Natasha Medici
- Department of Chemistry, Point Loma Nazarene University, San Diego, California, 92106, U.S.A
| | - Brittany Thomas
- Department of Chemistry, Point Loma Nazarene University, San Diego, California, 92106, U.S.A
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, U.S.A.,Author for correspondence: H. Jane Dyson, Phone: 1-858-784-2223, , Peter E. Wright, Phone: 1-858-784-9721,
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, U.S.A.,Author for correspondence: H. Jane Dyson, Phone: 1-858-784-2223, , Peter E. Wright, Phone: 1-858-784-9721,
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30
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Ginnard SM, Winkler AE, Mellado Fritz C, Bluhm T, Kemmer R, Gilliam M, Butkevich N, Abdrabbo S, Bricker K, Feiler J, Miller I, Zoerman J, El-Mohri Z, Khuansanguan P, Basch M, Petzold T, Kostoff M, Konopka S, Kociba B, Gillis T, Heyl DL, Trievel RC, Albaugh BN. Molecular investigation of the tandem Tudor domain and plant homeodomain histone binding domains of the epigenetic regulator UHRF2. Proteins 2021; 90:835-847. [PMID: 34766381 DOI: 10.1002/prot.26278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/25/2021] [Accepted: 11/07/2021] [Indexed: 11/12/2022]
Abstract
Ubiquitin-like containing PHD and ring finger (UHRF)1 and UHRF2 are multidomain epigenetic proteins that play a critical role in bridging crosstalk between histone modifications and DNA methylation. Both proteins contain two histone reader domains, called tandem Tudor domain (TTD) and plant homeodomain (PHD), which read the modification status on histone H3 to regulate DNA methylation and gene expression. To shed light on the mechanism of histone binding by UHRF2, we have undergone a detailed molecular investigation with the TTD, PHD and TTD-PHD domains and compared the binding activity to its UHRF1 counterpart. We found that unlike UHRF1 where the PHD is the primary binding contributor, the TTD of UHRF2 has modestly higher affinity toward the H3 tail, while the PHD has a weaker binding interaction. We also demonstrated that like UHRF1, the aromatic amino acids within the TTD are important for binding to H3K9me3 and a conserved aspartic acid within the PHD forms an ionic interaction with R2 of H3. However, while the aromatic amino acids in the TTD of UHRF1 contribute to selectivity, the analogous residues in UHRF2 contribute to both selectivity and affinity. We also discovered that the PHD of UHRF2 contains a distinct asparagine in the H3R2 binding pocket that lowers the binding affinity of the PHD by reducing a potential electrostatic interaction with the H3 tail. Furthermore, we demonstrate the PHD and TTD of UHRF2 cooperate to interact with the H3 tail and that dual domain engagement with the H3 tail relies on specific amino acids. Lastly, our data indicate that the unique stretch region in the TTD of UHRF2 can decrease the melting temperature of the TTD-PHD and represents a disordered region. Thus, these subtle but important mechanistic differences are potential avenues for selectively targeting the histone binding interactions of UHRF1 and UHRF2 with small molecules.
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Affiliation(s)
- Shane M Ginnard
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Alyssa E Winkler
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | | | - Tatum Bluhm
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Ray Kemmer
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Marisa Gilliam
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Nick Butkevich
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Sara Abdrabbo
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Kaitlyn Bricker
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Justin Feiler
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Isaak Miller
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Jenna Zoerman
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Zeineb El-Mohri
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Panida Khuansanguan
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Madyson Basch
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Timothy Petzold
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Matthew Kostoff
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Sean Konopka
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Brendon Kociba
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Thomas Gillis
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Deborah L Heyl
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brittany N Albaugh
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
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31
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Structural and thermodynamical insights into the binding and inhibition of FIH-1 by the N-terminal disordered region of Mint3. J Biol Chem 2021; 297:101304. [PMID: 34655613 PMCID: PMC8571082 DOI: 10.1016/j.jbc.2021.101304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
Mint3 is known to enhance aerobic ATP production, known as the Warburg effect, by binding to FIH-1. Since this effect is considered to be beneficial for cancer cells, the interaction is a promising target for cancer therapy. However, previous research has suggested that the interacting region of Mint3 with FIH-1 is intrinsically disordered, which makes investigation of this interaction challenging. Therefore, we adopted thermodynamic and structural studies in solution to clarify the structural and thermodynamical changes of Mint3 binding to FIH-1. First, using a combination of circular dichroism, nuclear magnetic resonance, and hydrogen/deuterium exchange–mass spectrometry (HDX-MS), we confirmed that the N-terminal half, which is the interacting part of Mint3, is mostly disordered. Next, we revealed a large enthalpy and entropy change in the interaction of Mint3 using isothermal titration calorimetry (ITC). The profile is consistent with the model that the flexibility of disordered Mint3 is drastically reduced upon binding to FIH-1. Moreover, we performed a series of ITC experiments with several types of truncated Mint3s, an effective approach since the interacting part of Mint3 is disordered, and identified amino acids 78 to 88 as a novel core site for binding to FIH-1. The truncation study of Mint3 also revealed the thermodynamic contribution of each part of Mint3 to the interaction with FIH-1, where the core sites contribute to the affinity (ΔG), while other sites only affect enthalpy (ΔH), by forming noncovalent bonds. This insight can serve as a foothold for further investigation of intrinsically disordered regions (IDRs) and drug development for cancer therapy.
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32
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Coordination of transcription, processing, and export of highly expressed RNAs by distinct biomolecular condensates. Emerg Top Life Sci 2021; 4:281-291. [PMID: 32338276 PMCID: PMC7733674 DOI: 10.1042/etls20190160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/30/2022]
Abstract
Genes under control of super-enhancers are expressed at extremely high levels and are frequently associated with nuclear speckles. Recent data suggest that the high concentration of unphosphorylated RNA polymerase II (Pol II) and Mediator recruited to super-enhancers create phase-separated condensates. Transcription initiates within or at the surface of these phase-separated droplets and the phosphorylation of Pol II, associated with transcription initiation and elongation, dissociates Pol II from these domains leading to engagement with nuclear speckles, which are enriched with RNA processing factors. The transitioning of Pol II from transcription initiation domains to RNA processing domains effectively co-ordinates transcription and processing of highly expressed RNAs which are then rapidly exported into the cytoplasm.
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33
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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34
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Enthalpy-Entropy Compensation in the Promiscuous Interaction of an Intrinsically Disordered Protein with Homologous Protein Partners. Biomolecules 2021; 11:biom11081204. [PMID: 34439869 PMCID: PMC8391806 DOI: 10.3390/biom11081204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) can engage in promiscuous interactions with their protein targets; however, it is not clear how this feature is encoded in the primary sequence of the IDPs and to what extent the surface properties and the shape of the binding cavity dictate the binding mode and the final bound conformation. Here we show, using a combination of nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), that the promiscuous interaction of the intrinsically disordered regulatory domain of the mitogen-activated protein kinase kinase MKK4 with p38α and JNK1 is facilitated by folding-upon-binding into two different conformations, despite the high sequence conservation and structural homology between p38α and JNK1. Our results support a model whereby the specific surface properties of JNK1 and p38α dictate the bound conformation of MKK4 and that enthalpy–entropy compensation plays a major role in maintaining comparable binding affinities for MKK4 towards the two kinases.
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35
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Clerc I, Sagar A, Barducci A, Sibille N, Bernadó P, Cortés J. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Comput Struct Biotechnol J 2021; 19:3817-3828. [PMID: 34285781 PMCID: PMC8273358 DOI: 10.1016/j.csbj.2021.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/15/2023] Open
Abstract
Intrinsically Disordered Proteins and Regions (IDPs/IDRs) are key components of a multitude of biological processes. Conformational malleability enables IDPs/IDRs to perform very specialized functions that cannot be accomplished by globular proteins. The functional role for most of these proteins is related to the recognition of other biomolecules to regulate biological processes or as a part of signaling pathways. Depending on the extent of disorder, the number of interacting sites and the type of partner, very different architectures for the resulting assemblies are possible. More recently, molecular condensates with liquid-like properties composed of multiple copies of IDPs and nucleic acids have been proven to regulate key processes in eukaryotic cells. The structural and kinetic details of disordered biomolecular complexes are difficult to unveil experimentally due to their inherent conformational heterogeneity. Computational approaches, alone or in combination with experimental data, have emerged as unavoidable tools to understand the functional mechanisms of this elusive type of assemblies. The level of description used, all-atom or coarse-grained, strongly depends on the size of the molecular systems and on the timescale of the investigated mechanism. In this mini-review, we describe the most relevant architectures found for molecular interactions involving IDPs/IDRs and the computational strategies applied for their investigation.
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Affiliation(s)
- Ilinka Clerc
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
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Abdulrahman DA, Meng X, Veit M. S-Acylation of Proteins of Coronavirus and Influenza Virus: Conservation of Acylation Sites in Animal Viruses and DHHC Acyltransferases in Their Animal Reservoirs. Pathogens 2021; 10:669. [PMID: 34072434 PMCID: PMC8227752 DOI: 10.3390/pathogens10060669] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 01/21/2023] Open
Abstract
Recent pandemics of zoonotic origin were caused by members of coronavirus (CoV) and influenza A (Flu A) viruses. Their glycoproteins (S in CoV, HA in Flu A) and ion channels (E in CoV, M2 in Flu A) are S-acylated. We show that viruses of all genera and from all hosts contain clusters of acylated cysteines in HA, S and E, consistent with the essential function of the modification. In contrast, some Flu viruses lost the acylated cysteine in M2 during evolution, suggesting that it does not affect viral fitness. Members of the DHHC family catalyze palmitoylation. Twenty-three DHHCs exist in humans, but the number varies between vertebrates. SARS-CoV-2 and Flu A proteins are acylated by an overlapping set of DHHCs in human cells. We show that these DHHC genes also exist in other virus hosts. Localization of amino acid substitutions in the 3D structure of DHHCs provided no evidence that their activity or substrate specificity is disturbed. We speculate that newly emerged CoVs or Flu viruses also depend on S-acylation for replication and will use the human DHHCs for that purpose. This feature makes these DHHCs attractive targets for pan-antiviral drugs.
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Affiliation(s)
- Dina A. Abdulrahman
- Department of Virology, Animal Health Research Institute (AHRI), Giza 12618, Egypt;
| | - Xiaorong Meng
- Institute of Virology, Veterinary Faculty, Free University Berlin, 14163 Berlin, Germany;
| | - Michael Veit
- Institute of Virology, Veterinary Faculty, Free University Berlin, 14163 Berlin, Germany;
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Bokor M, Tantos Á. Protein-Protein Connections-Oligomer, Amyloid and Protein Complex-By Wide Line 1H NMR. Biomolecules 2021; 11:biom11050757. [PMID: 34070204 PMCID: PMC8158481 DOI: 10.3390/biom11050757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/29/2021] [Accepted: 05/14/2021] [Indexed: 01/26/2023] Open
Abstract
The amount of bonds between constituting parts of a protein aggregate were determined in wild type (WT) and A53T α-synuclein (αS) oligomers, amyloids and in the complex of thymosin-β4–cytoplasmic domain of stabilin-2 (Tβ4-stabilin CTD). A53T αS aggregates have more extensive βsheet contents reflected by constant regions at low potential barriers in difference (to monomers) melting diagrams (MDs). Energies of the intermolecular interactions and of secondary structures bonds, formed during polymerization, fall into the 5.41 kJ mol−1 ≤ Ea ≤ 5.77 kJ mol−1 range for αS aggregates. Monomers lose more mobile hydration water while forming amyloids than oligomers. Part of the strong mobile hydration water–protein bonds break off and these bonding sites of the protein form intermolecular bonds in the aggregates. The new bonds connect the constituting proteins into aggregates. Amyloid–oligomer difference MD showed an overall more homogeneous solvent accessible surface of A53T αS amyloids. From the comparison of the nominal sum of the MDs of the constituting proteins to the measured MD of the Tβ4-stabilin CTD complex, the number of intermolecular bonds connecting constituent proteins into complex is 20(1) H2O/complex. The energies of these bonds are in the 5.40(3) kJ mol−1 ≤ Ea ≤ 5.70(5) kJ mol−1 range.
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Affiliation(s)
- Mónika Bokor
- Wigner Research Centre for Physics, Institute for Solid State Physics and Optics, 1121 Budapest, Hungary
- Correspondence: ; Tel.: +36-209939420
| | - Ágnes Tantos
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary;
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Sagar A, Herranz-Trillo F, Langkilde AE, Vestergaard B, Bernadó P. Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets. Structure 2021; 29:1074-1090.e4. [PMID: 33862013 DOI: 10.1016/j.str.2021.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Transient biomolecular interactions play crucial roles in many cellular signaling and regulation processes. However, deciphering the structure of these assemblies is challenging owing to the difficulties in isolating complexes from the individual partners. The additive nature of small-angle X-ray scattering (SAXS) data allows for probing the species present in these mixtures, but decomposition into structural and thermodynamic information is difficult. We present a chemometric approach enabling the decomposition of titration SAXS data into species-specific information. Using extensive synthetic SAXS data, we demonstrate that robust decomposition can be achieved for titrations with a maximum fraction of complex of 0.5 that can be extended to 0.3 when two orthogonal titrations are simultaneously analyzed. The effect of the structural features, titration points, relative concentrations, and noise are thoroughly analyzed. The validation of the strategy with experimental data highlights the power of the approach to provide unique insights into this family of biomolecular assemblies.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
| | - Fátima Herranz-Trillo
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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39
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Jin Y, Kotler JLM, Wang S, Huang B, Halpin JC, Street TO. The ER Chaperones BiP and Grp94 Regulate the Formation of Insulin-Like Growth Factor 2 (IGF2) Oligomers. J Mol Biol 2021; 433:166963. [PMID: 33811917 DOI: 10.1016/j.jmb.2021.166963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023]
Abstract
While cytosolic Hsp90 chaperones have been extensively studied, less is known about how the ER Hsp90 paralog Grp94 recognizes clients and influences client folding. Here, we examine how Grp94 and the ER Hsp70 paralog, BiP, influence the folding of insulin-like growth factor 2 (IGF2), an established client protein of Grp94. ProIGF2 is composed of a disulfide-bonded insulin-like hormone and a C-terminal E-peptide that has sequence characteristics of an intrinsically disordered region. BiP and Grp94 have a minimal influence on folding whereby both chaperones slow proIGF2 folding and do not substantially alter the disulfide-bonded folding intermediates, suggesting that BiP and Grp94 may have an additional influence unrelated to proIGF2 folding. Indeed, we made the unexpected discovery that the E-peptide region allows proIGF2 to form dynamic oligomers. ProIGF2 oligomers can transition from a dynamic state that is capable of exchanging monomers to an irreversibly aggregated state, providing a plausible role for BiP and Grp94 in regulating proIGF2 oligomerization. In contrast to the modest influence on folding, BiP and Grp94 have a stronger influence on proIGF2 oligomerization and these chaperones exert counteracting effects. BiP suppresses proIGF2 oligomerization while Grp94 can enhance proIGF2 oligomerization in a nucleotide-dependent manner. We propose that BiP and Grp94 regulate the assembly and dynamic behavior of proIGF2 oligomers, although the biological role of proIGF2 oligomerization is not yet known.
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Affiliation(s)
- Yi Jin
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Judy L M Kotler
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Shiyu Wang
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Bin Huang
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jackson C Halpin
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Timothy O Street
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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40
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Appadurai R, Nagesh J, Srivastava A. High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme. Nat Commun 2021; 12:958. [PMID: 33574233 PMCID: PMC7878814 DOI: 10.1038/s41467-021-21105-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Mapping free energy landscapes of complex multi-funneled metamorphic proteins and weakly-funneled intrinsically disordered proteins (IDPs) remains challenging. While rare-event sampling molecular dynamics simulations can be useful, they often need to either impose restraints or reweigh the generated data to match experiments. Here, we present a parallel-tempering method that takes advantage of accelerated water dynamics and allows efficient and accurate conformational sampling across a wide variety of proteins. We demonstrate the improved sampling efficiency by benchmarking against standard model systems such as alanine di-peptide, TRP-cage and β-hairpin. The method successfully scales to large metamorphic proteins such as RFA-H and to highly disordered IDPs such as Histatin-5. Across the diverse proteins, the calculated ensemble averages match well with the NMR, SAXS and other biophysical experiments without the need to reweigh. By allowing accurate sampling across different landscapes, the method opens doors for sampling free energy landscape of complex uncharted proteins.
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Affiliation(s)
- Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Jayashree Nagesh
- Solid State & Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.
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di Rienzo V, Imanifard Z, Mascio I, Gasser CS, Skinner DJ, Pierri CL, Marini M, Fanelli V, Sabetta W, Montemurro C, Bellin D. Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation. HORTICULTURE RESEARCH 2021; 8:29. [PMID: 33518713 PMCID: PMC7848007 DOI: 10.1038/s41438-021-00467-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/06/2023]
Abstract
Seedlessness represents a highly appreciated trait in table grapes. Based on an interesting case of seedless fruit production described in the crop species Annona squamosa, we focused on the Vitis vinifera INNER NO OUTER (INO) gene as a candidate. This gene encodes a transcription factor belonging to the YABBY family involved in the determination of abaxial identity in several organs. In Arabidopsis thaliana, this gene was shown to be essential for the formation and asymmetric growth of the ovule outer integument and its mutation leads to a phenotypic defect of ovules and failure in seed formation. In this study, we identified in silico the V. vinifera orthologue and investigated its phylogenetic relationship to INO genes from other species and its expression in different organs in seeded and seedless varieties. Applying cross-species complementation, we have tested its functionality in the Arabidopsis ino-1 mutant. We show that the V. vinifera INO successfully rescues the ovule outer integument growth and seeds set and also partially complements the outer integument asymmetric growth in the Arabidopsis mutant, differently from orthologues from other species. These data demonstrate that VviINO retains similar activity and protein targets in grapevine as in Arabidopsis. Potential implications for grapevine breeding are discussed.
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Affiliation(s)
- Valentina di Rienzo
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
| | - Zahra Imanifard
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
| | - Charles S Gasser
- Department of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Debra J Skinner
- Department of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry Molecular and Structural Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70126 Bari, Italy
- Spin off BROWSer S.r.l. (https://browser-bioinf.com/) c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona 4, 70126, Bari, Italy
| | - Martina Marini
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy
| | - Wilma Sabetta
- Institute of Biosciences and Bioresources of the National Research Council (IBBR-CNR), Via Amendola 165/A, 70125, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, Section of Genetics and Breeding, University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy.
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, via Amendola 165/A, 70125, Bari, Italy.
- Institute for Sustainable Plant Protection-Support Unit Bari, National Research Council of Italy (CNR), Via Amendola 165/A, 70125 Bari, Italy.
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.
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42
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PiP 2 favors an α-helical structure of non-recombinant Hsp12 of Saccharomyces cerevisiae. Protein Expr Purif 2021; 181:105830. [PMID: 33485946 DOI: 10.1016/j.pep.2021.105830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 11/23/2022]
Abstract
Hsp12 is a small heat shock protein of Saccharomyces cerevisiae upregulated in response to various stresses. Non recombinant Hsp12 has been purified and characterized. Using circular dichroism (CD), Isothermal Titration Calorimetry (ITC) and Differential Scanning Calorimetry (DSC), it has been demonstrated that the native Hsp12 is monomeric and intrinsically disordered (IDP). Hsp12 gains in structure in the presence of specific lipids (PiP2). The helical form binds to liposomes models membrane with high affinity, leading to their rigidification. These results suggest that hydrophobic and ionic interactions are involved. Hsp12 is most likely a membrane chaperone expressed during stresses in Saccharomyces cerevisiae.
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43
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Jana T, Brodsky S, Barkai N. Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites. Trends Genet 2021; 37:421-432. [PMID: 33414013 DOI: 10.1016/j.tig.2020.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors (TFs) regulate gene expression by binding DNA sequences recognized by their DNA-binding domains (DBDs). DBD-recognized motifs are short and highly abundant in genomes. The ability of TFs to bind a specific subset of motif-containing sites, and to do so rapidly upon activation, is fundamental for gene expression in all eukaryotes. Despite extensive interest, our understanding of the TF-target search process is fragmented; although binding specificity and detection speed are two facets of this same process, trade-offs between them are rarely addressed. In this opinion article, we discuss potential speed-specificity trade-offs in the context of existing models. We further discuss the recently described 'distributed specificity' paradigm, suggesting that intrinsically disordered regions (IDRs) promote specificity while reducing the TF-target search time.
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Affiliation(s)
- Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Tan F, Sun N, Zhang L, Wu J, Xiao S, Tan Q, Uversky VN, Liu Y. Functional characterization of an unknown soybean intrinsically disordered protein in vitro and in Escherichia coli. Int J Biol Macromol 2021; 166:538-549. [PMID: 33137381 DOI: 10.1016/j.ijbiomac.2020.10.211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess a wide range of biological function in all organisms, however the specific functions of most IDPs are still unknown. Soybean LOC protein, LOC for short, is a heat-stable protein, which is more abundant in the stress-resistant radicles. Sequence alignment and phylogenetic analysis showed that LOC is a functionally unknown protein and conserved in Fabaceae. LOC, being enriched in most disorder-promoting residues and depleted in most order-promoting residues, was predicted to contain high levels of intrinsic disorder by several commonly used computational tools. However, it was also predicted to contain two disorder-based protein-protein binding sites and two short α-helical segments. The circular dichroism spectroscopic analysis showed that this protein is mostly disordered in water, but can form more α-helical structure in the presence of SDS and TFE. Functional in vitro studies showed that the LOC protein is able to prevent lactate dehydrogenase inactivation by freeze-thaw at a molar ratio of 10:1. Furthermore, in vivo analyses revealed the survival rate of Escherichia coli over-expressing LOC protein under the conditions of osmotic stress was noticeably increased in comparison with the control. These observations suggest that the intrinsically disordered protein LOC might serve as a chaperone and/or cell protector.
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Affiliation(s)
- Fangmei Tan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Nan Sun
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Linsong Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Jiahui Wu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Shifeng Xiao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Qiulong Tan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, Florida, USA; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow, region, Russia.
| | - Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China.
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Lermyte F. Roles, Characteristics, and Analysis of Intrinsically Disordered Proteins: A Minireview. Life (Basel) 2020; 10:E320. [PMID: 33266184 PMCID: PMC7761095 DOI: 10.3390/life10120320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a growing understanding that a significant fraction of the eukaryotic proteome is intrinsically disordered, and that these conformationally dynamic proteins play a myriad of vital biological roles in both normal and pathological states. In this review, selected examples of intrinsically disordered proteins are highlighted, with particular attention for a few which are relevant in neurological disorders and in viral infection. Next, the underlying causes for the intrinsic disorder are discussed, along with computational methods used to predict whether a given amino acid sequence is likely to adopt a folded or unfolded state in the solution. Finally, biophysical methods for the analysis of intrinsically disordered proteins will be discussed, as well as the unique challenges they pose in this context due to their highly dynamic nature.
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Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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46
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Chong S, Mir M. Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions. J Mol Biol 2020; 433:166724. [PMID: 33248138 DOI: 10.1016/j.jmb.2020.11.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/14/2020] [Accepted: 11/19/2020] [Indexed: 01/03/2023]
Abstract
A substantial portion of the proteome consists of intrinsically disordered regions (IDRs) that do not fold into well-defined 3D structures yet perform numerous biological functions and are associated with a broad range of diseases. It has been a long-standing enigma how different IDRs successfully execute their specific functions. Further putting a spotlight on IDRs are recent discoveries of functionally relevant biomolecular assemblies, which in some cases form through liquid-liquid phase separation. At the molecular level, the formation of biomolecular assemblies is largely driven by weak, multivalent, but selective IDR-IDR interactions. Emerging experimental and computational studies suggest that the primary amino acid sequences of IDRs encode a variety of their interaction behaviors. In this review, we focus on findings and insights that connect sequence-derived features of IDRs to their conformations, propensities to form biomolecular assemblies, selectivity of interaction partners, functions in the context of physiology and disease, and regulation of function. We also discuss directions of future research to facilitate establishing a comprehensive sequence-function paradigm that will eventually allow prediction of selective interactions and specificity of function mediated by IDRs.
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Affiliation(s)
- Shasha Chong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, United States; The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, United States.
| | - Mustafa Mir
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, United States
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47
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Reddy ST, Uversky VN, Costa-Filho AJ. Biophysical characterization of intrinsically disordered human Golgi matrix protein GRASP65. Int J Biol Macromol 2020; 162:1982-1993. [DOI: 10.1016/j.ijbiomac.2020.08.126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/30/2020] [Accepted: 08/14/2020] [Indexed: 01/21/2023]
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48
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Brown CJ, Verma CS, Lane DP, Lama D. Conformational ordering of intrinsically disordered peptides for targeting translation initiation. Biochim Biophys Acta Gen Subj 2020; 1865:129775. [PMID: 33122085 DOI: 10.1016/j.bbagen.2020.129775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/14/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Intrinsically disordered regions (IDRs) in proteins can regulate their activity by facilitating protein-protein interactions (PPIs) as exemplified in the recruitment of the eukaryotic translation initiation factor 4E (eIF4E) protein by the protein eIF4G. Deregulation of this PPI module is central to a broad spectrum of cancer related malignancies and its targeted inhibition through bioactive peptides is a promising strategy for therapeutic intervention. METHODS We employed molecular dynamics simulations coupled with biophysical assays to rationally develop peptide derivatives from the intrinsically disordered eIF4G scaffold by incorporating non-natural amino acids that facilitates disorder-to-order transition. RESULTS The conformational heterogeneity of these peptides and the degree of structural reorganization required to adopt the optimum mode of interaction with eIF4E underscores their differential binding affinities. The presence of a pre-structured local helical element in the ensemble of structures was instrumental in the efficient docking of the peptides on to the protein surface. The formation of Y4: P38 hydrogen-bond interaction between the peptide and eIF4E is a rate limiting event in the efficient recognition of the protein since it occurs through the disordered region of the peptide. CONCLUSIONS These insights were exploited to further design features into the peptide to propagate bound-state conformations in solution which resulted in the generation of a potent eIF4E binder. GENERAL SIGNIFICANCE The study illustrates the molecular basis of eIF4E recognition by a disordered epitope from eIF4G and its modulation to generate peptides that can potentially attenuate translation initiation in oncology.
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Affiliation(s)
- Christopher J Brown
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, 138648, Singapore.
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, 637551, Singapore
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, 138648, Singapore; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Biomedicum Quarter 7B-C Solnavägen 9, 17165 Solna, Sweden
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Biomedicum Quarter 7B-C Solnavägen 9, 17165 Solna, Sweden.
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49
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Chasing coevolutionary signals in intrinsically disordered proteins complexes. Sci Rep 2020; 10:17962. [PMID: 33087759 PMCID: PMC7578644 DOI: 10.1038/s41598-020-74791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/27/2020] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins/regions (IDPs/IDRs) are crucial components of the cell, they are highly abundant and participate ubiquitously in a wide range of biological functions, such as regulatory processes and cell signaling. Many of their important functions rely on protein interactions, by which they trigger or modulate different pathways. Sequence covariation, a powerful tool for protein contact prediction, has been applied successfully to predict protein structure and to identify protein–protein interactions mostly of globular proteins. IDPs/IDRs also mediate a plethora of protein–protein interactions, highlighting the importance of addressing sequence covariation-based inter-protein contact prediction of this class of proteins. Despite their importance, a systematic approach to analyze the covariation phenomena of intrinsically disordered proteins and their complexes is still missing. Here we carry out a comprehensive critical assessment of coevolution-based contact prediction in IDP/IDR complexes and detail the challenges and possible limitations that emerge from their analysis. We found that the coevolutionary signal is faint in most of the complexes of disordered proteins but positively correlates with the interface size and binding affinity between partners. In addition, we discuss the state-of-art methodology by biological interpretation of the results, formulate evaluation guidelines and suggest future directions of development to the field.
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Yin G, Zhang J, Nair V, Truong V, Chaia A, Petela J, Harrison J, Gorfe AA, Campbell SL. KRAS Ubiquitination at Lysine 104 Retains Exchange Factor Regulation by Dynamically Modulating the Conformation of the Interface. iScience 2020; 23:101448. [PMID: 32882514 PMCID: PMC7479270 DOI: 10.1016/j.isci.2020.101448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/13/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
RAS proteins function as highly regulated molecular switches that control cellular growth. In addition to regulatory proteins, RAS undergoes a number of posttranslational modifications (PTMs) that regulate its activity. Lysine 104, a hot spot for multiple PTMs, is a highly conserved residue that forms key interactions that stabilize the RAS helix-2(H2)/helix-3(H3) interface. Mutation at 104 attenuates interaction with guanine nucleotide exchange factors (GEFs), whereas ubiquitination at lysine 104 retains GEF regulation. To elucidate how ubiquitination modulates RAS function, we generated monoubiquitinated KRAS at 104 using chemical biology approaches and conducted biochemical, NMR, and computational analyses. We find that ubiquitination promotes a new dynamic interaction network and alters RAS conformational dynamics to retain GEF function. These findings reveal a mechanism by which ubiquitination can regulate protein function.
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Affiliation(s)
- Guowei Yin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Jerry Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vinay Nair
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vinh Truong
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Angelo Chaia
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Johnny Petela
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph Harrison
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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