1
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Hurali DT, Banerjee M, Ballal A. Unravelling the involvement of protein disorder in cyanobacterial stress responses. Int J Biol Macromol 2024; 277:133934. [PMID: 39025183 DOI: 10.1016/j.ijbiomac.2024.133934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
This study has explored the involvement of Intrinsically Disordered Proteins (IDPs) in cyanobacterial stress response. IDPs possess distinct physicochemical properties, which allow them to execute diverse functions. Anabaena PCC 7120, the model photosynthetic, nitrogen-fixing cyanobacterium encodes 688 proteins (11 % of the total proteome) with at least one intrinsically disordered region (IDR). Of these, 130 proteins that showed >30 % overall disorder were designated as IDPs. Physico-chemical analysis, showed these IDPs to adopt shapes ranging from 'globular' to 'tadpole-like'. Upon exposure to NaCl, 41 IDP-encoding genes were found to be differentially expressed. Surprisingly, most of these were induced, indicating the importance of IDP-accumulation in overcoming salt stress. Subsequently, six IDPs were identified to be induced by multiple stresses (salt, ammonium and selenite). Interestingly, the presence of these 6-multiple stress-induced IDPs was conserved in filamentous cyanobacteria. Utilizing the experimental proteomic data of Anabaena, these 6 IDPs were found to interact with many proteins involved in diverse pathways, underscoring their physiological importance as protein hubs. This study lays the framework for IDP-related research in Anabaena by (a) identifying, as well as physiochemically characterizing, all the disordered proteins and (b) uncovering a subset of IDPs that are likely to be critical in adaptation to environmental stresses.
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Affiliation(s)
- Deepak T Hurali
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
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2
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Parra RG, Freiberger MI, Poley-Gil M, Fernandez-Martin M, Radusky L, Ruiz-Serra V, Wolynes P, Ferreiro D, Valencia A. Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families. Nucleic Acids Res 2024; 52:W233-W237. [PMID: 38587198 PMCID: PMC11223790 DOI: 10.1093/nar/gkae244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.
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Affiliation(s)
- R Gonzalo Parra
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Maria I Freiberger
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Miriam Poley-Gil
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Miguel Fernandez-Martin
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Victoria Ruiz-Serra
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Peter G Wolynes
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Diego U Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Alfonso Valencia
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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3
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Muradyan N, Arakelov V, Sargsyan A, Paronyan A, Arakelov G, Nazaryan K. Impact of mutations on the stability of SARS-CoV-2 nucleocapsid protein structure. Sci Rep 2024; 14:5870. [PMID: 38467657 PMCID: PMC10928099 DOI: 10.1038/s41598-024-55157-8] [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: 10/30/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 is known to participate in various host cellular processes, including interferon inhibition, RNA interference, apoptosis, and regulation of virus life cycles. Additionally, it has potential as a diagnostic antigen and/or immunogen. Our research focuses on examining structural changes caused by mutations in the N protein. We have modeled the complete tertiary structure of native and mutated forms of the N protein using Alphafold2. Notably, the N protein contains 3 disordered regions. The focus was on investigating the impact of mutations on the stability of the protein's dimeric structure based on binding free energy calculations (MM-PB/GB-SA) and RMSD fluctuations after MD simulations. The results demonstrated that 28 mutations out of 37 selected mutations analyzed, compared with wild-type N protein, resulted in a stable dimeric structure, while 9 mutations led to destabilization. Our results are important to understand the tertiary structure of the N protein dimer of SARS-CoV-2 and the effect of mutations on it, their behavior in the host cell, as well as for the research of other viruses belonging to the same genus additionally, to anticipate potential strategies for addressing this viral illness․.
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Affiliation(s)
- Nelli Muradyan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia (NAS RA), 0014, Yerevan, Armenia
| | - Vahram Arakelov
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia (NAS RA), 0014, Yerevan, Armenia
| | - Arsen Sargsyan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia (NAS RA), 0014, Yerevan, Armenia
- Russian-Armenian University, 0051, Yerevan, Armenia
| | - Adrine Paronyan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia (NAS RA), 0014, Yerevan, Armenia
- Russian-Armenian University, 0051, Yerevan, Armenia
| | - Grigor Arakelov
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia (NAS RA), 0014, Yerevan, Armenia.
- Russian-Armenian University, 0051, Yerevan, Armenia.
| | - Karen Nazaryan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia (NAS RA), 0014, Yerevan, Armenia
- Russian-Armenian University, 0051, Yerevan, Armenia
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4
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Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Local energetic frustration conservation in protein families and superfamilies. Nat Commun 2023; 14:8379. [PMID: 38104123 PMCID: PMC10725452 DOI: 10.1038/s41467-023-43801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a methodology to analyze local frustration patterns within protein families and superfamilies that allows us to uncover constraints related to stability and function, and identify differential frustration patterns in families with a common ancestry. We analyze these signals in very well studied protein families such as PDZ, SH3, ɑ and β globins and RAS families. Recent advances in protein structure prediction make it possible to analyze a vast majority of the protein space. An automatic and unsupervised proteome-wide analysis on the SARS-CoV-2 virus demonstrates the potential of our approach to enhance our understanding of the natural phenotypic diversity of protein families beyond single protein instances. We apply our method to modify biophysical properties of natural proteins based on their family properties, as well as perform unsupervised analysis of large datasets to shed light on the physicochemical signatures of poorly characterized proteins such as the ones belonging to emergent pathogens.
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Affiliation(s)
- Maria I Freiberger
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Victoria Ruiz-Serra
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Camila Pontes
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Miguel Romero-Durana
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, 8331150, Chile
| | - Cesar A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, 8331150, Chile
| | - Claudio D Schuster
- Laboratorio de Bioinformática, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Marcelo A Marti
- Laboratorio de Bioinformática, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Peter G Wolynes
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Diego U Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - R Gonzalo Parra
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
| | - Alfonso Valencia
- Computational Biology Group, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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5
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Skriver K, Theisen FF, Kragelund BB. Conformational entropy in molecular recognition of intrinsically disordered proteins. Curr Opin Struct Biol 2023; 83:102697. [PMID: 37716093 DOI: 10.1016/j.sbi.2023.102697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023]
Abstract
Broad conformational ensembles make intrinsically disordered proteins or regions entropically intriguing. Although methodologically challenging and understudied, emerging studies into their changes in conformational entropy (ΔS°conf) upon complex formation have provided both quantitative and qualitative insight. Recent work based on thermodynamics from isothermal titration calorimetry and NMR spectroscopy uncovers an expanded repertoire of regulatory mechanisms, where ΔS°conf plays roles in partner selection, state behavior, functional buffering, allosteric regulation, and drug design. We highlight these mechanisms to display the large entropic reservoir of IDPs for the regulation of molecular communication. We call upon the field to make efforts to contribute to this insight as more studies are needed for forwarding mechanistic decoding of intrinsically disordered proteins and their complexes.
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Affiliation(s)
- Karen Skriver
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Frederik Friis Theisen
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark. https://twitter.com/@FrederikTheisen
| | - Birthe B Kragelund
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
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6
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Zhou X, Song H, Li J. Residue-Frustration-Based Prediction of Protein-Protein Interactions Using Machine Learning. J Phys Chem B 2022; 126:1719-1727. [PMID: 35170967 DOI: 10.1021/acs.jpcb.1c10525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of protein-protein interactions (PPIs) is important in understanding the function of proteins. However, it is still a challenge to investigate the transient protein-protein interaction by experiments. Hence, the computational prediction for protein-protein interactions draws growing attention. Statistics-based features have been widely used in the studies of protein structure prediction and protein folding. Due to the scarcity of experimental data of PPI, it is difficult to construct a conventional statistical feature for PPI prediction, and the application of statistics-based features is very limited in this field. In this paper, we explored the application of frustration, a statistical potential, in PPI prediction. By comparing the energetic contribution of the extra stabilization energy from a given residue pair in the native protein with the statistics of the energies, we obtained the residue pair's frustration index. By calculating the number of residue pairs with a high frustration index, the highly frustrated density, a residue-frustration-based feature, was then obtained to describe the tendency of residues to be involved in PPI. Highly frustrated density, as well as structure-based features, were then used to describe protein residues and combined with the long short-term memory (LSTM) neural network to predict PPI residue pairs. Our model correctly predicted 75% dimers when only the top 2‰ residue pairs were selected in each dimer. Our model, which considers the statistics-based features, is significantly different from the models based on the chemical features of residues. We found that frustration can effectively describe the tendency of residue to be involved in PPI. Frustration-based features can replace chemical features to combine with machine learning and realize the better performance of PPI prediction. It reveals the great potential of statistical potential such as frustration in PPI prediction.
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Affiliation(s)
- Xiaozhou Zhou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Haoyu Song
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China
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7
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Rausch AO, Freiberger MI, Leonetti CO, Luna DM, Radusky LG, Wolynes PG, Ferreiro DU, Parra RG. FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations. Bioinformatics 2021; 37:3038-3040. [PMID: 33720293 DOI: 10.1093/bioinformatics/btab176] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/19/2021] [Accepted: 03/11/2021] [Indexed: 02/02/2023] Open
Abstract
SUMMARY Once folded, natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they are highly frustrated. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here, we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and molecular dynamics (MD) trajectories, allowing straightforward integration of local frustration analysis into pipelines for protein structural analysis. AVAILABILITY AND IMPLEMENTATION https://github.com/proteinphysiologylab/frustratometeR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Atilio O Rausch
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Entre Ríos E3100XAD, Argentina
| | - Maria I Freiberger
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Cesar O Leonetti
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Diego M Luna
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Entre Ríos E3100XAD, Argentina
| | - Leandro G Radusky
- Center for Genomic Regulation, Barcelona Institute for Science and Technology, Barcelona 08003, Spain
| | - Peter G Wolynes
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Diego U Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica - IQUIBICEN/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - R Gonzalo Parra
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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8
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Chang M, Wilson CJ, Karunatilleke NC, Moselhy MH, Karttunen M, Choy WY. Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism. J Chem Theory Comput 2021; 17:3145-3156. [PMID: 33861593 DOI: 10.1021/acs.jctc.0c01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2)-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity, thereby reducing the efficacy of both chemotherapeutics and radiotherapies. Key to this antioxidant pathway is the interaction between Nrf2 and CREB binding protein (CBP), mediated by the Neh4 and Neh5 domains of Nrf2. Disruption of this interaction via small-molecule therapeutics could negate the effects of aberrant Nrf2 upregulation. Due to the disordered nature of these domains, there remains no three-dimensional structure of Neh4 or Neh5, making structure-based drug design a challenge. Here, we performed 48 μs of unbiased molecular dynamics (MD) simulations with the Amber99SB*-ILDNP and CHARMM36m force fields and circular dichroism (CD) spectropolarimetry experiments to elucidate the free-state structures of these domains; no previous data regarding their conformational landscapes exists. There are two main findings: First, we find Neh5 to be markedly more disordered than Neh4, which has nine residues in the middle of the domain showing α-helical propensity, thus pointing to Neh4 and Neh5 having different binding mechanisms. Second, the two force fields show strong differences for the glutamic acid-rich Neh5 peptide but are in reasonable agreement for Neh4, which has no glutamic acid. The CHARMM36m force field agrees more closely with the CD results.
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Affiliation(s)
- Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Carter J Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Nadun Chanaka Karunatilleke
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Mohamed Hesham Moselhy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Computer Science, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
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9
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Tan J, Zhang L, Hsieh MC, Goodwin JT, Grover MA, Lynn DG. Chemical control of peptide material phase transitions. Chem Sci 2021; 12:3025-3031. [PMID: 34164071 PMCID: PMC8179288 DOI: 10.1039/d0sc03666h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network. Substrate initiated assembly of a dynamic chemical network.![]()
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Affiliation(s)
- Junjun Tan
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Li Zhang
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Ming-Chien Hsieh
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA .,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - Jay T Goodwin
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - David G Lynn
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
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10
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Zhu M, Ou D, Khan MH, Zhao S, Zhu Z, Niu L. Structural insights into the formation of oligomeric state by a type I Hsp40 chaperone. Biochimie 2020; 176:45-51. [PMID: 32621942 DOI: 10.1016/j.biochi.2020.06.009] [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: 05/16/2019] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 10/23/2022]
Abstract
Molecular chaperones can prevent and repair protein misfolding and aggregation to maintain protein homeostasis in cells. Hsp40 chaperones interact with unfolded client proteins via the dynamic multivalent interaction (DMI) mechanism with their multiple client-binding sites. Here we report that a type I Hsp40 chaperone from Streptococcus pneumonia (spHsp40) forms a concentration-independent polydispersity oligomer state in solution. The crystal structure of spHsp40 determined at 2.75 Å revealed that each monomer has a type I Hsp40 structural fold containing a zinc finger domain and C-terminal domains I and II (CTD I and CTD II). Subsequent quaternary structure analysis using a PISA server generated two dimeric models. The interface mutational analysis suggests the conserved C-terminal dimeric motif as a basis for dimer formation and that the novel dimeric interaction between a client-binding site in CTD I and the zinc finger domain promotes the formation of the spHsp40 oligomeric state. In vitro functional analysis demonstrated that spHsp40 oligomer is fully active and possess the optimal activity in stimulating the ATPase activity of spHsp70. The oligomer state of type I Hsp40 and its formation might be important in understanding Hsp40 function and its interaction with client proteins.
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Affiliation(s)
- Min Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China
| | - Dingmin Ou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China
| | - Muhammad Hidayatullah Khan
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China
| | - Shasha Zhao
- Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610075, China
| | - Zhongliang Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China.
| | - Liwen Niu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China; Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, 230026, China.
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11
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Gorman SD, Winston DS, Sahu D, Boehr DD. Different Solvent and Conformational Entropy Contributions to the Allosteric Activation and Inhibition Mechanisms of Yeast Chorismate Mutase. Biochemistry 2020; 59:2528-2540. [DOI: 10.1021/acs.biochem.0c00277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Scott D. Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dennis S. Winston
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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12
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Weng J, Wang W. Dynamic multivalent interactions of intrinsically disordered proteins. Curr Opin Struct Biol 2020; 62:9-13. [DOI: 10.1016/j.sbi.2019.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022]
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13
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Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng Des Sel 2019; 32:489-501. [PMID: 32626892 PMCID: PMC7462040 DOI: 10.1093/protein/gzaa012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/08/2023] Open
Abstract
Adenylate kinase (AK) orthologs with a range of thermostabilities were subjected to random circular permutation, and deep mutational scanning was used to evaluate where new protein termini were nondisruptive to activity. The fraction of circularly permuted variants that retained function in each library correlated with AK thermostability. In addition, analysis of the positional tolerance to new termini, which increase local conformational flexibility, showed that bonds were either functionally sensitive to cleavage across all homologs, differentially sensitive, or uniformly tolerant. The mobile AMP-binding domain, which displays the highest calculated contact energies, presented the greatest tolerance to new termini across all AKs. In contrast, retention of function in the lid and core domains was more dependent upon AK melting temperature. These results show that family permutation profiling identifies primary structure that has been selected by evolution for dynamics that are critical to activity within an enzyme family. These findings also illustrate how deep mutational scanning can be applied to protein homologs in parallel to differentiate how topology, stability, and local energetics govern mutational tolerance.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, TX 77005, USA
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Alicia M Jones
- Biochemistry and Cell Biology Graduate Program, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, TX 77005, USA
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, TX 77005, USA
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14
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Nyqvist I, Dogan J. Characterization of the dynamics and the conformational entropy in the binding between TAZ1 and CTAD-HIF-1α. Sci Rep 2019; 9:16557. [PMID: 31719609 PMCID: PMC6851107 DOI: 10.1038/s41598-019-53067-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/26/2019] [Indexed: 11/09/2022] Open
Abstract
The interaction between the C-terminal transactivation domain of HIF-1α (CTAD-HIF-1α) and the transcriptional adapter zinc binding 1 (TAZ1) domain of CREB binding protein participate in the initiation of gene transcription during hypoxia. Unbound CTAD-HIF-1α is disordered but undergoes a disorder-to-order transition upon binding to TAZ1. We have here performed NMR side chain and backbone relaxation studies on TAZ1 and side chain relaxation measurements on CTAD-HIF-1α in order to investigate the role of picosecond to nanosecond dynamics. We find that the internal motions are significantly affected upon binding, both on the side chain and the backbone level. The dynamic response corresponds to a conformational entropy change that contributes substantially to the binding thermodynamics for both binding partners. Furthermore, the conformational entropy change for the well-folded TAZ1 varies upon binding to different IDP targets. We further identify a cluster consisting of side chains in bound TAZ1 and CTAD-HIF-1α that experience extensive dynamics and are part of the binding region that involves the N-terminal end of the LPQL motif in CTAD-HIF-1α; a feature that might have an important role in the termination of the hypoxic response.
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Affiliation(s)
- Ida Nyqvist
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden.
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15
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Yang J, Gao M, Xiong J, Su Z, Huang Y. Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Sci 2019; 28:1952-1965. [PMID: 31441158 PMCID: PMC6798136 DOI: 10.1002/pro.3718] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
The sequence-structure-function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well-defined three-dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.
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Affiliation(s)
- Jing Yang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Meng Gao
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Junwen Xiong
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Zhengding Su
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Yongqi Huang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
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16
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Gao M, Yang J, Liu S, Su Z, Huang Y. Intrinsically Disordered Transactivation Domains Bind to TAZ1 Domain of CBP via Diverse Mechanisms. Biophys J 2019; 117:1301-1310. [PMID: 31521329 DOI: 10.1016/j.bpj.2019.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 02/06/2023] Open
Abstract
CREB-binding protein is a multidomain transcriptional coactivator whose transcriptional adaptor zinc-binding 1 (TAZ1) domain mediates interactions with a number of intrinsically disordered transactivation domains (TADs), including the CREB-binding protein/p300-interacting transactivator with ED-rich tail, the hypoxia inducible factor 1α, p53, the signal transducer and activator of transcription 2, and the NF-κB p65 subunit. These five disordered TADs undergo partial disorder-to-order transitions upon binding TAZ1, forming fuzzy complexes with helical segments. Interestingly, they wrap around TAZ1 with different orientations and occupy the binding sites with various orders. To elucidate the microscopic molecular details of the binding processes of TADs with TAZ1, in this work, we carried out extensive molecular dynamics simulations using a coarse-grained topology-based model. After careful calibration of the models to reproduce the residual helical contents and binding affinities, our simulations were able to recapitulate the experimentally observed flexibility profiles. Although great differences exist in the complex structures, we found similarities between hypoxia inducible factor 1α and signal transducer and activator of transcription 2 as well as between CREB-binding protein/p300-interacting transactivator with ED-rich tail and NF-κB p65 subunit in the binding kinetics and binding thermodynamics. Although the origins of similarities and differences in the binding mechanisms remain unclear, our results provide some clues that indicate that binding of TADs to TAZ1 could be templated by the target as well as encoded by the TADs.
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Affiliation(s)
- Meng Gao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Jing Yang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Sen Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China; Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China.
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17
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Neira JL, Palomino-Schätzlein M, Ricci C, Ortore MG, Rizzuti B, Iovanna JL. Dynamics of the intrinsically disordered protein NUPR1 in isolation and in its fuzzy complexes with DNA and prothymosin α. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140252. [PMID: 31325636 DOI: 10.1016/j.bbapap.2019.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins (IDPs) explore diverse conformations in their free states and, a few of them, also in their molecular complexes. This functional plasticity is essential for the function of IDPs, although their dynamics in both free and bound states is poorly understood. NUPR1 is a protumoral multifunctional IDP, activated during the acute phases of pancreatitis. It interacts with DNA and other IDPs, such as prothymosin α (ProTα), with dissociation constants of ~0.5 μM, and a 1:1 stoichiometry. We studied the structure and picosecond-to-nanosecond (ps-ns) dynamics by using both NMR and SAXS in: (i) isolated NUPR1; (ii) the NUPR1/ProTα complex; and (iii) the NUPR1/double stranded (ds) GGGCGCGCCC complex. Our SAXS findings show that NUPR1 remained disordered when bound to either partner, adopting a worm-like conformation; the fuzziness of bound NUPR1 was also pinpointed by NMR. Residues with the largest values of the relaxation rates (R1, R1ρ, R2 and ηxy), in the free and bound species, were mainly clustered around the 30s region of the sequence, which agree with one of the protein hot-spots already identified by site-directed mutagenesis. Not only residues in this region had larger relaxation rates, but they also moved slower than the rest of the molecule, as indicated by the reduced spectral density approach (RSDA). Upon binding, the energy landscape of NUPR1 was not funneled down to a specific, well-folded conformation, but rather its backbone flexibility was kept, with distinct motions occurring at the hot-spot region.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain.
| | | | - Caterina Ricci
- Department of Life and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, 60131 Ancona, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, 60131 Ancona, Italy
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
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18
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Entropy and Information within Intrinsically Disordered Protein Regions. ENTROPY 2019; 21:e21070662. [PMID: 33267376 PMCID: PMC7515160 DOI: 10.3390/e21070662] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-structure-function paradigm to IDRs and motivates the development of new methods to extract information from IDR sequences. We argue that the information in IDR sequences cannot be fully revealed through positional conservation, which largely measures stable structural contacts and interaction motifs. Instead, considerations of evolutionary conservation of molecular features can reveal the full extent of information in IDRs. Experimental quantification of the large conformational entropy of IDRs is challenging but can be approximated through the extent of conformational sampling measured by a combination of NMR spectroscopy and lower-resolution structural biology techniques, which can be further interpreted with simulations. Conformational entropy and other biophysical features can be modulated by post-translational modifications that provide functional advantages to IDRs by tuning their energy landscapes and enabling a variety of functional interactions and modes of regulation. The diverse mosaic of functional states of IDRs and their conformational features within complexes demands novel metrics of information, which will reflect the complicated sequence-conformational ensemble-function relationship of IDRs.
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19
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Nyqvist I, Andersson E, Dogan J. Role of Conformational Entropy in Molecular Recognition by TAZ1 of CBP. J Phys Chem B 2019; 123:2882-2888. [PMID: 30860376 DOI: 10.1021/acs.jpcb.9b01343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The globular transcriptional adapter zinc binding 1 (TAZ1) domain of CREB binding protein participates in protein-protein interactions that are involved in transcriptional regulation. TAZ1 binds numerous targets, of which many are intrinsically disordered proteins that undergo a disorder-to-order transition to various degrees. One such target is the disordered transactivation domain of transcription factor RelA (TAD-RelA), which with its interaction with TAZ1 is involved in transcriptional regulation of genes in NF-κB signaling. We have here performed nuclear magnetic resonance backbone and side-chain relaxation studies to investigate the influence of RelA-TA2 (residues 425-490 in TAD-RelA) binding on the subnanosecond internal motions of TAZ1. We find a considerable dynamic response on both the backbone and side-chain levels, which corresponds to a conformational entropy change that contributes significantly to the binding energetics. We further show that the microscopic origins of the dynamic response of TAZ1 vary depending on the target. This study demonstrates that folded protein domains that are able to interact with various targets are not dynamically passive but can have a significant role in the motional response upon target association.
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Affiliation(s)
- Ida Nyqvist
- Department of Biochemistry and Biophysics , Stockholm University , SE-10691 Stockholm , Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology , Uppsala University , SE-75123 Uppsala , Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics , Stockholm University , SE-10691 Stockholm , Sweden
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20
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Berlow RB, Martinez-Yamout MA, Dyson HJ, Wright PE. Role of Backbone Dynamics in Modulating the Interactions of Disordered Ligands with the TAZ1 Domain of the CREB-Binding Protein. Biochemistry 2019; 58:1354-1362. [PMID: 30775911 DOI: 10.1021/acs.biochem.8b01290] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The intrinsically disordered transactivation domains of HIF-1α and CITED2 compete for binding of the TAZ1 domain of the CREB-binding protein by a unidirectional allosteric mechanism involving direct competition for shared binding sites, ternary complex formation, and TAZ1 conformational changes. To gain insight into the mechanism by which CITED2 displaces HIF-1α from TAZ1, we used nuclear magnetic resonance spin relaxation methods to obtain an atomic-level description of the picosecond to nanosecond backbone dynamics that contribute to TAZ1 binding and competition. We show that HIF-1α and CITED2 adopt different dynamics in their complexes with TAZ1, with flexibility observed for HIF-1α in regions that would maintain accessibility for CITED2 to bind to TAZ1 and facilitate subsequent HIF-1α dissociation. In contrast, critical regions of CITED2 adopt a rigid structure in its complex with TAZ1, minimizing the ability of HIF-1α to compete for binding. We also find that TAZ1, previously thought to be a rigid scaffold for binding of disordered protein ligands, displays altered backbone dynamics in its various bound states. TAZ1 is more rigid in its CITED2-bound state than in its free state or in complex with HIF-1α, with increased rigidity observed not only in the CITED2 binding site but also in regions of TAZ1 that undergo conformational changes between the HIF-1α- and CITED2-bound structures. Taken together, these data suggest that backbone dynamics in TAZ1, as well as in the HIF-1α and CITED2 ligands, play a role in modulating the occupancy of TAZ1 and highlight the importance of characterizing both binding partners in molecular interactions.
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Affiliation(s)
- Rebecca B Berlow
- 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 , United States
| | - Maria A Martinez-Yamout
- 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 , United States
| | - 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 , United States
| | - 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 , United States
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21
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Schneider R, Blackledge M, Jensen MR. Elucidating binding mechanisms and dynamics of intrinsically disordered protein complexes using NMR spectroscopy. Curr Opin Struct Biol 2018; 54:10-18. [PMID: 30316104 DOI: 10.1016/j.sbi.2018.09.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 01/10/2023]
Abstract
Advances in characterizing complexes of intrinsically disordered proteins (IDPs) have led to the discovery of a remarkably diverse interaction landscape that includes folding-upon-binding, highly dynamic complexes, multivalent interactions as well as regulatory switches controlled by post-translational modifications. Nuclear magnetic resonance (NMR) spectroscopy has in recent years made significant contributions to this field by describing the binding mechanisms and mapping conformational dynamics on multiple time scales. Importantly, this progress has been associated with specific methodological developments in NMR, for example in exchange techniques, allowing challenging biological systems to be studied at atomic resolution. In general, the level of dynamics observed in IDP complexes does not correlate with binding affinities, demonstrating the intricate relationship between conformational dynamics and IDP regulatory function.
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Affiliation(s)
- Robert Schneider
- Univ. Lille, CNRS, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
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22
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Jemth P, Karlsson E, Vögeli B, Guzovsky B, Andersson E, Hultqvist G, Dogan J, Güntert P, Riek R, Chi CN. Structure and dynamics conspire in the evolution of affinity between intrinsically disordered proteins. SCIENCE ADVANCES 2018; 4:eaau4130. [PMID: 30397651 PMCID: PMC6200366 DOI: 10.1126/sciadv.aau4130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/13/2018] [Indexed: 05/10/2023]
Abstract
In every established species, protein-protein interactions have evolved such that they are fit for purpose. However, the molecular details of the evolution of new protein-protein interactions are poorly understood. We have used nuclear magnetic resonance spectroscopy to investigate the changes in structure and dynamics during the evolution of a protein-protein interaction involving the intrinsically disordered CREBBP (CREB-binding protein) interaction domain (CID) and nuclear coactivator binding domain (NCBD) from the transcriptional coregulators NCOA (nuclear receptor coactivator) and CREBBP/p300, respectively. The most ancient low-affinity "Cambrian-like" [540 to 600 million years (Ma) ago] CID/NCBD complex contained less secondary structure and was more dynamic than the complexes from an evolutionarily younger "Ordovician-Silurian" fish ancestor (ca. 440 Ma ago) and extant human. The most ancient Cambrian-like CID/NCBD complex lacked one helix and several interdomain interactions, resulting in a larger solvent-accessible surface area. Furthermore, the most ancient complex had a high degree of millisecond-to-microsecond dynamics distributed along the entire sequences of both CID and NCBD. These motions were reduced in the Ordovician-Silurian CID/NCBD complex and further redistributed in the extant human CID/NCBD complex. Isothermal calorimetry experiments show that complex formation is enthalpically favorable and that affinity is modulated by a largely unfavorable entropic contribution to binding. Our data demonstrate how changes in structure and motion conspire to shape affinity during the evolution of a protein-protein complex and provide direct evidence for the role of structural, dynamic, and frustrational plasticity in the evolution of interactions between intrinsically disordered proteins.
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Affiliation(s)
- Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
- Corresponding author. (C.N.C.); (P.J.)
| | - Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Brenda Guzovsky
- Protein Physiology Lab, FCEyN-Universidad de Buenos Aires, IQUIBICEN/CONICET, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Greta Hultqvist
- Department of Pharmaceutical Biosciences, Uppsala University, BMC Box 591, SE-75124 Uppsala, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, Switzerland
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
- Corresponding author. (C.N.C.); (P.J.)
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