1
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Melikishvili M, Fried MG, Fondufe-Mittendorf YN. Cooperative nucleic acid binding by Poly ADP-ribose polymerase 1. Sci Rep 2024; 14:7530. [PMID: 38553566 PMCID: PMC10980755 DOI: 10.1038/s41598-024-58076-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Poly (ADP)-ribose polymerase 1 (PARP1) is an abundant nuclear protein well-known for its role in DNA repair yet also participates in DNA replication, transcription, and co-transcriptional splicing, where DNA is undamaged. Thus, binding to undamaged regions in DNA and RNA is likely a part of PARP1's normal repertoire. Here we describe analyses of PARP1 binding to two short single-stranded DNAs, a single-stranded RNA, and a double stranded DNA. The investigations involved comparing the wild-type (WT) full-length enzyme with mutants lacking the catalytic domain (∆CAT) or zinc fingers 1 and 2 (∆Zn1∆Zn2). All three protein types exhibited monomeric characteristics in solution and formed saturated 2:1 complexes with single-stranded T20 and U20 oligonucleotides. These complexes formed without accumulation of 1:1 intermediates, a pattern suggestive of positive binding cooperativity. The retention of binding activities by ∆CAT and ∆Zn1∆Zn2 enzymes suggests that neither the catalytic domain nor zinc fingers 1 and 2 are indispensable for cooperative binding. In contrast, when a double stranded 19mer DNA was tested, WT PARP1 formed a 4:1 complex while the ∆Zn1Zn2 mutant binding saturated at 1:1 stoichiometry. These deviations from the 2:1 pattern observed with T20 and U20 oligonucleotides show that PARP's binding mechanism can be influenced by the secondary structure of the nucleic acid. Our studies show that PARP1:nucleic acid interactions are strongly dependent on the nucleic acid type and properties, perhaps reflecting PARP1's ability to respond differently to different nucleic acid ligands in cells. These findings lay a platform for understanding how the functionally versatile PARP1 recognizes diverse oligonucleotides within the realms of chromatin and RNA biology.
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Affiliation(s)
- Manana Melikishvili
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Michael G Fried
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
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2
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Lemieux P, Bradley D, Dubé AK, Dionne U, Landry CR. Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins. Genetics 2024; 226:iyad175. [PMID: 37793087 PMCID: PMC10763533 DOI: 10.1093/genetics/iyad175] [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: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 10/06/2023] Open
Abstract
Protein-protein interactions (PPIs) drive many cellular processes. Some interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of 2 paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the preduplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the most recent ancestor of the 2 domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that a SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity.
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Affiliation(s)
- Pascale Lemieux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec, Université Laval, Québec, QC, Canada G1R 2J6
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada M5G 1X5
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
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3
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Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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4
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Soya N, Xu H, Roldan A, Yang Z, Ye H, Jiang F, Premchandar A, Veit G, Cole SPC, Kappes J, Hegedüs T, Lukacs GL. Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling. Nat Commun 2023; 14:6868. [PMID: 37891162 PMCID: PMC10611759 DOI: 10.1038/s41467-023-42586-8] [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: 11/16/2022] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR posttranslational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their posttranslational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding.
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Affiliation(s)
- Naoto Soya
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Haijin Xu
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Ariel Roldan
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Zhengrong Yang
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Haoxin Ye
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Fan Jiang
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Aiswarya Premchandar
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Guido Veit
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada
| | - Susan P C Cole
- Division of Cancer Biology and Genetics, Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Kingston, ON, Canada
| | - John Kappes
- Heersink School of Medicine, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Tamás Hegedüs
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085, Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Gergely L Lukacs
- Department of Physiology and Biochemistry, McGill University, Montréal, QC, Canada.
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5
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Soya N, Xu H, Roldan A, Yang Z, Ye H, Jiang F, Premchandar A, Veit G, Cole SPC, Kappes J, Hegedus T, Lukacs GL. Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563107. [PMID: 37905074 PMCID: PMC10614980 DOI: 10.1101/2023.10.19.563107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR post-translational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their post-translational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding. One-Sentence Summary Allosteric interdomain communication and its modulation are critical determinants of ABCC-transporters post-translational conformational biogenesis, misfolding, and pharmacological rescue.
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6
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Sidhanta SPD, Sowdhamini R, Srinivasan N. Comparative analysis of permanent and transient domain-domain interactions in multi-domain proteins. Proteins 2023. [PMID: 37828826 DOI: 10.1002/prot.26581] [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: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 10/14/2023]
Abstract
Protein domains are structural, functional, and evolutionary units. These domains bring out the diversity of functionality by means of interactions with other co-existing domains and provide stability. Hence, it is important to study intra-protein inter-domain interactions from the perspective of types of interactions. Domains within a chain could interact over short timeframes or permanently, rather like protein-protein interactions (PPIs). However, no systematic study has been carried out between two classes, namely permanent and transient domain-domain interactions. In this work, we studied 263 two-domain proteins, belonging to either of these classes and their interfaces on the basis of several factors, such as interface area and details of interactions (number, strength, and types of interactions). We also characterized them based on residue conservation at the interface, correlation of residue motions across domains, its involvement in repeat formation, and their involvement in particular molecular processes. Finally, we could analyze the interactions arising from domains in two-domain monomeric proteins, and we observed significant differences between these two classes of domain interactions and a few similarities. This study will help to obtain a better understanding of structure-function and folding principles of multi-domain proteins.
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Affiliation(s)
| | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Computational Approaches to Protein Science, National Centre for Biological Sciences, Bangalore, India
- Computational Biology, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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7
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Choudhary P, Anyango S, Berrisford J, Tolchard J, Varadi M, Velankar S. Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data. Sci Data 2023; 10:204. [PMID: 37045837 PMCID: PMC10097656 DOI: 10.1038/s41597-023-02101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorporates residue-level annotations from many other biological resources. SIFTS data is available in various formats like XML, CSV and TSV format or also accessible via the PDBe REST API but always maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. Here, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProtKB, Pfam, SCOP2, and CATH residue-level annotations directly into the PDBx/mmCIF files from the PDB archive. With the integrated UniProtKB annotations, these files now provide consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended dictionary yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at the residue level resulting in better data interoperability, supporting improved data analysis and visualisation.
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Grants
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley) National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley NSF | National Science Board (NSB)
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Affiliation(s)
- Preeti Choudhary
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - John Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Trumpington, Cambridge, CB2 0AA, UK
| | - James Tolchard
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Claude Bernard University, Villeurbanne, Lyon, 69100, France
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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8
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Oh J, Durai P, Kannan P, Park J, Yeon YJ, Lee WK, Park K, Seo MH. Domain-wise dissection of thermal stability enhancement in multidomain proteins. Int J Biol Macromol 2023; 237:124141. [PMID: 36958447 DOI: 10.1016/j.ijbiomac.2023.124141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023]
Abstract
Stability is critical for the proper functioning of all proteins. Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering.
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Affiliation(s)
- Jisung Oh
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Prasannavenkatesh Durai
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea
| | - Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea
| | - Jaehui Park
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Chungbuk 28160, South Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
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9
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Xie J, Pan G, Li Y, Lai L. How protein topology controls allosteric regulations. J Chem Phys 2023; 158:105102. [PMID: 36922138 DOI: 10.1063/5.0138279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Allostery is an important regulatory mechanism of protein functions. Among allosteric proteins, certain protein structure types are more observed. However, how allosteric regulation depends on protein topology remains elusive. In this study, we extracted protein topology graphs at the fold level and found that known allosteric proteins mainly contain multiple domains or subunits and allosteric sites reside more often between two or more domains of the same fold type. Only a small fraction of fold-fold combinations are observed in allosteric proteins, and homo-fold-fold combinations dominate. These analyses imply that the locations of allosteric sites including cryptic ones depend on protein topology. We further developed TopoAlloSite, a novel method that uses the kernel support vector machine to predict the location of allosteric sites on the overall protein topology based on the subgraph-matching kernel. TopoAlloSite successfully predicted known cryptic allosteric sites in several allosteric proteins like phosphopantothenoylcysteine synthetase, spermidine synthase, and sirtuin 6, demonstrating its power in identifying cryptic allosteric sites without performing long molecular dynamics simulations or large-scale experimental screening. Our study demonstrates that protein topology largely determines how its function can be allosterically regulated, which can be used to find new druggable targets and locate potential binding sites for rational allosteric drug design.
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Affiliation(s)
- Juan Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Gaoxiang Pan
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yibo Li
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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10
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Diaz-Parga P, Gould A, de Alba E. Natural and engineered inflammasome adapter proteins reveal optimum linker length for self-assembly. J Biol Chem 2022; 298:102501. [PMID: 36116550 PMCID: PMC9640978 DOI: 10.1016/j.jbc.2022.102501] [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: 04/07/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The inflammasome is a multiprotein complex that triggers the activation of proinflammatory cytokines. The adapter ASC and its isoform ASCb mediate inflammasome assembly via self-association and oligomerization with other inflammasome proteins by homotypic interactions of their two identical Death Domains, PYD and CARD, connected by a linker of different length: 23 (ASC) and 4 (ASCb) amino acids long. However, ASC is a more potent inflammasome activator compared to ASCb. Thus, adapter isoforms might be involved in the regulation of the inflammatory response. As previously reported, ASC's faster and less polydisperse self-association compared to ASCb points to interdomain flexibility resulting from the linker length as a key factor in inflammasome regulation. To test the influence of linker length in self-association, we have engineered the isoform ASC3X with identical PYD and CARD connected by a 69 amino acid-long linker (i.e., three-times longer than ASC's linker). Real-time NMR and dynamic light scattering data indicate that ASC3X polymerization is less effective and more polydisperse compared to ASC or ASCb. However, transmission electron micrographs show that ASC3X can polymerize into filaments. Comparative interdomain dynamics of the three isoforms obtained from NMR relaxation data reveal that ASCb tumbles as a rod, whereas the PYD and CARD of ASC and ASC3X tumble independently with marginally higher interdomain flexibility in ASC3X. Altogether, our data suggest that ASC's linker length is optimized for self-association by allowing enough flexibility to favor intermolecular homotypic interactions but simultaneously keeping both domains sufficiently close for essential participation in filament formation.
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Affiliation(s)
- Pedro Diaz-Parga
- Department of Bioengineering, School of Engineering, University of California Merced, California, USA; Quantitative Systems Biology PhD Program, University of California Merced, California, USA
| | - Andrea Gould
- Department of Bioengineering, School of Engineering, University of California Merced, California, USA
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California Merced, California, USA.
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11
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Laursen L, Inturi R, Østergaard S, Jemth P. Determinants of affinity, specificity, and phase separation in a supramodule from Post-synaptic density protein 95. iScience 2022; 25:105069. [PMID: 36157580 PMCID: PMC9490041 DOI: 10.1016/j.isci.2022.105069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
The post-synaptic density (PSD) is a phase-separated membraneless compartment of proteins including PSD-95 that undergoes morphological alteration in response to synaptic activity. Here, we investigated the interactome of a three-domain supramodule, PDZ3-SH3-GK (PSG) from PSD-95 using bioinformatics to identify potential binding partners, and biophysical methods to characterize the interaction with peptides from these proteins. PSG and the single PDZ3 domain bound similar peptides, but with different specificity. Furthermore, we found that the protein ADGRB1 formed liquid droplets with the PSG supramodule, extending the model for PSD formation. Moreover, certain mutations, introduced outside of the binding pocket in PDZ3, increased the affinity and specificity of the interaction and the size of liquid droplets. Other mutations within the ligand binding pocket lead to a new binding motif specificity. Our results show how the context in terms of supertertiary structure modulates affinity, specificity, and phase separation, and how these properties can evolve by point mutation. Identification of potential binding partners for PSD-95 in the post-synaptic density ADGRB1 and PSD-95 undergo liquid-liquid phase separation (LLPS) Single domain PDZ3 cannot induce LLPS and binds weakly to ADGRB1 and SynGap Supertertiary structure alters the affinity, specificity, and phase separation
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Affiliation(s)
- Louise Laursen
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Søren Østergaard
- Global Research Technology, Novo Nordisk A/S, Novo Nordisk Research Park, 2760 Maalov, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
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12
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Bacala R, Hatcher DW, Perreault H, Fu BX. Challenges and opportunities for proteomics and the improvement of bread wheat quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153743. [PMID: 35749977 DOI: 10.1016/j.jplph.2022.153743] [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: 02/28/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Wheat remains a critical global food source, pressured by climate change and the need to maximize yield, improve processing and nutritional quality and ensure safety. An enormous amount of research has been conducted to understand gluten protein composition and structure in relation to end-use quality, yet progress has become stagnant. This is mainly due to the need and inability to biochemically characterize the intact functional glutenin polymer in order to correlate to quality, necessitating reduction to monomeric subunits and a loss of contextual information. While some individual gluten proteins might have a positive or negative influence on gluten quality, it is the sum total of these proteins, their relative and absolute expression, their sub-cellular trafficking, the amount and size of glutenin polymers, and ratios between gluten protein classes that define viscoelasticity of gluten. The sub-cellular trafficking of gluten proteins during seed maturation is still not completely clear and there is evidence of dual pathways and therefore different destinations for proteins, either constitutively or temporally. The trafficking of proteins is also unclear in endosperm cells as they undergo programmed cell death; Golgi disappear around 12 DPA but protein filling continues at least to 25 DPA. Modulation of the timing of cellular events will invariably affect protein deposition and therefore gluten strength and function. Existing and emerging proteomics technologies such as proteoform profiling and top-down proteomics offer new tools to study gluten protein composition as a whole system and identify compositional patterns that can modify gluten structure with improved functionality.
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Affiliation(s)
- Ray Bacala
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Dave W Hatcher
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada
| | - Héléne Perreault
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Bin Xiao Fu
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; Department of Food and Human Nutritional Sciences, 209 - 35 Chancellor's Circle, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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13
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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14
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Gromiha MM, Orengo CA, Sowdhamini R, Thornton AJM. Srinivasan (1962-2021) in Bioinformatics and beyond. Bioinformatics 2022; 38:2377-2379. [PMID: 35134112 PMCID: PMC9004639 DOI: 10.1093/bioinformatics/btac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Christine A Orengo
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bangalore, Karnataka 560065, India,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India,Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
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15
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Coyote-Maestas W, Nedrud D, Suma A, He Y, Matreyek KA, Fowler DM, Carnevale V, Myers CL, Schmidt D. Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling. Nat Commun 2021; 12:7114. [PMID: 34880224 PMCID: PMC8654947 DOI: 10.1038/s41467-021-27342-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
Protein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about biophysical mechanisms that determine whether protein domains can be combined into viable protein folds. Here, we use massively parallel insertional mutagenesis to determine compatibility of over 300,000 domain recombination variants of the Inward Rectifier K+ channel Kir2.1 with channel surface expression. Our data suggest that genomic and biophysical mechanisms acted in concert to favor gain of large, structured domain at protein termini during ion channel evolution. We use machine learning to build a quantitative biophysical model of domain compatibility in Kir2.1 that allows us to derive rudimentary rules for designing domain insertion variants that fold and traffic to the cell surface. Positional Kir2.1 responses to motif insertion clusters into distinct groups that correspond to contiguous structural regions of the channel with distinct biophysical properties tuned towards providing either folding stability or gating transitions. This suggests that insertional profiling is a high-throughput method to annotate function of ion channel structural regions.
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Affiliation(s)
- Willow Coyote-Maestas
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - David Nedrud
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Antonio Suma
- grid.264727.20000 0001 2248 3398Department of Chemistry, Temple University, Philadelphia, PA 19122 USA
| | - Yungui He
- grid.17635.360000000419368657Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455 USA
| | - Kenneth A. Matreyek
- grid.67105.350000 0001 2164 3847Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Douglas M. Fowler
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98115 USA ,grid.34477.330000000122986657Department of Bioengineering, University of Washington, Seattle, WA 98115 USA
| | - Vincenzo Carnevale
- grid.264727.20000 0001 2248 3398Department of Chemistry, Temple University, Philadelphia, PA 19122 USA
| | - Chad L. Myers
- grid.17635.360000000419368657Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, 55455, USA.
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16
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Born A, Soetbeer J, Breitgoff F, Henen MA, Sgourakis N, Polyhach Y, Nichols PJ, Strotz D, Jeschke G, Vögeli B. Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance. J Am Chem Soc 2021; 143:16055-16067. [PMID: 34579531 DOI: 10.1021/jacs.1c06289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States.,Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nikolaos Sgourakis
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Dean Strotz
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
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17
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Mulnaes D, Golchin P, Koenig F, Gohlke H. TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning. J Chem Theory Comput 2021; 17:4599-4613. [PMID: 34161735 DOI: 10.1021/acs.jctc.1c00129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. Current domain boundary prediction methods differ in terms of boundary definition, methodology, and training databases resulting in disparate performance for different proteins. We developed TopDomain, an exhaustive metapredictor, that uses deep neural networks to combine multisource information from sequence- and homology-based features of over 50 primary predictors. For this purpose, we developed a new domain boundary data set termed the TopDomain data set, in which the true annotations are informed by SCOPe annotations, structural domain parsers, human inspection, and deep learning. We benchmark TopDomain against 2484 targets with 3354 boundaries from the TopDomain test set and achieve F1 scores of 78.4% and 73.8% for multidomain boundary prediction within ±20 residues and ±10 residues of the true boundary, respectively. When examined on targets from CASP11-13 competitions, TopDomain achieves F1 scores of 47.5% and 42.8% for multidomain proteins. TopDomain significantly outperforms 15 widely used, state-of-the-art ab initio and homology-based domain boundary predictors. Finally, we implemented TopDomainTMC, which accurately predicts whether domain parsing is necessary for the target protein.
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Affiliation(s)
- Daniel Mulnaes
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Pegah Golchin
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Filip Koenig
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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18
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Decoding LncRNAs. Cancers (Basel) 2021; 13:cancers13112643. [PMID: 34072257 PMCID: PMC8199187 DOI: 10.3390/cancers13112643] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been considered as unimportant additions to the transcriptome. Yet, in light of numerous studies, it has become clear that ncRNAs play important roles in development, health and disease. Long-ignored, long non-coding RNAs (lncRNAs), ncRNAs made of more than 200 nucleotides have gained attention due to their involvement as drivers or suppressors of a myriad of tumours. The detailed understanding of some of their functions, structures and interactomes has been the result of interdisciplinary efforts, as in many cases, new methods need to be created or adapted to characterise these molecules. Unlike most reviews on lncRNAs, we summarize the achievements on lncRNA studies by taking into consideration the approaches for identification of lncRNA functions, interactomes, and structural arrangements. We also provide information about the recent data on the involvement of lncRNAs in diseases and present applications of these molecules, especially in medicine.
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19
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Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1. Sci Rep 2021; 11:1034. [PMID: 33441818 PMCID: PMC7806782 DOI: 10.1038/s41598-020-80524-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
TDP-43 and hnRNPA1 contain tandemly-tethered RNA-recognition-motif (RRM) domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), alzheimer's disease (AD) and Multisystem proteinopathy (MSP). Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: (1) upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. (2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity slightly higher to the tethered than isolated forms. (3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1–RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.
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20
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Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, DeGrado WF. Allosteric cooperation in a de novo-designed two-domain protein. Proc Natl Acad Sci U S A 2020; 117:33246-33253. [PMID: 33318174 PMCID: PMC7776816 DOI: 10.1073/pnas.2017062117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis-Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter Km and a 7-fold decrease in kcat These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Nathan Schmidt
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - James Lincoff
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Zachary X Widel
- Department of Chemistry, Duke University, Durham, NC 27708-0346
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Lijun Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055 Shenzhen, China
- DLX Scientific, Lawrence, KS 66049
| | | | - Michael Grabe
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy;
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001;
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21
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Dokainish HM, Sugita Y. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. Int J Mol Sci 2020; 22:ijms22010270. [PMID: 33383937 PMCID: PMC7796230 DOI: 10.3390/ijms22010270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 11/26/2022] Open
Abstract
Conformational transitions in multidomain proteins are essential for biological functions. The Apo conformations are typically open and flexible, while the Holo states form more compact conformations stabilized by protein-ligand interactions. Unfortunately, the atomically detailed mechanisms for such open-closed conformational changes are difficult to be accessed experimentally as well as computationally. To simulate the transitions using atomistic molecular dynamics (MD) simulations, efficient conformational sampling algorithms are required. In this work, we propose a new approach based on generalized replica-exchange with solute tempering (gREST) for exploring the open-closed conformational changes in multidomain proteins. Wherein, selected surface charged residues in a target protein are defined as the solute region in gREST simulation and the solute temperatures are different in replicas and exchanged between them to enhance the domain motions. This approach is called gREST selected surface charged residues (gREST_SSCR) and is applied to the Apo and Holo states of ribose binding protein (RBP) in solution. The conformational spaces sampled with gREST_SSCR are much wider than those with the conventional MD, sampling open-closed conformational changes while maintaining RBP domains’ stability. The free-energy landscapes of RBP in the Apo and Holo states are drawn along with twist and hinge angles of the two moving domains. The inter-domain salt-bridges that are not observed in the experimental structures are also important in the intermediate states during the conformational changes.
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Affiliation(s)
- Hisham M. Dokainish
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- RIKEN Center for Computational Science, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Correspondence: ; Tel.: +81-48-462-1407
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22
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Tandon H, de Brevern AG, Srinivasan N. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure 2020; 29:371-384.e3. [PMID: 33306961 DOI: 10.1016/j.str.2020.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and structures of their corresponding unbound forms to evaluate dynamics changes induced by binding. Fifty-five percent of cases showed significant dynamics change away from the interfaces. This change is not always accompanied by an observed structural change. Binding of protein partner is found to alter inter-residue communication within the tertiary structure in about 90% of cases. Also, residue motions accessible to proteins in unbound form were not always maintained in the bound form. Further analyses revealed functional roles for the distant site where dynamics change was observed. Overall, the results presented here strongly suggest that alteration of protein dynamics due to binding of a partner protein commonly occurs.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, 75739 Paris, France; Univ Paris, UMR_S 1134, 75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), 75739 Paris, France; Laboratoire d'Excellence GR-Ex, 75739 Paris, France
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23
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Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020; 9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023] Open
Abstract
The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
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Schiebenhoefer H, Schallert K, Renard BY, Trappe K, Schmid E, Benndorf D, Riedel K, Muth T, Fuchs S. A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. Nat Protoc 2020; 15:3212-3239. [PMID: 32859984 DOI: 10.1038/s41596-020-0368-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.
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Affiliation(s)
- Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Hasso Plattner Institute, Faculty for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Hasso Plattner Institute, Faculty for Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Emanuel Schmid
- ID Computational & Data Science Support, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Katharina Riedel
- Center for Functional Genomics of Microbes (CFGM), Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thilo Muth
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Section S.3 eScience, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Stephan Fuchs
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.
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25
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Understanding the Effect of Multiple Domain Deletion in DNA Polymerase I from Geobacillus Sp. Strain SK72. Catalysts 2020. [DOI: 10.3390/catal10080936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic polymerase activity with additional traits that used isothermal amplification. However, the 3′-5′ exonuclease domain that carries a proofreading activity was disabled. Yet, the structure remained attached to the 5′-3′ polymerization domain without affecting its ability. The purpose of this non-functional domain still remains scarce. It either gives negative effects or provides structural support to the DNA polymerase. Here, we compared the effect of deleting each domain against the polymerase activity. The recombinant wild type and its variants were successfully purified and characterized. Interestingly, SK72-Exo (a large fragment excluding the 5′-3′ exonuclease domain) exhibited better catalytic activity than the native SK72 (with all three domains) at similar optimum temperature and pH profile, and it showed longer stability at 70 °C. Meanwhile, SK72-Exo2 (polymerization domain without both the 5′-3′ and 3′-5′ exonuclease domain) displayed the lowest activity with an optimum at 40 °C and favored a more neutral environment. It was also the least stable among the variants, with almost no activity at 50 °C for the first 10 min. In conclusion, cutting both exonuclease domains in DNA polymerase I has a detrimental effect on the polymerization activity and structural stability.
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26
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Coyote-Maestas W, Nedrud D, Okorafor S, He Y, Schmidt D. Targeted insertional mutagenesis libraries for deep domain insertion profiling. Nucleic Acids Res 2020; 48:e11. [PMID: 31745561 PMCID: PMC6954442 DOI: 10.1093/nar/gkz1110] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/22/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Domain recombination is a key principle in protein evolution and protein engineering, but inserting a donor domain into every position of a target protein is not easily experimentally accessible. Most contemporary domain insertion profiling approaches rely on DNA transposons, which are constrained by sequence bias. Here, we establish Saturated Programmable Insertion Engineering (SPINE), an unbiased, comprehensive, and targeted domain insertion library generation technique using oligo library synthesis and multi-step Golden Gate cloning. Through benchmarking to MuA transposon-mediated library generation on four ion channel genes, we demonstrate that SPINE-generated libraries are enriched for in-frame insertions, have drastically reduced sequence bias as well as near-complete and highly-redundant coverage. Unlike transposon-mediated domain insertion that was severely biased and sparse for some genes, SPINE generated high-quality libraries for all genes tested. Using the Inward Rectifier K+ channel Kir2.1, we validate the practical utility of SPINE by constructing and comparing domain insertion permissibility maps. SPINE is the first technology to enable saturated domain insertion profiling. SPINE could help explore the relationship between domain insertions and protein function, and how this relationship is shaped by evolutionary forces and can be engineered for biomedical applications.
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Affiliation(s)
- Willow Coyote-Maestas
- Dept. of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Nedrud
- Dept. of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Steffan Okorafor
- Dept. of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yungui He
- Dept. of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Schmidt
- Dept. of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
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27
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Yazhini A, Srinivasan N. How good are comparative models in the understanding of protein dynamics? Proteins 2020; 88:874-888. [PMID: 31999374 DOI: 10.1002/prot.25879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/04/2020] [Accepted: 01/25/2020] [Indexed: 12/27/2022]
Abstract
The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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28
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Abstract
Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Using single-molecule force spectroscopy, we have defined how stabilizing interfaces among the domains of elongation factor G (EF-G) shape its folding pathway. Contrary to the expectation that multidomain proteins fold sequentially as they emerge from the ribosome, we find that folding cannot be completed until the full protein has been synthesized. This posttranslational folding mechanism results in a propensity for misfolding. It is dictated by an energetic coupling among domains that enables conformational flexibility crucial for EF-G function. EF-G thus provides an example of how distinct biological ends—robust folding and functionally important flexibility—come into conflict during protein biogenesis. Large proteins with multiple domains are thought to fold cotranslationally to minimize interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. However, multidomain protein folding and the energetics of domain interactions remain poorly understood. In elongation factor G (EF-G), a highly conserved protein composed of 5 domains, the 2 N-terminal domains form a stably structured unit cotranslationally. Using single-molecule optical tweezers, we have defined the steps leading to fully folded EF-G. We find that the central domain III of EF-G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N-terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C-terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C-terminal neighbors disrupts cotranslational folding and imposes a posttranslational mechanism on the folding of the C-terminal part of EF-G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large-scale conformational transitions that are part of the EF-G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF-G function, complicates the folding of this large multidomain protein.
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29
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Naveenkumar N, Sowdhamini R, Srinivasan N. Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family. FEBS Open Bio 2019; 9:1848-1859. [PMID: 31436855 PMCID: PMC6823287 DOI: 10.1002/2211-5463.12725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/09/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022] Open
Abstract
Homologous domains embedded in multidomain proteins of different domain architectures (DA) may exhibit subtle, but important, differences in their structure and function. Here, we consider two multidomain proteins, Arf nucleotide binding site opener (ARNO) and G protein‐coupled receptor kinase 2 (GRK2), which have very different DAs, but both contain pleckstrin homology (PH) domains. We analyzed the roles of residues selectively conserved in these subfamilies of PH domains from ARNO and GRK2 proteins. DA‐specific residues in PH domain are found to contribute to structural and functional specialization of ARNO and GRK2 in terms of (a) specific intra‐ and interprotein interactions; (b) specificity for phospholipids; and (c) participation in conformational excursions, leading to various functional forms. Our approach can also be applied to subfamilies of other protein families to identify subfamily‐specific residues and their specialized roles.
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Affiliation(s)
- Nagarajan Naveenkumar
- National Centre for Biological Sciences, TIFR, Bangalore, India.,Bharathidasan University, Tiruchirappalli, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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30
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On the perturbation nature of allostery: sites, mutations, and signal modulation. Curr Opin Struct Biol 2019; 56:18-27. [DOI: 10.1016/j.sbi.2018.10.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/27/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
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31
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Naveenkumar N, Kumar G, Sowdhamini R, Srinivasan N, Vishwanath S. Fold combinations in multi-domain proteins. Bioinformation 2019; 15:342-350. [PMID: 31249437 PMCID: PMC6589474 DOI: 10.6026/97320630015342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 01/21/2023] Open
Abstract
Domain-domain interactions in multi-domain proteins play an important role in the combined function of individual domains for the overall biological activity of the protein. The functions of the tethered domains are often coupled and hence, limited numbers of domain architectures with defined folds are known in nature. Therefore, it is of interest to document the available fold-fold combinations and their preference in multi-domain proteins. Hence, we analyzed all multi-domain proteins with known structures in the protein databank and observed that only about 860 fold-fold combinations are present among them. Analyses of multi-domain proteins represented in sequence database result in recognition of 29,860 fold-fold combinations and it accounts for only 2.8% of the theoretically possible 1,036,080 (1439C2) fold-fold combinations. The observed preference for fold-fold combinations in multi-domain proteins is interesting in the context of multiple functions through structural adaptation by gene fusion.
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Affiliation(s)
- Nagarajan Naveenkumar
- National Center for Biological Science, GKVK Campus, Bengaluru, Karnataka, India - 560065
- Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India - 560012
| | - Gayatri Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India - 560012
| | - Ramanathan Sowdhamini
- National Center for Biological Science, GKVK Campus, Bengaluru, Karnataka, India - 560065
| | | | - Sneha Vishwanath
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India - 560012
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32
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Troilo F, Bonetti D, Bignon C, Longhi S, Gianni S. Understanding Intramolecular Crosstalk in an Intrinsically Disordered Protein. ACS Chem Biol 2019; 14:337-341. [PMID: 30715849 DOI: 10.1021/acschembio.8b01055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The interaction between NTAIL and XD from the measles virus represents a paradigmatic example of molecular recognition between an intrinsically disordered protein and a folded partner. By binding to XD, a small portion of NTAIL (classically denoted as MoRE) undergoes a disorder-to-order transition, populating an α-helical structure, while the reminder of the protein remains disordered. Here, we demonstrate an unexpected crosstalk between such a disordered region and the adjacent molecular recognition element (MoRE). This result was obtained by producing a series of truncation and site-directed variants of NTAIL while measuring the effects on the kinetics of folding and binding. We show that the disordered region of NTAIL exerts its inhibitory role by slowing the folding step of the MoRE, thereby tuning the affinity of the interaction.
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Affiliation(s)
- Francesca Troilo
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Christophe Bignon
- Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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