1
|
Hernández-Sánchez A, Páez-Pérez ED, Alfaro-Saldaña E, Olivares-Illana V, García-Meza JV. Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV. J Microbiol Biotechnol 2024; 34:527-537. [PMID: 38346803 PMCID: PMC11016768 DOI: 10.4014/jmb.2310.10033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 04/17/2024]
Abstract
Pilins are protein subunits of pili. The pilins of type IV pili (T4P) in pathogenic bacteria are well characterized, but anything is known about the T4P proteins in acidophilic chemolithoautotrophic microorganisms such as the genus Acidithiobacillus. The interest in T4P of A. thiooxidans is because of their possible role in cell recruitment and bacterial aggregation on the surface of minerals during biooxidation of sulfide minerals. In this study we present a successful ad hoc methodology for the heterologous expression and purification of extracellular proteins such as the minor pilin PilV of the T4P of A. thiooxidans, a pilin exposed to extreme conditions of acidity and high oxidation-reduction potentials, and that interact with metal sulfides in an environment rich in dissolved minerals. Once obtained, the model structure of A. thiooxidans PilV revealed the core basic architecture of T4P pilins. Because of the acidophilic condition, we carried out in silico characterization of the protonation status of acidic and basic residues of PilV in order to calculate the ionization state at specific pH values and evaluated their pH stability. Further biophysical characterization was done using UV-visible and fluorescence spectroscopy and the results showed that PilV remains soluble and stable even after exposure to significant changes of pH. PilV has a unique amino acid composition that exhibits acid stability, with significant biotechnology implications such as biooxidation of sulfide minerals. The biophysics profiles of PilV open new paradigms about resilient proteins and stimulate the study of other pilins from extremophiles.
Collapse
Affiliation(s)
- Araceli Hernández-Sánchez
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, San Luis Potosí, 78210, SLP, México
| | - Edgar D. Páez-Pérez
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, San Luis Potosí, 78210, SLP, México
| | - Elvia Alfaro-Saldaña
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, San Luis Potosí, 78210, SLP, México
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y Cáncer. Instituto de Física, Universidad Autónoma de San Luis Potosí, Av. Parque Chapultepec 1570, Privadas del Pedregal, San Luis Potosí, 78210, SLP, México
| | - J. Viridiana García-Meza
- Geomicrobiología, Metalurgia, Universidad Autónoma de San Luis Potosí, Sierra Leona 550, San Luis Potosí, 78210, SLP, México
| |
Collapse
|
2
|
Gómez-Mínguez Y, Palacios-Abella A, Costigliolo-Rojas C, Barber M, Hernández-Villa L, Úrbez C, Alabadí D. The prefoldin-like protein AtURI exhibits characteristics of intrinsically disordered proteins. FEBS Lett 2024; 598:556-570. [PMID: 38302844 DOI: 10.1002/1873-3468.14811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024]
Abstract
The prefoldin-like protein UNCONVENTIONAL PREFOLDIN RPB5 INTERACTOR (URI) participates in diverse cellular functions, including protein homeostasis, transcription, translation, and signal transduction. Thus, URI is a highly versatile protein, although the molecular basis of this versatility remains unknown. In this work, we show that Arabidopsis thaliana (Arabidopsis) URI (AtURI) possesses a large intrinsically disordered region (IDR) spanning most of the C-terminal part of the protein, a feature conserved in yeast and human orthologs. Our findings reveal two key characteristics of disordered proteins in AtURI: promiscuity in interacting with partners and protein instability. We propose that these two features contribute to providing AtURI with functional versatility.
Collapse
Affiliation(s)
- Yaiza Gómez-Mínguez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | | | | | | | | | - Cristina Úrbez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| |
Collapse
|
3
|
Hannon CE, Eisen MB. Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors. eLife 2024; 12:RP88221. [PMID: 38275292 PMCID: PMC10945700 DOI: 10.7554/elife.88221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
Collapse
Affiliation(s)
- Colleen E Hannon
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| |
Collapse
|
4
|
García-Morales A, Balleza D. Non-canonical helical transitions and conformational switching are associated with characteristic flexibility and disorder indices in TRP and Kv channels. Channels (Austin) 2023; 17:2212349. [PMID: 37196183 DOI: 10.1080/19336950.2023.2212349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023] Open
Abstract
Structural evidence and much experimental data have demonstrated the presence of non-canonical helical substructures (π and 310) in regions of great functional relevance both in TRP as in Kv channels. Through an exhaustive compositional analysis of the sequences underlying these substructures, we find that each of them is associated with characteristic local flexibility profiles, which in turn are implicated in significant conformational rearrangements and interactions with specific ligands. We found that α-to-π helical transitions are associated with patterns of local rigidity whereas α-to-310 transitions are mainly leagued with high local flexibility profiles. We also study the relationship between flexibility and protein disorder in the transmembrane domain of these proteins. By contrasting these two parameters, we located regions showing a sort of structural discrepancy between these similar but not identical protein attributes. Notably, these regions are presumably implicated in important conformational rearrangements during the gating in those channels. In that sense, finding these regions where flexibility and disorder are not proportional allows us to detect regions with potential functional dynamism. From this point of view, we highlighted some conformational rearrangements that occur during ligand binding events, the compaction, and refolding of the outer pore loops in several TRP channels, as well as the well-known S4 motion in Kv channels.
Collapse
Affiliation(s)
| | - Daniel Balleza
- Unidad de Investigación y desarrollo en Alimentos, Instituto Tecnológico de Veracruz. Tecnológico Nacional de México, Veracruz, MEXICO
| |
Collapse
|
5
|
Peterson BG, Hwang J, Russ JE, Schroeder JW, Freddolino PL, Baldridge RD. Deep mutational scanning highlights a role for cytosolic regions in Hrd1 function. Cell Rep 2023; 42:113451. [PMID: 37980570 PMCID: PMC10751623 DOI: 10.1016/j.celrep.2023.113451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/21/2023] Open
Abstract
Misfolded endoplasmic reticulum (ER) proteins are degraded through a process called ER-associated degradation (ERAD). Soluble, lumenal ERAD targets are recognized, retrotranslocated across the ER membrane, ubiquitinated, extracted from the membrane, and degraded by the proteasome using an ERAD pathway containing a ubiquitin ligase called Hrd1. To determine how Hrd1 mediates these processes, we developed a deep mutational scanning approach to identify residues involved in Hrd1 function, including those exclusively required for lumenal degradation. We identify several regions required for different Hrd1 functions. Most surprisingly, we find two cytosolic regions of Hrd1 required for lumenal ERAD substrate degradation. Using in vivo and in vitro approaches, we define roles for disordered regions between structural elements that are required for Hrd1 autoubiquitination and substrate interaction. Our results demonstrate that disordered cytosolic regions promote substrate retrotranslocation by controlling Hrd1 activation and establishing directionality of retrotranslocation for lumenal substrate across the ER membrane.
Collapse
Affiliation(s)
- Brian G Peterson
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jiwon Hwang
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jennifer E Russ
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jeremy W Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - P Lydia Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ryan D Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA.
| |
Collapse
|
6
|
Hatzianestis IH, Mountourakis F, Stavridou S, Moschou PN. Plant condensates: no longer membrane-less? Trends Plant Sci 2023; 28:1101-1112. [PMID: 37183142 DOI: 10.1016/j.tplants.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
Cellular condensation is a reinvigorated area of study in biology, with scientific discussions focusing mainly on the forces that drive condensate formation, properties, and functions. Usually, condensates are called 'membrane-less' to highlight the absence of a surrounding membrane and the lack of associated contacts. In this opinion article we take a different direction, focusing on condensates that may be interfacing with membranes and their possible functions. We also highlight changes in condensate material properties brought about by condensate-membrane interactions, proposing how condensates-membrane interfaces could potentially affect interorganellar communication, development, and growth, but also adaptation in an evolutionary context. We would thus like to stimulate research in this area, which is much less understood in plants compared with the animal field.
Collapse
Affiliation(s)
- Ioannis H Hatzianestis
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Fanourios Mountourakis
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | | | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
| |
Collapse
|
7
|
Narwani TJ, Sharma G, de Brevern AG. Editorial: Flexibility in the genome and proteome: an adaptive toolkit for organisms. Front Genet 2023; 14:1229315. [PMID: 37485333 PMCID: PMC10361655 DOI: 10.3389/fgene.2023.1229315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Affiliation(s)
- Tarun Jairaj Narwani
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Gaurav Sharma
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangāreddi, Telangana, India
| | - Alexandre G. de Brevern
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| |
Collapse
|
8
|
Kumar R, Acharya V. Effector protein structures: a tale of evolutionary relationship. Trends Plant Sci 2023; 28:746-748. [PMID: 37127498 DOI: 10.1016/j.tplants.2023.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
Effector proteins are highly diverse, often lacking similarity in their protein sequences, making it challenging to determine their biological function. Using AlphaFold2 (AF2), Seong and Krasileva recently found that effector structures, but not sequences, share commonality. This helps further understanding of effector evolution across fungal species and reveals unique sequence-unrelated, structurally similar, effector families.
Collapse
Affiliation(s)
- Ravi Kumar
- Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Acharya
- Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
9
|
Lemire BD, Uppuluri P. Coding Sequence Insertions in Fungal Genomes are Intrinsically Disordered and can Impart Functionally-Important Properties on the Host Protein. bioRxiv 2023:2023.04.06.535715. [PMID: 37066283 PMCID: PMC10104129 DOI: 10.1101/2023.04.06.535715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Insertion and deletion mutations (indels) are important mechanisms of generating protein diversity. Indels in coding sequences are under considerable selective pressure to maintain reading frames and to preserve protein function, but once generated, indels provide raw material for the acquisition of new protein properties and functions. We reported recently that coding sequence insertions in the Candida albicans NDU1 protein, a mitochondrial protein involved in the assembly of the NADH:ubiquinone oxidoreductase are imperative for respiration, biofilm formation and pathogenesis. NDU1 inserts are specific to CTG-clade fungi, absent in human ortholog and successfully harnessed as drug targets. Here, we present the first comprehensive report investigating indels and clade-defining insertions (CDIs) in fungal proteomes. We investigated 80 ascomycete proteomes encompassing CTG clade species, the Saccharomycetaceae family, the Aspergillaceae family and the Herpotrichiellaceae (black yeasts) family. We identified over 30,000 insertions, 4,000 CDIs and 2,500 clade-defining deletions (CDDs). Insert sizes range from 1 to over 1,000 residues in length, while maximum deletion length is 19 residues. Inserts are strikingly over-represented in protein kinases, and excluded from structural domains and transmembrane segments. Inserts are predicted to be highly disordered. The amino acid compositions of the inserts are highly depleted in hydrophobic residues and enriched in polar residues. An indel in the Saccharomyces cerevisiae Sth1 protein, the catalytic subunit of the RSC (Remodel the Structure of Chromatin) complex is predicted to be disordered until it forms a ß-strand upon interaction. This interaction performs a vital role in RSC-mediated transcriptional regulation, thereby expanding protein function.
Collapse
Affiliation(s)
- Bernard D. Lemire
- Department of Biochemistry, University of Alberta, Edmonton, Canada (retired)
| | - Priya Uppuluri
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| |
Collapse
|
10
|
Peterson BG, Hwang J, Russ JE, Schroeder J, Freddolino PL, Baldridge RD. Deep mutational scanning highlights a new role for cytosolic regions in Hrd1 function. bioRxiv 2023:2023.04.03.535444. [PMID: 37066402 PMCID: PMC10103981 DOI: 10.1101/2023.04.03.535444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Misfolded endoplasmic reticulum proteins are degraded through a process called endoplasmic reticulum associated degradation (ERAD). Soluble, lumenal ERAD targets are recognized, retrotranslocated across the ER membrane, ubiquitinated, extracted from the membrane, and degraded by the proteasome using an ERAD pathway containing a ubiquitin ligase called Hrd1. To determine how Hrd1 mediates these processes, we developed a deep mutational scanning approach to identify residues involved in Hrd1 function, including those exclusively required for lumenal degradation. We identified several regions required for different Hrd1 functions. Most surprisingly, we found two cytosolic regions of Hrd1 required for lumenal ERAD substrate degradation. Using in vivo and in vitro approaches, we defined roles for disordered regions between structural elements that were required for Hrd1's ability to autoubiquitinate and interact with substrate. Our results demonstrate that disordered cytosolic regions promote substrate retrotranslocation by controlling Hrd1 activation and establishing directionality of retrotranslocation for lumenal substrate across the endoplasmic reticulum membrane.
Collapse
Affiliation(s)
- Brian G. Peterson
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jiwon Hwang
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jennifer E. Russ
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School
| | - Ryan D. Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| |
Collapse
|
11
|
Lyons H, Veettil RT, Pradhan P, Fornero C, De La Cruz N, Ito K, Eppert M, Roeder RG, Sabari BR. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 2023; 186:327-345.e28. [PMID: 36603581 PMCID: PMC9910284 DOI: 10.1016/j.cell.2022.12.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/15/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023]
Abstract
Components of transcriptional machinery are selectively partitioned into specific condensates, often mediated by protein disorder, yet we know little about how this specificity is achieved. Here, we show that condensates composed of the intrinsically disordered region (IDR) of MED1 selectively partition RNA polymerase II together with its positive allosteric regulators while excluding negative regulators. This selective compartmentalization is sufficient to activate transcription and is required for gene activation during a cell-state transition. The IDRs of partitioned proteins are necessary and sufficient for selective compartmentalization and require alternating blocks of charged amino acids. Disrupting this charge pattern prevents partitioning, whereas adding the pattern to proteins promotes partitioning with functional consequences for gene activation. IDRs with similar patterned charge blocks show similar partitioning and function. These findings demonstrate that disorder-mediated interactions can selectively compartmentalize specific functionally related proteins from a complex mixture of biomolecules, leading to regulation of a biochemical pathway.
Collapse
Affiliation(s)
- Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reshma T Veettil
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christy Fornero
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nancy De La Cruz
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, the Rockefeller University, New York, NY 10065, USA
| | - Mikayla Eppert
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, the Rockefeller University, New York, NY 10065, USA
| | - Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
12
|
Eicher JE, Brom JA, Wang S, Sheiko SS, Atkin JM, Pielak GJ. Secondary structure and stability of a gel-forming tardigrade desiccation-tolerance protein. Protein Sci 2022; 31:e4495. [PMID: 36335581 PMCID: PMC9679978 DOI: 10.1002/pro.4495] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/08/2022]
Abstract
Protein-based pharmaceuticals are increasingly important, but their inherent instability necessitates a "cold chain" requiring costly refrigeration during production, shipment, and storage. Drying can overcome this problem, but most proteins need the addition of stabilizers, and some cannot be successfully formulated. Thus, there is a need for new, more effective protective molecules. Cytosolically, abundant heat-soluble proteins from tardigrades are both fundamentally interesting and a promising source of inspiration; these disordered, monodisperse polymers form hydrogels whose structure may protect client proteins during drying. We used attenuated total reflectance Fourier transform infrared spectroscopy, differential scanning calorimetry, and small-amplitude oscillatory shear rheometry to characterize gelation. A 5% (wt/vol) gel has a strength comparable with human skin, and melts cooperatively and reversibly near body temperature with an enthalpy comparable with globular proteins. We suggest that the dilute protein forms α-helical coiled coils and increasing their concentration drives gelation via intermolecular β-sheet formation.
Collapse
Affiliation(s)
- Jonathan E. Eicher
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Julia A. Brom
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Shikun Wang
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Sergei S. Sheiko
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Joanna M. Atkin
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| |
Collapse
|
13
|
Fenton M, Borcherds W, Chen L, Anbanandam A, Levy R, Chen J, Daughdrill G. The MDMX Acidic Domain Uses Allovalency to Bind Both p53 and MDMX. J Mol Biol 2022; 434:167844. [PMID: 36181774 PMCID: PMC9644833 DOI: 10.1016/j.jmb.2022.167844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 01/10/2023]
Abstract
Autoinhibition of p53 binding to MDMX requires two short-linear motifs (SLiMs) containing adjacent tryptophan (WW) and tryptophan-phenylalanine (WF) residues. NMR spectroscopy was used to show the WW and WF motifs directly compete for the p53 binding site on MDMX and circular dichroism spectroscopy was used to show the WW motif becomes helical when it is bound to the p53 binding domain (p53BD) of MDMX. Binding studies using isothermal titration calorimetry showed the WW motif is a stronger inhibitor of p53 binding than the WF motif when they are both tethered to p53BD by the natural disordered linker. We also investigated how the WW and WF motifs interact with the DNA binding domain (DBD) of p53. Both motifs bind independently to similar sites on DBD that overlap the DNA binding site. Taken together our work defines a model for complex formation between MDMX and p53 where a pair of disordered SLiMs bind overlapping sites on both proteins.
Collapse
Affiliation(s)
- Malissa Fenton
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Lihong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612, United States
| | - Asokan Anbanandam
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Robin Levy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Jiandong Chen
- Molecular Oncology Department, Moffitt Cancer Center, Tampa, FL 33612, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, United States.
| |
Collapse
|
14
|
Abstract
Predictions for millions of protein three-dimensional structures are only a few clicks away since the release of AlphaFold2 results for UniProt. However, many proteins have so-called intrinsically disordered regions (IDRs) that do not adopt unique structures in isolation. These IDRs are associated with several diseases, including Alzheimer’s Disease. We showed that three recent disorder measures of AlphaFold2 predictions (pLDDT, “experimentally resolved” prediction and “relative solvent accessibility”) correlated to some extent with IDRs. However, expert methods predict IDRs more reliably by combining complex machine learning models with expert-crafted input features and evolutionary information from multiple sequence alignments (MSAs). MSAs are not always available, especially for IDRs, and are computationally expensive to generate, limiting the scalability of the associated tools. Here, we present the novel method SETH that predicts residue disorder from embeddings generated by the protein Language Model ProtT5, which explicitly only uses single sequences as input. Thereby, our method, relying on a relatively shallow convolutional neural network, outperformed much more complex solutions while being much faster, allowing to create predictions for the human proteome in about 1 hour on a consumer-grade PC with one NVIDIA GeForce RTX 3060. Trained on a continuous disorder scale (CheZOD scores), our method captured subtle variations in disorder, thereby providing important information beyond the binary classification of most methods. High performance paired with speed revealed that SETH’s nuanced disorder predictions for entire proteomes capture aspects of the evolution of organisms. Additionally, SETH could also be used to filter out regions or proteins with probable low-quality AlphaFold2 3D structures to prioritize running the compute-intensive predictions for large data sets. SETH is freely publicly available at: https://github.com/Rostlab/SETH.
Collapse
Affiliation(s)
- Dagmar Ilzhöfer
- Faculty of Informatics, TUM (Technical University of Munich), Munich, Germany
| | - Michael Heinzinger
- Faculty of Informatics, TUM (Technical University of Munich), Munich, Germany,Center of Doctoral Studies in Informatics and Its Applications (CeDoSIA), TUM Graduate School, Garching, Germany,*Correspondence: Michael Heinzinger,
| | - Burkhard Rost
- Faculty of Informatics, TUM (Technical University of Munich), Munich, Germany,Institute for Advanced Study (TUM-IAS), TUM (Technical University of Munich), Garching, Germany,TUM School of Life Sciences Weihenstephan (WZW), TUM (Technical University of Munich), Freising, Germany
| |
Collapse
|
15
|
Stejskal L, Kalemera MD, Lewis CB, Palor M, Walker L, Daviter T, Lees WD, Moss DS, Kremyda-Vlachou M, Kozlakidis Z, Gallo G, Bailey D, Rosenberg W, Illingworth CJR, Shepherd AJ, Grove J. An entropic safety catch controls hepatitis C virus entry and antibody resistance. eLife 2022; 11:e71854. [PMID: 35796426 PMCID: PMC9333995 DOI: 10.7554/elife.71854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
E1 and E2 (E1E2), the fusion proteins of Hepatitis C Virus (HCV), are unlike that of any other virus yet described, and the detailed molecular mechanisms of HCV entry/fusion remain unknown. Hypervariable region-1 (HVR-1) of E2 is a putative intrinsically disordered protein tail. Here, we demonstrate that HVR-1 has an autoinhibitory function that suppresses the activity of E1E2 on free virions; this is dependent on its conformational entropy. Thus, HVR-1 is akin to a safety catch that prevents premature triggering of E1E2 activity. Crucially, this mechanism is turned off by host receptor interactions at the cell surface to allow entry. Mutations that reduce conformational entropy in HVR-1, or genetic deletion of HVR-1, turn off the safety catch to generate hyper-reactive HCV that exhibits enhanced virus entry but is thermally unstable and acutely sensitive to neutralising antibodies. Therefore, the HVR-1 safety catch controls the efficiency of virus entry and maintains resistance to neutralising antibodies. This discovery provides an explanation for the ability of HCV to persist in the face of continual immune assault and represents a novel regulatory mechanism that is likely to be found in other viral fusion machinery.
Collapse
Affiliation(s)
- Lenka Stejskal
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Mphatso D Kalemera
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Charlotte B Lewis
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Machaela Palor
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Lucas Walker
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Tina Daviter
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
- Shared Research Facilities, The Institute of Cancer ResearchLondonUnited Kingdom
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - David S Moss
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | | | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health OrganizationLyonFrance
| | | | | | - William Rosenberg
- Division of Medicine, Institute for Liver and Digestive Health, University College LondonLondonUnited Kingdom
| | - Christopher JR Illingworth
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Institut für Biologische Physik, Universität zu KölnCologneGermany
- MRC Biostatistics Unit, University of CambridgeCambridgeUnited Kingdom
| | - Adrian J Shepherd
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Joe Grove
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| |
Collapse
|
16
|
Jara KA, Loening NM, Reardon PN, Yu Z, Woonnimani P, Brooks C, Vesely CH, Barbar EJ. Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein. eLife 2022; 11:80217. [PMID: 36416224 PMCID: PMC9771362 DOI: 10.7554/elife.80217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
As the only major retrograde transporter along microtubules, cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to the function of this motor protein complex is dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150Glued and nuclear distribution protein (NudE) at overlapping sites of its intrinsically disordered N-terminal domain. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulates IC interactions with p150Glued and NudE. Using IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in binding affinity of IC to p150Glued and a loss of binding to NudE for constructs containing the entire N-terminal domain as well as for full-length constructs when compared to the tight binding observed with short IC constructs. We attribute this difference to autoinhibition caused by long-range intramolecular interactions between the N-terminal single α-helix of IC, the common site for p150Glued, and NudE binding, and residues closer to the end of the N-terminal domain. Reconstitution of IC subcomplexes demonstrates that autoinhibition is differentially regulated by light chains binding, underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.
Collapse
Affiliation(s)
- Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | | | - Patrick N Reardon
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States,Oregon State University NMR FacilityCorvallisUnited States
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Prajna Woonnimani
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Coban Brooks
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Cat H Vesely
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| |
Collapse
|
17
|
Hsiao AS. Plant Protein Disorder: Spatial Regulation, Broad Specificity, Switch of Signaling and Physiological Status. Front Plant Sci 2022; 13:904446. [PMID: 35685011 PMCID: PMC9171514 DOI: 10.3389/fpls.2022.904446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/10/2022] [Indexed: 05/14/2023]
Affiliation(s)
- An-Shan Hsiao
- *Correspondence: An-Shan Hsiao ; orcid.org/0000-0002-2485-9034
| |
Collapse
|
18
|
Kim M, Bezprozvanny I. Conformational Models of APP Processing by Gamma Secretase Based on Analysis of Pathogenic Mutations. Int J Mol Sci 2021; 22:13600. [PMID: 34948396 DOI: 10.3390/ijms222413600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/27/2022] Open
Abstract
Proteolytic processing of amyloid precursor protein (APP) plays a critical role in the pathogenesis of Alzheimer’s disease (AD). Sequential cleavage of APP by β and γ secretases leads to the generation of Aβ40 (non-amyloidogenic) and Aβ42 (amyloidogenic) peptides. Presenilin-1 (PS1) or presenilin-2 (PS2) play the role of a catalytic subunit of γ-secretase. Multiple familial AD (FAD) mutations in APP, PS1, or PS2 result in an increased Aβ42:Aβ40 ratio and the accumulation of toxic Aβ42 oligomers and plaques in patient brains. In this study, we perform molecular modeling of the APP complex with γ-secretase and analyze potential effects of FAD mutations in APP and PS1. We noticed that all FAD mutations in the APP transmembrane domain are predicted to cause an increase in the local disorder of its secondary structure. Based on structural analysis of known γ-secretase structures, we propose that APP can form a complex with γ-secretase in 2 potential conformations—M1 and M2. In conformation, the M1 transmembrane domain of APP forms a contact with the perimembrane domain that follows transmembrane domain 6 (TM6) in the PS1 structure. In conformation, the M2 transmembrane domain of APP forms a contact with transmembrane domain 7 (TM7) in the PS1 structure. By analyzing the effects of PS1-FAD mutations on the local protein disorder index, we discovered that these mutations increase the conformational flexibility of M2 and reduce the conformational flexibility of M1. Based on these results, we propose that M2 conformation, but not M1 conformation, of the γ secretase complex with APP leads to the amyloidogenic (Aβ42-generating) processing of APP. Our model predicts that APP processing in M1 conformation is favored by curved membranes, such as the membranes of early endosomes. In contrast, APP processing in M2 conformation is likely to be favored by relatively flat membranes, such as membranes of late endosomes and plasma membranes. These predictions are consistent with published biochemical analyses of APP processing at different subcellular locations. Our results also suggest that specific inhibitors of Aβ42 production could be potentially developed by selectively targeting the M2 conformation of the γ secretase complex with APP.
Collapse
|
19
|
Makarov M, Meng J, Tretyachenko V, Srb P, Březinová A, Giacobelli VG, Bednárová L, Vondrášek J, Dunker AK, Hlouchová K. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. Protein Sci 2021; 30:1022-1034. [PMID: 33739538 PMCID: PMC8040869 DOI: 10.1002/pro.4068] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/07/2022]
Abstract
The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.
Collapse
Affiliation(s)
- Mikhail Makarov
- Department of Cell Biology, Faculty of ScienceCharles University, BIOCEVPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Jingwei Meng
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Vyacheslav Tretyachenko
- Department of Cell Biology, Faculty of ScienceCharles University, BIOCEVPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Anna Březinová
- Proteomics Core Facility, BIOCEV, Faculty of Science, Charles UniversityPragueCzech Republic
| | | | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - A. Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Klára Hlouchová
- Department of Cell Biology, Faculty of ScienceCharles University, BIOCEVPragueCzech Republic
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| |
Collapse
|
20
|
Chui AJ, Griswold AR, Taabazuing CY, Orth EL, Gai K, Rao SD, Ball DP, Hsiao JC, Bachovchin DA. Activation of the CARD8 Inflammasome Requires a Disordered Region. Cell Rep 2020; 33:108264. [PMID: 33053349 PMCID: PMC7594595 DOI: 10.1016/j.celrep.2020.108264] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/25/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Several cytosolic pattern-recognition receptors (PRRs) form multiprotein complexes called canonical inflammasomes in response to intracellular danger signals. Canonical inflammasomes recruit and activate caspase-1 (CASP1), which in turn cleaves and activates inflammatory cytokines and gasdermin D (GSDMD), inducing pyroptotic cell death. Inhibitors of the dipeptidyl peptidases DPP8 and DPP9 (DPP8/9) activate both the human NLRP1 and CARD8 inflammasomes. NLRP1 and CARD8 have different N-terminal regions but have similar C-terminal regions that undergo autoproteolysis to generate two non-covalently associated fragments. Here, we show that DPP8/9 inhibition activates a proteasomal degradation pathway that targets disordered and misfolded proteins for destruction. CARD8’s N terminus contains a disordered region of ~160 amino acids that is recognized and destroyed by this degradation pathway, thereby freeing its C-terminal fragment to activate CASP1 and induce pyroptosis. Thus, CARD8 serves as an alarm to signal the activation of a degradation pathway for disordered and misfolded proteins. Inflammasomes are multiprotein complexes that detect intracellular danger signals and stimulate powerful immune responses. DPP8/9 inhibitors activate the CARD8 inflammasome through an unknown mechanism. Here, Chui et al. show that DPP8/9 inhibitors induce the degradation of many disordered and misfolded proteins. CARD8 has an N-terminal disordered region that is degraded upon DPP8/9 inhibition, triggering inflammasome formation.
Collapse
Affiliation(s)
- Ashley J Chui
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew R Griswold
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Cornelius Y Taabazuing
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth L Orth
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kuo Gai
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sahana D Rao
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel P Ball
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeffrey C Hsiao
- Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel A Bachovchin
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
21
|
Gianni S, Jemth P. Affinity versus specificity in coupled binding and folding reactions. Protein Eng Des Sel 2020; 32:355-357. [PMID: 31397874 DOI: 10.1093/protein/gzz020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 01/08/2023] Open
Abstract
Intrinsically disordered protein regions may fold upon binding to an interaction partner. It is often argued that such coupled binding and folding enables the combination of high specificity with low affinity. The basic tenet is that an unfavorable folding equilibrium will make the overall binding weaker while maintaining the interaction interface. While theoretically solid, we argue that this concept may be misleading for intrinsically disordered proteins. In fact, experimental evidence suggests that interactions of disordered regions usually involve extended conformations. In such cases, the disordered region is exceptionally unlikely to fold into a bound conformation in the absence of its binding partner. Instead, these disordered regions can bind to their partners in multiple different conformations and then fold into the native bound complex, thus, if anything, increasing the affinity through folding. We concede that (de)stabilization of native structural elements such as helices will modulate affinity, but this could work both ways, decreasing or increasing the stability of the complex. Moreover, experimental data show that intrinsically disordered binding regions display a range of affinities and specificities dictated by the particular side chains and length of the disordered region and not necessarily by the fact that they are disordered. We find it more likely that intrinsically disordered regions are common in protein-protein interactions because they increase the repertoire of binding partners, providing an accessible route to evolve interactions rather than providing a stability-affinity trade-off.
Collapse
Affiliation(s)
- Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome 00185, Italy
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, SE-75123 Uppsala, Sweden
| |
Collapse
|
22
|
Sridhar A, Farr SE, Portella G, Schlick T, Orozco M, Collepardo-Guevara R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proc Natl Acad Sci U S A 2020; 117:7216-24. [PMID: 32165536 DOI: 10.1073/pnas.1910044117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1-a ubiquitous nucleosome-binding protein-remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.
Collapse
|
23
|
Manguy J, Shields DC. Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles. R Soc Open Sci 2019; 6:190939. [PMID: 31824707 PMCID: PMC6837221 DOI: 10.1098/rsos.190939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Milk alpha-, beta- and kappa-casein proteins assemble into casein micelles in breast epithelial cells. The glycomacropeptide (GMP) tails of kappa-casein that extend from the surface of the micelle are key to assembly and aggregation. Aggregation is triggered by stomach pepsin cleavage of GMP from para-kappa-casein (PKC). While one casein micelle model emphasizes the importance of hydrophobic interactions, another focuses on polar residues. We performed an evolutionary analysis of kappa-casein primary sequence and predicted features that potentially impact on protein interactions. We noted more rapid change in the earlier period (166 to 60 Ma). Pepsin and plasmin cleavage sites were avoided in the GMP, which may partly explain its amino acid composition. Short tandem repeats have led to modest expansions of PKC, and to large GMP expansions, suggesting the GMP is less length constrained. Amino acid compositional constraints were assessed across species. Polarity and hydrophobicity properties were insufficient to explain differences between PKC and GMP. Among polar residues, threonine dominates the GMP, compared to serine, probably reflecting its preference for O-glycosylation over phosphorylation. Glutamine, enriched in the bovine PQ-rich region, is not positionally conserved in other species. Among hydrophobic residues, isoleucine is clearly preferred over leucine in the GMP, and patches of hydrophobicity are not markedly positionally conserved. PKC tyrosine and charged residues showed stronger conservation of position, suggesting a role for pi-interactions, seen in other structurally dynamic protein membraneless assemblies. Independent acquisitions of cysteines are consistent with a trend of increasing stabilization of multimers by covalent disulphide bonds, over evolutionary time. In conclusion, kappa-casein compositional and positional constraints appear to be influenced by modification preferences, protease evasion and protein-protein interactions.
Collapse
Affiliation(s)
- Jean Manguy
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Denis C. Shields
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
24
|
Bracha D, Walls MT, Wei MT, Zhu L, Kurian M, Avalos JL, Toettcher JE, Brangwynne CP. Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. Cell 2018; 175:1467-1480.e13. [PMID: 30500534 DOI: 10.1016/j.cell.2018.10.048] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 08/10/2018] [Accepted: 10/23/2018] [Indexed: 11/24/2022]
Abstract
Liquid-liquid phase separation plays a key role in the assembly of diverse intracellular structures. However, the biophysical principles by which phase separation can be precisely localized within subregions of the cell are still largely unclear, particularly for low-abundance proteins. Here, we introduce an oligomerizing biomimetic system, "Corelets," and utilize its rapid and quantitative light-controlled tunability to map full intracellular phase diagrams, which dictate the concentrations at which phase separation occurs and the transition mechanism, in a protein sequence dependent manner. Surprisingly, both experiments and simulations show that while intracellular concentrations may be insufficient for global phase separation, sequestering protein ligands to slowly diffusing nucleation centers can move the cell into a different region of the phase diagram, resulting in localized phase separation. This diffusive capture mechanism liberates the cell from the constraints of global protein abundance and is likely exploited to pattern condensates associated with diverse biological processes. VIDEO ABSTRACT.
Collapse
|
25
|
Abstract
Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of the sequences of these clusters, we were able to link between sequence, structure, and disorder information. We introduced several parameters as measures of fluctuations at a given MSA site and used these as representative of the sequence and structure entropy at that site. In general, we found a tendency for negative correlations between disorder and structure, and significant positive correlations between disorder and the fluctuations in the system. We also found evidence for residue-type conservation for those residues proximate to potentially disordered sites. Mutation at the disorder site itself appear to be allowed. In addition, we found positive correlation for disorder and accessible surface area, validating that disordered residues occur in exposed regions of proteins. Finally, we also found that fluctuations in the dihedral angles at the original mutated residue and disorder are positively correlated while dihedral angle fluctuations in spatially proximal residues are negatively correlated with disorder. Our results seem to indicate permissible variability in the disordered site, but greater rigidity in the parts of the protein with which the disordered site interacts. This is another indication that disordered residues are involved in protein function.
Collapse
|
26
|
Loos MS, Ramakrishnan R, Vranken W, Tsirigotaki A, Tsare EP, Zorzini V, Geyter JD, Yuan B, Tsamardinos I, Klappa M, Schymkowitz J, Rousseau F, Karamanou S, Economou A. Structural Basis of the Subcellular Topology Landscape of Escherichia coli. Front Microbiol 2019; 10:1670. [PMID: 31404336 PMCID: PMC6677119 DOI: 10.3389/fmicb.2019.01670] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Cellular proteomes are distributed in multiple compartments: on DNA, ribosomes, on and inside membranes, or they become secreted. Structural properties that allow polypeptides to occupy subcellular niches, particularly to after crossing membranes, remain unclear. We compared intrinsic and extrinsic features in cytoplasmic and secreted polypeptides of the Escherichia coli K-12 proteome. Structural features between the cytoplasmome and secretome are sharply distinct, such that a signal peptide-agnostic machine learning tool distinguishes cytoplasmic from secreted proteins with 95.5% success. Cytoplasmic polypeptides are enriched in aliphatic, aromatic, charged and hydrophobic residues, unique folds and higher early folding propensities. Secretory polypeptides are enriched in polar/small amino acids, β folds, have higher backbone dynamics, higher disorder and contact order and are more often intrinsically disordered. These non-random distributions and experimental evidence imply that evolutionary pressure selected enhanced secretome flexibility, slow folding and looser structures, placing the secretome in a distinct protein class. These adaptations protect the secretome from premature folding during its cytoplasmic transit, optimize its lipid bilayer crossing and allowed it to acquire cell envelope specific chemistries. The latter may favor promiscuous multi-ligand binding, sensing of stress and cell envelope structure changes. In conclusion, enhanced flexibility, slow folding, looser structures and unique folds differentiate the secretome from the cytoplasmome. These findings have wide implications on the structural diversity and evolution of modern proteomes and the protein folding problem.
Collapse
Affiliation(s)
- Maria S Loos
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Reshmi Ramakrishnan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, Free University of Brussels, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel and Center for Structural Biology, Brussels, Belgium
| | - Alexandra Tsirigotaki
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Evrydiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Valentina Zorzini
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jozefien De Geyter
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Biao Yuan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ioannis Tsamardinos
- Gnosis Data Analysis PC, Heraklion, Greece.,Department of Computer Science, University of Crete, Heraklion, Greece
| | - Maria Klappa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Joost Schymkowitz
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,Gnosis Data Analysis PC, Heraklion, Greece
| |
Collapse
|
27
|
Cable J, Brangwynne C, Seydoux G, Cowburn D, Pappu RV, Castañeda CA, Berchowitz LE, Chen Z, Jonikas M, Dernburg A, Mittag T, Fawzi NL. Phase separation in biology and disease-a symposium report. Ann N Y Acad Sci 2019; 1452:3-11. [PMID: 31199001 DOI: 10.1111/nyas.14126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 01/28/2023]
Abstract
Phase separation of multivalent protein and RNA molecules enables cells the formation of reversible nonstoichiometric, membraneless assemblies. These assemblies, referred to as biomolecular condensates, help with the spatial organization and compartmentalization of cellular matter. Each biomolecular condensate is defined by a distinct macromolecular composition. Distinct condensates have distinct preferential locations within cells, and they are associated with distinct biological functions, including DNA replication, RNA metabolism, signal transduction, synaptic transmission, and stress response. Several proteins found in biomolecular condensates have also been implicated in disease, including Huntington's disease, amyotrophic lateral sclerosis, and several types of cancer. Disease-associated mutations in these proteins have been found to affect the material properties of condensates as well as the driving forces for phase separation. Understanding the intrinsic and extrinsic forces driving the formation and dissolution of biomolecular condensates via spontaneous and driven phase separation is an important step in understanding the processes associated with biological regulation in health and disease.
Collapse
Affiliation(s)
| | - Clifford Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Cowburn
- Departments of Biochemistry and Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Science and Engineering of Living Systems, McKelvey School of Engineering, St. Louis, Missouri
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Program in Neuroscience, Syracuse University, Syracuse, New York
| | - Luke E Berchowitz
- Departments of Genetics and Development, Columbia University, New York, New York
| | - Zhijuan Chen
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Martin Jonikas
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Abby Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island
| |
Collapse
|
28
|
Yruela I, Contreras-Moreira B, Dunker AK, Niklas KJ. Evolution of Protein Ductility in Duplicated Genes of Plants. Front Plant Sci 2018; 9:1216. [PMID: 30177944 PMCID: PMC6109787 DOI: 10.3389/fpls.2018.01216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality.
Collapse
Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology, Joint Unit to CSIC, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology, Joint Unit to CSIC, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Zaragoza, Spain
| | - A. Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Karl J. Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
29
|
Pallarès I, de Groot NS, Iglesias V, Sant'Anna R, Biosca A, Fernàndez-Busquets X, Ventura S. Discovering Putative Prion-Like Proteins in Plasmodium falciparum: A Computational and Experimental Analysis. Front Microbiol 2018; 9:1737. [PMID: 30131778 PMCID: PMC6090025 DOI: 10.3389/fmicb.2018.01737] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022] Open
Abstract
Prions are a singular subset of proteins able to switch between a soluble conformation and a self-perpetuating amyloid state. Traditionally associated with neurodegenerative diseases, increasing evidence indicates that organisms exploit prion-like mechanisms for beneficial purposes. The ability to transit between conformations is encoded in the so-called prion domains, long disordered regions usually enriched in glutamine/asparagine residues. Interestingly, Plasmodium falciparum, the parasite that causes the most virulent form of malaria, is exceptionally rich in proteins bearing long Q/N-rich sequence stretches, accounting for roughly 30% of the proteome. This biased composition suggests that these protein regions might correspond to prion-like domains (PrLDs) and potentially form amyloid assemblies. To investigate this possibility, we performed a stringent computational survey for Q/N-rich PrLDs on P. falciparum. Our data indicate that ∼10% of P. falciparum protein sequences have prionic signatures, and that this subproteome is enriched in regulatory proteins, such as transcription factors and RNA-binding proteins. Furthermore, we experimentally demonstrate for several of the identified PrLDs that, despite their disordered nature, they contain inner short sequences able to spontaneously self-assemble into amyloid-like structures. Although the ability of these sequences to nucleate the conformational conversion of the respective full-length proteins should still be demonstrated, our analysis suggests that, as previously described for other organisms, prion-like proteins might also play a functional role in P. falciparum.
Collapse
Affiliation(s)
- Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natalia S de Groot
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ricardo Sant'Anna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Biosca
- Nanomalaria Group, Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Barcelona Institute for Global Health, Barcelona Centre for International Health Research (Hospital Clínic - Universitat de Barcelona), Barcelona, Spain.,Institute of Nanoscience and Nanotechnology, University of Barcelona, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Barcelona Institute for Global Health, Barcelona Centre for International Health Research (Hospital Clínic - Universitat de Barcelona), Barcelona, Spain.,Institute of Nanoscience and Nanotechnology, University of Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
30
|
Klasberg S, Bitard-Feildel T, Callebaut I, Bornberg-Bauer E. Origins and structural properties of novel and de novo protein domains during insect evolution. FEBS J 2018; 285:2605-2625. [PMID: 29802682 DOI: 10.1111/febs.14504] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 04/12/2018] [Accepted: 05/11/2018] [Indexed: 12/11/2022]
Abstract
Over long time scales, protein evolution is characterized by modular rearrangements of protein domains. Such rearrangements are mainly caused by gene duplication, fusion and terminal losses. To better understand domain emergence mechanisms we investigated 32 insect genomes covering a speciation gradient ranging from ~ 2 to ~ 390 mya. We use established domain models and foldable domains delineated by hydrophobic cluster analysis (HCA), which does not require homologous sequences, to also identify domains which have likely arisen de novo, that is, from previously noncoding DNA. Our results indicate that most novel domains emerge terminally as they originate from ORF extensions while fewer arise in middle arrangements, resulting from exonization of intronic or intergenic regions. Many novel domains rapidly migrate between terminal or middle positions and single- and multidomain arrangements. Young domains, such as most HCA-defined domains, are under strong selection pressure as they show signals of purifying selection. De novo domains, linked to ancient domains or defined by HCA, have higher degrees of intrinsic disorder and disorder-to-order transition upon binding than ancient domains. However, the corresponding DNA sequences of the novel domains of de novo origins could only rarely be found in sister genomes. We conclude that novel domains are often recruited by other proteins and undergo important structural modifications shortly after their emergence, but evolve too fast to be characterized by cross-species comparisons alone.
Collapse
Affiliation(s)
- Steffen Klasberg
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Germany
| | - Tristan Bitard-Feildel
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Germany
| |
Collapse
|
31
|
Berlow RB, Dyson HJ, Wright PE. Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation. J Mol Biol 2018; 430:2309-2320. [PMID: 29634920 DOI: 10.1016/j.jmb.2018.04.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022]
Abstract
Allosteric regulatory processes are implicated at all levels of biological function. Recent advances in our understanding of the diverse and functionally significant class of intrinsically disordered proteins have identified a multitude of ways in which disordered proteins function within the confines of the allosteric paradigm. Allostery within or mediated by intrinsically disordered proteins ensures robust and efficient signal integration through mechanisms that would be extremely unfavorable or even impossible for globular protein interaction partners. Here, we highlight recent examples that indicate the breadth of biological outcomes that can be achieved through allosteric regulation by intrinsically disordered proteins. Ongoing and future work in this rapidly evolving area of research will expand our appreciation of the central role of intrinsically disordered proteins in ensuring the fidelity and efficiency of cellular regulation.
Collapse
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, CA 92037, USA
| | - 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, CA 92037, USA
| | - 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, CA 92037, USA.
| |
Collapse
|
32
|
Tsirigotaki A, Chatzi KE, Koukaki M, De Geyter J, Portaliou AG, Orfanoudaki G, Sardis MF, Trelle MB, Jørgensen TJD, Karamanou S, Economou A. Long-Lived Folding Intermediates Predominate the Targeting-Competent Secretome. Structure 2018; 26:695-707.e5. [PMID: 29606594 DOI: 10.1016/j.str.2018.03.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/02/2018] [Accepted: 03/08/2018] [Indexed: 10/17/2022]
Abstract
Secretory preproteins carry signal peptides fused amino-terminally to mature domains. They are post-translationally targeted to cross the plasma membrane in non-folded states with the help of translocases, and fold only at their final destinations. The mechanism of this process of postponed folding is unknown, but is generally attributed to signal peptides and chaperones. We herein demonstrate that, during targeting, most mature domains maintain loosely packed folding intermediates. These largely soluble states are signal peptide independent and essential for translocase recognition. These intermediates are promoted by mature domain features: residue composition, elevated disorder, and reduced hydrophobicity. Consequently, a mature domain folds slower than its cytoplasmic structural homolog. Some mature domains could not evolve stable, loose intermediates, and hence depend on signal peptides for slow folding to the detriment of solubility. These unique features of secretory proteins impact our understanding of protein trafficking, folding, and aggregation, and thus place them in a distinct class.
Collapse
Affiliation(s)
- Alexandra Tsirigotaki
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Katerina E Chatzi
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Marina Koukaki
- Institute of Molecular Biology and Biotechnology, FoRTH, University of Crete, 70013 Heraklion, Crete, Greece
| | - Jozefien De Geyter
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Athina G Portaliou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FoRTH, University of Crete, 70013 Heraklion, Crete, Greece
| | - Marios Frantzeskos Sardis
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Morten Beck Trelle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| |
Collapse
|
33
|
Grossman-Haham I, Rosenblum G, Namani T, Hofmann H. Slow domain reconfiguration causes power-law kinetics in a two-state enzyme. Proc Natl Acad Sci U S A 2018; 115:513-8. [PMID: 29298911 DOI: 10.1073/pnas.1714401115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein dynamics are typically captured well by rate equations that predict exponential decays for two-state reactions. Here, we describe a remarkable exception. The electron-transfer enzyme quiescin sulfhydryl oxidase (QSOX), a natural fusion of two functionally distinct domains, switches between open- and closed-domain arrangements with apparent power-law kinetics. Using single-molecule FRET experiments on time scales from nanoseconds to milliseconds, we show that the unusual open-close kinetics results from slow sampling of an ensemble of disordered domain orientations. While substrate accelerates the kinetics, thus suggesting a substrate-induced switch to an alternative free energy landscape of the enzyme, the power-law behavior is also preserved upon electron load. Our results show that the slow sampling of open conformers is caused by a variety of interdomain interactions that imply a rugged free energy landscape, thus providing a generic mechanism for dynamic disorder in multidomain enzymes.
Collapse
|
34
|
Krüger TPJ, Malý P, Alexandre MTA, Mančal T, Büchel C, van Grondelle R. How reduced excitonic coupling enhances light harvesting in the main photosynthetic antennae of diatoms. Proc Natl Acad Sci U S A 2017; 114:E11063-71. [PMID: 29229806 DOI: 10.1073/pnas.1714656115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strong excitonic interactions are a key design strategy in photosynthetic light harvesting, expanding the spectral cross-section for light absorption and creating considerably faster and more robust excitation energy transfer. These molecular excitons are a direct result of exceptionally densely packed pigments in photosynthetic proteins. The main light-harvesting complexes of diatoms, known as fucoxanthin-chlorophyll proteins (FCPs), are an exception, displaying surprisingly weak excitonic coupling between their chlorophyll (Chl) a's, despite a high pigment density. Here, we show, using single-molecule spectroscopy, that the FCP complexes of Cyclotella meneghiniana switch frequently into stable, strongly emissive states shifted 4-10 nm toward the red. A few percent of isolated FCPa complexes and ∼20% of isolated FCPb complexes, on average, were observed to populate these previously unobserved states, percentages that agree with the steady-state fluorescence spectra of FCP ensembles. Thus, the complexes use their enhanced sensitivity to static disorder to increase their light-harvesting capability in a number of ways. A disordered exciton model based on the structure of the main plant light-harvesting complex explains the red-shifted emission by strong localization of the excitation energy on a single Chl a pigment in the terminal emitter domain due to very specific pigment orientations. We suggest that the specific construction of FCP gives the complex a unique strategy to ensure that its light-harvesting function remains robust in the fluctuating protein environment despite limited excitonic interactions.
Collapse
|
35
|
Woodcock JM, Goodwin KL, Sandow JJ, Coolen C, Perugini MA, Webb AI, Pitson SM, Lopez AF, Carver JA. Role of salt bridges in the dimer interface of 14-3-3ζ in dimer dynamics, N-terminal α-helical order, and molecular chaperone activity. J Biol Chem 2017; 293:89-99. [PMID: 29109150 DOI: 10.1074/jbc.m117.801019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/24/2017] [Indexed: 11/06/2022] Open
Abstract
The 14-3-3 family of intracellular proteins are dimeric, multifunctional adaptor proteins that bind to and regulate the activities of many important signaling proteins. The subunits within 14-3-3 dimers are predicted to be stabilized by salt bridges that are largely conserved across the 14-3-3 protein family and allow the different isoforms to form heterodimers. Here, we have examined the contributions of conserved salt-bridging residues in stabilizing the dimeric state of 14-3-3ζ. Using analytical ultracentrifugation, our results revealed that Asp21 and Glu89 both play key roles in dimer dynamics and contribute to dimer stability. Furthermore, hydrogen-deuterium exchange coupled with mass spectrometry showed that mutation of Asp21 promoted disorder in the N-terminal helices of 14-3-3ζ, suggesting that this residue plays an important role in maintaining structure across the dimer interface. Intriguingly, a D21N 14-3-3ζ mutant exhibited enhanced molecular chaperone ability that prevented amorphous protein aggregation, suggesting a potential role for N-terminal disorder in 14-3-3ζ's poorly understood chaperone action. Taken together, these results imply that disorder in the N-terminal helices of 14-3-3ζ is a consequence of the dimer-monomer dynamics and may play a role in conferring chaperone function to 14-3-3ζ protein.
Collapse
Affiliation(s)
- Joanna M Woodcock
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000.
| | - Katy L Goodwin
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005
| | - Jarrod J Sandow
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052
| | - Carl Coolen
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Andrew I Webb
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000
| | - Angel F Lopez
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000
| | - John A Carver
- Research School of Chemistry, Australian National University, Acton, Australian Capital Territory 2601, Australia
| |
Collapse
|
36
|
Bornberg-Bauer E, Schmitz J, Heberlein M. Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'. Biochem Soc Trans 2015; 43:867-73. [PMID: 26517896 DOI: 10.1042/BST20150089] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Proteins are the workhorses of the cell and, over billions of years, they have evolved an amazing plethora of extremely diverse and versatile structures with equally diverse functions. Evolutionary emergence of new proteins and transitions between existing ones are believed to be rare or even impossible. However, recent advances in comparative genomics have repeatedly called some 10%-30% of all genes without any detectable similarity to existing proteins. Even after careful scrutiny, some of those orphan genes contain protein coding reading frames with detectable transcription and translation. Thus some proteins seem to have emerged from previously non-coding 'dark genomic matter'. These 'de novo' proteins tend to be disordered, fast evolving, weakly expressed but also rapidly assuming novel and physiologically important functions. Here we review mechanisms by which 'de novo' proteins might be created, under which circumstances they may become fixed and why they are elusive. We propose a 'grow slow and moult' model in which first a reading frame is extended, coding for an initially disordered and non-globular appendage which, over time, becomes more structured and may also become associated with other proteins.
Collapse
|
37
|
Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. Acta Crystallogr F Struct Biol Commun 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
Collapse
Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
| |
Collapse
|
38
|
Tantos A, Kalmar L, Tompa P. The role of structural disorder in cell cycle regulation, related clinical proteomics, disease development and drug targeting. Expert Rev Proteomics 2016; 12:221-33. [PMID: 25976105 DOI: 10.1586/14789450.2015.1042866] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding the molecular mechanisms of the regulation of cell cycle is a central issue in molecular cell biology, due to its fundamental role in the existence of cells. The regulatory circuits that make decisions on when a cell should divide are very complex and particularly subtly balanced in eukaryotes, in which the harmony of many different cells in an organism is essential for life. Several hundred proteins are involved in these processes, and a great deal of studies attests that most of them have functionally relevant intrinsic structural disorder. Structural disorder imparts many functional advantages on these proteins, and we discuss it in detail that it is involved in all key steps from signaling through the cell membrane to regulating transcription of proteins that execute timely responses to an ever-changing environment.
Collapse
Affiliation(s)
- Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | | | | |
Collapse
|
39
|
Abstract
Recent experiments established that a culture of
Saccharomyces cerevisiae (baker’s yeast) survives sudden high temperatures by specifically duplicating the entire chromosome III and two chromosomal fragments (from IV and XII). Heat shock proteins (HSPs) are not significantly over-abundant in the duplication. In contrast, we suggest a simple algorithm to “
postdict” the experimental results: Find a small enough chromosome with minimal protein disorder and duplicate this region. This algorithm largely explains all observed duplications. In particular, all regions duplicated in the experiment reduced the overall content of protein disorder. The differential analysis of the functional makeup of the duplication remained inconclusive. Gene Ontology (GO) enrichment suggested over-representation in processes related to reproduction and nutrient uptake. Analyzing the protein-protein interaction network (PPI) revealed that few network-central proteins were duplicated. The predictive hypothesis hinges upon the concept of reducing proteins with long regions of disorder in order to become less sensitive to heat shock attack.
Collapse
Affiliation(s)
- Esmeralda Vicedo
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Experimental Physics, Division of Biophysics, University of Warsaw, Warsaw, Poland
| | - Zofia Gasik
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Graduate School of Information Science in Health, TUM, Munich, Germany
| | - Yu-An Dong
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Systems Biology, Shanghai University, Shanghai, China
| | - Tatyana Goldberg
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Advanced Study, TUM, Munich, Germany ; Institute for Food and Plant Sciences WZW, TUM, Freising, Germany
| |
Collapse
|
40
|
Schmidt HB, Görlich D. Transport Selectivity of Nuclear Pores, Phase Separation, and Membraneless Organelles. Trends Biochem Sci 2016; 41:46-61. [PMID: 26705895 DOI: 10.1016/j.tibs.2015.11.001] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022]
Abstract
Nuclear pore complexes (NPCs) provide a selective passageway for receptor-mediated active transport between nucleus and cytoplasm, while maintaining the distinct molecular compositions of both compartments at large. In this review we discuss how NPCs gain a remarkable sorting selectivity from non-globular FG domains and their phase separation into dense polymer meshworks. The resulting sieve-like FG hydrogels are effective barriers to normal macromolecules but are at the same time highly permeable to shuttling nuclear transport receptors, which bind to FG motifs as well as to their designated cargoes. Phase separation driven by disordered protein domains was recently also recognized as being pivotal to the formation of membraneless organelles, making it an important emerging principle in cell biology.
Collapse
|
41
|
Widjaja M, Berry IJ, Pont EJ, Padula MP, Djordjevic SP. P40 and P90 from Mpn142 are Targets of Multiple Processing Events on the Surface of Mycoplasma pneumoniae. Proteomes 2015; 3:512-37. [PMID: 28248283 DOI: 10.3390/proteomes3040512] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 12/02/2015] [Accepted: 12/07/2015] [Indexed: 12/18/2022] Open
Abstract
Mycoplasma pneumoniae is a significant cause of community acquired pneumonia globally. Despite having a genome less than 1 Mb in size, M. pneumoniae presents a structurally sophisticated attachment organelle that (i) provides cell polarity, (ii) directs adherence to receptors presented on respiratory epithelium, and (iii) plays a major role in cell motility. The major adhesins, P1 (Mpn141) and P30 (Mpn453), are localised to the tip of the attachment organelle by the surface accessible cleavage fragments P90 and P40 derived from Mpn142. Two events play a defining role in the formation of P90 and P40; removal of a leader peptide at position 26 (23SLA↓NTY28) during secretion to the cell surface and cleavage at amino acid 455 (452GPL↓RAG457) generating P40 and P90. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) analysis of tryptic peptides generated by digesting size-fractionated cell lysates of M. pneumoniae identified 15 cleavage fragments of Mpn142 ranging in mass from 9–84 kDa. Further evidence for the existence of cleavage fragments of Mpn142 was generated by mapping tryptic peptides to proteins recovered from size fractionated eluents from affinity columns loaded with heparin, fibronectin, fetuin, actin, plasminogen and A549 surface proteins as bait. To define the sites of cleavage in Mpn142, neo-N-termini in cell lysates of M. pneumoniae were dimethyl-labelled and characterised by LC-MS/MS. Our data suggests that Mpn142 is cleaved to generate adhesins that are auxiliary to P1 and P30.
Collapse
|
42
|
Perdigão N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, Schafferhans A, O'Donoghue SI. Unexpected features of the dark proteome. Proc Natl Acad Sci U S A 2015; 112:15898-903. [PMID: 26578815 DOI: 10.1073/pnas.1508380112] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.
Collapse
|
43
|
Volpato V, Alshomrani B, Pollastri G. Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets. Int J Mol Sci 2015; 16:19868-85. [PMID: 26307973 PMCID: PMC4581330 DOI: 10.3390/ijms160819868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 12/02/2022] Open
Abstract
Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins. Although predictors of disorder have been shown to achieve relatively high rates of correct classification of these segments, improvements over the the years have been slow, and accurate methods are needed that are capable of accommodating the ever-increasing amount of structurally-determined protein sequences to try to boost predictive performances. In this paper, we propose a predictor for short disordered regions based on bidirectional recurrent neural networks and tested by rigorous five-fold cross-validation on a large, non-redundant dataset collected from MobiDB, a new comprehensive source of protein disorder annotations. The system exploits sequence and structural information in the forms of frequency profiles, predicted secondary structure and solvent accessibility and direct disorder annotations from homologous protein structures (templates) deposited in the Protein Data Bank. The contributions of sequence, structure and homology information result in large improvements in predictive accuracy. Additionally, the large scale of the training set leads to low false positive rates, making our systems a robust and efficient way to address high-throughput disorder prediction.
Collapse
Affiliation(s)
- Viola Volpato
- School of Computer Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Adaptive and Complex Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Badr Alshomrani
- School of Computer Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Adaptive and Complex Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Gianluca Pollastri
- School of Computer Science, University College Dublin, Belfield, Dublin 4, Ireland.
- Adaptive and Complex Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| |
Collapse
|
44
|
Kurotani A, Sakurai T. In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae. Int J Mol Sci 2015; 16:19812-35. [PMID: 26307970 PMCID: PMC4581327 DOI: 10.3390/ijms160819812] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/12/2015] [Accepted: 08/13/2015] [Indexed: 12/23/2022] Open
Abstract
Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.
Collapse
Affiliation(s)
- Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| |
Collapse
|
45
|
Lu HC, Chung SS, Fornili A, Fraternali F. Anatomy of protein disorder, flexibility and disease-related mutations. Front Mol Biosci 2015; 2:47. [PMID: 26322316 PMCID: PMC4532925 DOI: 10.3389/fmolb.2015.00047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/29/2015] [Indexed: 01/23/2023] Open
Abstract
Integration of protein structural information with human genetic variation and pathogenic mutations is essential to understand molecular mechanisms associated with the effects of polymorphisms on protein interactions and cellular processes. We investigate occurrences of non-synonymous SNPs in ordered and disordered protein regions by systematic mapping of common variants and disease-related SNPs onto these regions. We show that common variants accumulate in disordered regions; conversely pathogenic variants are significantly depleted in disordered regions. These different occurrences of pathogenic and common SNPs can be attributed to a negative selection on random mutations in structurally highly constrained regions. New approaches in the study of quantitative effects of pathogenic-related mutations should effectively account for all the possible contexts and relative functional constraints in which the sequence variation occurs.
Collapse
Affiliation(s)
- Hui-Chun Lu
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK
| | - Sun Sook Chung
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK ; Department of Haematological Medicine, King's College London London, UK
| | - Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK ; School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK
| |
Collapse
|
46
|
Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda MLM, de Visser JAGM, Fraser JS, Tawfik DS. Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder. J Mol Biol 2015; 427:2396-409. [PMID: 26004540 DOI: 10.1016/j.jmb.2015.05.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 12/28/2022]
Abstract
Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiveness of sign epistasis--a complete reversion of mutational effects, particularly in protein evolution--yet its molecular basis remains poorly understood. We describe the structural basis of sign epistasis between G238S and R164S, two adaptive mutations in TEM-1 β-lactamase--an enzyme that endows antibiotics resistance. Separated by 10 Å, these mutations initiate two separate trajectories toward increased hydrolysis rates and resistance toward second and third-generation cephalosporins antibiotics. Both mutations allow the enzyme's active site to adopt alternative conformations and accommodate the new antibiotics. By solving the corresponding set of crystal structures, we found that R164S causes local disorder whereas G238S induces discrete conformations. When combined, the mutations in 238 and 164 induce local disorder whereby nonproductive conformations that perturb the enzyme's catalytic preorganization dominate. Specifically, Asn170 that coordinates the deacylating water molecule is misaligned, in both the free form and the inhibitor-bound double mutant. This local disorder is not restored by stabilizing global suppressor mutations and thus leads to an evolutionary cul-de-sac. Conformational dynamism therefore underlines the reshaping potential of protein's structures and functions but also limits protein evolvability because of the fragility of the interactions networks that maintain protein structures.
Collapse
Affiliation(s)
- Eynat Dellus-Gur
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mikael Elias
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Emilia Caselli
- Department of Chemistry, University of Modena, Modena 41100, Italy
| | - Fabio Prati
- Department of Chemistry, University of Modena, Modena 41100, Italy
| | - Merijn L M Salverda
- Institute for Translational Vaccinology (Intravacc), Bilthoven 3720 AL, The Netherlands
| | - J Arjan G M de Visser
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen 6700 AH, The Netherlands
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
47
|
Abstract
Phosphorylation offers a dynamic way to regulate protein activity and subcellular localization, which is achieved through its reversibility and fast kinetics. Adding or removing a dianionic phosphate group somewhere on a protein often changes the protein’s structural properties, its stability and dynamics. Moreover, the majority of signaling pathways involve an extensive set of protein–protein interactions, and phosphorylation can be used to regulate and modulate protein–protein binding. Losses of phosphorylation sites, as a result of disease mutations, might disrupt protein binding and deregulate signal transduction. In this paper we focus on the effects of phosphorylation on protein stability, dynamics, and binding. We describe several physico-chemical mechanisms of protein regulation through phosphorylation and pay particular attention to phosphorylation in protein complexes and phosphorylation in the context of disorder–order and order–disorder transitions. Finally we assess the role of multiple phosphorylation sites in a protein molecule, their possible cooperativity and function.
Collapse
Affiliation(s)
- Hafumi Nishi
- Graduate School of Medical Life Science, Yokohama City University Yokohama Japan
| | - Alexey Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD USA
| |
Collapse
|
48
|
Yao Q, Gao J, Bollinger C, Thelen JJ, Xu D. Predicting and analyzing protein phosphorylation sites in plants using musite. Front Plant Sci 2012; 3:186. [PMID: 22934099 PMCID: PMC3423629 DOI: 10.3389/fpls.2012.00186] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 07/31/2012] [Indexed: 05/29/2023]
Abstract
Although protein phosphorylation sites can be reliably identified with high-resolution mass spectrometry, the experimental approach is time-consuming and resource-dependent. Furthermore, it is unlikely that an experimental approach could catalog an entire phosphoproteome. Computational prediction of phosphorylation sites provides an efficient and flexible way to reveal potential phosphorylation sites and provide hypotheses in experimental design. Musite is a tool that we previously developed to predict phosphorylation sites based solely on protein sequence. However, it was not comprehensively applied to plants. In this study, the phosphorylation data from Arabidopsis thaliana, B. napus, G. max, M. truncatula, O. sativa, and Z. mays were collected for cross-species testing and the overall plant-specific prediction as well. The results show that the model for A. thaliana can be extended to other organisms, and the overall plant model from Musite outperforms the current plant-specific prediction tools, Plantphos, and PhosphAt, in prediction accuracy. Furthermore, a comparative study of predicted phosphorylation sites across orthologs among different plants was conducted to reveal potential evolutionary features. A bipolar distribution of isolated, non-conserved phosphorylation sites, and highly conserved ones in terms of the amino acid type was observed. It also shows that predicted phosphorylation sites conserved within orthologs do not necessarily share more sequence similarity in the flanking regions than the background, but they often inherit protein disorder, a property that does not necessitate high sequence conservation. Our analysis also suggests that the phosphorylation frequencies among serine, threonine, and tyrosine correlate with their relative proportion in disordered regions. Musite can be used as a web server (http://musite.net) or downloaded as an open-source standalone tool (http://musite.sourceforge.net/).
Collapse
Affiliation(s)
- Qiuming Yao
- Department of Computer Science, University of MissouriColumbia, MO, USA
- Bond Life Science Center, University of MissouriColumbia, MO, USA
| | - Jianjiong Gao
- Computational Biology Center, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
| | - Curtis Bollinger
- Department of Computer Science, University of MissouriColumbia, MO, USA
- Bond Life Science Center, University of MissouriColumbia, MO, USA
| | - Jay J. Thelen
- Bond Life Science Center, University of MissouriColumbia, MO, USA
- Department of Biochemistry, University of MissouriColumbia, MO, USA
| | - Dong Xu
- Department of Computer Science, University of MissouriColumbia, MO, USA
- Bond Life Science Center, University of MissouriColumbia, MO, USA
| |
Collapse
|
49
|
Abstract
Carbon distribution is responsible for stability and structure of proteins. Arrangement of carbon along the protein sequence is
depends on how the amino acids are organized and is guided by mRNAs. An atomic level revision is important for understanding
these codes. This will ultimately help in identification of disorders and suggest mutations. For this purpose a carbon distribution
analysis program has been developed. This program captures the hydrophobic / hydrophilic / disordered regions in a protein. The
program gives accurate results. The calculations are precise and sensitive to single amino acid resolution. This program is to help in
mutational studies leading to protein stabilisation.
Collapse
Affiliation(s)
- Ekambaram Rajasekaran
- Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore 641114
| |
Collapse
|
50
|
Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions. J Proteome Res 2012; 11:2968-81. [PMID: 22390342 PMCID: PMC3402239 DOI: 10.1021/pr300041t] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein interactions are critical determinants of insect transmission for viruses in the family Luteoviridae. Two luteovirid structural proteins, the capsid protein (CP) and the readthrough protein (RTP), contain multiple functional domains that regulate virus transmission. There is no structural information available for these economically important viruses. We used Protein Interaction Reporter (PIR) technology, a strategy that uses chemical cross-linking and high resolution mass spectrometry, to discover topological features of the Potato leafroll virus (PLRV) CP and RTP that are required for the diverse biological functions of PLRV virions. Four cross-linked sites were repeatedly detected, one linking CP monomers, two within the RTP, and one linking the RTP and CP. Virus mutants with triple amino acid deletions immediately adjacent to or encompassing the cross-linked sites were defective in virion stability, RTP incorporation into the capsid, and aphid transmission. Plants infected with a new, infectious PLRV mutant lacking 26 amino acids encompassing a cross-linked site in the RTP exhibited a delay in the appearance of systemic infection symptoms. PIR technology provided the first structural insights into luteoviruses which are crucially lacking and are involved in vector-virus and plant-virus interactions. These are the first cross-linking measurements on any infectious, insect-transmitted virus.
Collapse
Affiliation(s)
- Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Michelle Cilia
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
| | - Chad R. Weisbrod
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Ho-Jong Ju
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
- Department of Agricultural Biology and Plant Medicinal Research Center, College of Agricultural & Life Sciences, Chonbuk National University, 664-14 Deokjin-Dong 1Ga Deokjin-Gu Jeonju Jeonbuk 561-756, South Korea
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Stewart M. Gray
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| |
Collapse
|