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Harvey SR, Gadkari VV, Ruotolo BT, Russell DH, Wysocki VH, Zhou M. Expanding Native Mass Spectrometry to the Masses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:646-652. [PMID: 38303101 DOI: 10.1021/jasms.3c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
At the 33rd ASMS Sanibel Meeting, on Membrane Proteins and Their Complexes, a morning roundtable discussion was held discussing the current challenges facing the field of native mass spectrometry and approaches to expanding the field to nonexperts. This Commentary summarizes the discussion and current initiatives to address these challenges.
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Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77844, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Mowei Zhou
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310058, China
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2
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Merges GE, Arévalo L, Kovacevic A, Lohanadan K, de Rooij DG, Simon C, Jokwitz M, Witke W, Schorle H. Actl7b deficiency leads to mislocalization of LC8 type dynein light chains and disruption of murine spermatogenesis. Development 2023; 150:dev201593. [PMID: 37800308 PMCID: PMC10652042 DOI: 10.1242/dev.201593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
Actin-related proteins (Arps) are classified according to their similarity to actin and are involved in diverse cellular processes. ACTL7B is a testis-specific Arp, and is highly conserved in rodents and primates. ACTL7B is specifically expressed in round and elongating spermatids during spermiogenesis. Here, we have generated an Actl7b-null allele in mice to unravel the role of ACTL7B in sperm formation. Male mice homozygous for the Actl7b-null allele (Actl7b-/-) were infertile, whereas heterozygous males (Actl7b+/-) were fertile. Severe spermatid defects, such as detached acrosomes, disrupted membranes and flagella malformations start to appear after spermiogenesis step 9 in Actl7b-/- mice, finally resulting in spermatogenic arrest. Abnormal spermatids were degraded and levels of autophagy markers were increased. Co-immunoprecipitation with mass spectrometry experiments identified an interaction between ACTL7B and the LC8 dynein light chains DYNLL1 and DYNLL2, which are first detected in step 9 spermatids and mislocalized when ACTL7B is absent. Our data unequivocally establish that mutations in ACTL7B are directly related to male infertility, pressing for additional research in humans.
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Affiliation(s)
- Gina E. Merges
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany
| | - Lena Arévalo
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany
| | - Andjela Kovacevic
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany
| | - Keerthika Lohanadan
- Department of Molecular Cell Biology, Institute for Cell Biology, University of Bonn, 53121 Bonn, Germany
| | - Dirk G. de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Carla Simon
- Cell Migration Unit, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
| | - Melanie Jokwitz
- Cell Migration Unit, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
| | - Walter Witke
- Cell Migration Unit, Institute of Genetics, University of Bonn, 53115 Bonn, Germany
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany
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3
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Rolland AD, Takata T, Donor MT, Lampi KJ, Prell JS. Eye lens β-crystallins are predicted by native ion mobility-mass spectrometry and computations to form compact higher-ordered heterooligomers. Structure 2023; 31:1052-1064.e3. [PMID: 37453416 PMCID: PMC10528727 DOI: 10.1016/j.str.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
Eye lens α- and β-/γ-crystallin proteins are not replaced after fiber cell denucleation and maintain lens transparency and refractive properties. The exceptionally high (∼400-500 mg/mL) concentration of crystallins in mature lens tissue and multiple other factors impede precise characterization of β-crystallin interactions, oligomer composition, size, and topology. Native ion mobility-mass spectrometry is used here to probe β-crystallin association and provide insight into homo- and heterooligomerization kinetics for these proteins. These experiments include separation and characterization of higher-order β-crystallin oligomers and illustrate the unique advantages of native IM-MS. Recombinantly expressed βB1, βB2, and βA3 isoforms are found to have different homodimerization propensities, and only βA3 forms larger homooligomers. Heterodimerization of βB2 with βA3 occurs ∼3 times as fast as that of βB1 with βA3, and βB1 and βB2 heterodimerize less readily. Ion mobility experiments, molecular dynamics simulations, and PISA analysis together reveal that observed oligomers are consistent with predominantly compact, ring-like topologies.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA
| | - Takumi Takata
- Kyoto University, Research Reactor Institute 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Micah T Donor
- Department of Biological & Molecular Sciences, George Fox University, 414 N Meridian St, Newberg, OR 97132, USA
| | - Kirsten J Lampi
- Integrative Biosciences, School of Dentistry, 3181 SW Sam Jackson Park Road, Oregon Health & Science University, Portland, OR 97239-3098, USA.
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA; Materials Science Institute, 1252 University of Oregon, Eugene, OR 97403-1252, USA.
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4
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Estelle AB, George A, Barbar EJ, Zuckerman DM. Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS Comput Biol 2023; 19:e1011059. [PMID: 37083599 PMCID: PMC10155966 DOI: 10.1371/journal.pcbi.1011059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/03/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Multistep protein-protein interactions underlie most biological processes, but their characterization through methods such as isothermal titration calorimetry (ITC) is largely confined to simple models that provide little information on the intermediate, individual steps. In this study, we primarily examine the essential hub protein LC8, a small dimer that binds disordered regions of 100+ client proteins in two symmetrical grooves at the dimer interface. Mechanistic details of LC8 binding have remained elusive, hampered in part by ITC data analyses employing simple models that treat bivalent binding as a single event with a single binding affinity. We build on existing Bayesian ITC approaches to quantify thermodynamic parameters for multi-site binding interactions impacted by significant uncertainty in protein concentration. Using a two-site binding model, we identify positive cooperativity with high confidence for LC8 binding to multiple client peptides. In contrast, application of an identical model to the two-site binding between the coiled-coil NudE dimer and the intermediate chain of dynein reveals little evidence of cooperativity. We propose that cooperativity in the LC8 system drives the formation of saturated induced-dimer structures, the functional units of most LC8 complexes. In addition to these system-specific findings, our work advances general ITC analysis in two ways. First, we describe a previously unrecognized mathematical ambiguity in concentrations in standard binding models and clarify how it impacts the precision with which binding parameters are determinable in cases of high uncertainty in analyte concentrations. Second, building on observations in the LC8 system, we develop a system-agnostic heat map of practical parameter identifiability calculated from synthetic data which demonstrates that the ability to determine microscopic binding parameters is strongly dependent on both the parameters themselves and experimental conditions. The work serves as a foundation for determination of multi-step binding interactions, and we outline best practices for Bayesian analysis of ITC experiments.
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Affiliation(s)
- Aidan B Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - August George
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
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5
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Walker DR, Jara KA, Rolland AD, Brooks C, Hare W, Swansiger AK, Reardon PN, Prell JS, Barbar EJ. Linker Length Drives Heterogeneity of Multivalent Complexes of Hub Protein LC8 and Transcription Factor ASCIZ. Biomolecules 2023; 13:404. [PMID: 36979339 PMCID: PMC10046861 DOI: 10.3390/biom13030404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
LC8, a ubiquitous and highly conserved hub protein, binds over 100 proteins involved in numerous cellular functions, including cell death, signaling, tumor suppression, and viral infection. LC8 binds intrinsically disordered proteins (IDPs), and although several of these contain multiple LC8 binding motifs, the effects of multivalency on complex formation are unclear. Drosophila ASCIZ has seven motifs that vary in sequence and inter-motif linker lengths, especially within subdomain QT2-4 containing the second, third, and fourth LC8 motifs. Using isothermal-titration calorimetry, analytical-ultracentrifugation, and native mass-spectrometry of QT2-4 variants, with methodically deactivated motifs, we show that inter-motif spacing and specific motif sequences combine to control binding affinity and compositional heterogeneity of multivalent duplexes. A short linker separating strong and weak motifs results in stable duplexes but forms off-register structures at high LC8 concentrations. Contrastingly, long linkers engender lower cooperativity and heterogeneous complexation at low LC8 concentrations. Accordingly, two-mers, rather than the expected three-mers, dominate negative-stain electron-microscopy images of QT2-4. Comparing variants containing weak-strong and strong-strong motif combinations demonstrates sequence also regulates IDP/LC8 assembly. The observed trends persist for trivalent ASCIZ subdomains: QT2-4, with long and short linkers, forms heterogeneous complexes, whereas QT4-6, with similar mid-length linkers, forms homogeneous complexes. Implications of linker length variations for function are discussed.
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Affiliation(s)
- Douglas R. Walker
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Kayla A. Jara
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Amber D. Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Coban Brooks
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Wendy Hare
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew K. Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Patrick N. Reardon
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- NMR Facility, Oregon State University, Corvallis, OR 97331, USA
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Elisar J. Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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Howe J, Weeks A, Reardon P, Barbar E. Multivalent binding of the hub protein LC8 at a newly discovered site in 53BP1. Biophys J 2022; 121:4433-4442. [PMID: 36335430 PMCID: PMC9748353 DOI: 10.1016/j.bpj.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/28/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Tumor suppressor p53 binding protein 1 (53BP1) is a scaffolding protein involved in poly-ADP ribose polymerase inhibitor hypersensitivity in BRCA1-negative cancers. 53BP1 plays a critical role in the DNA damage response and relies on its oligomerization to create foci that promote repair of DNA double-strand breaks. Previous work shows that mutation of either the oligomerization domain or the dynein light chain 8 (LC8)-binding sites of 53BP1 results in reduced accumulation of 53BP1 at double-strand breaks. Mutation of both abolishes focus formation almost completely. Here, we show that, contrary to current literature, 53BP1 contains three LC8-binding sites, all of which are conserved in mammals. Isothermal titration calorimetry measuring binding affinity of 53BP1 variants with LC8 shows that the third LC8-binding site has a high affinity and can bind LC8 in the absence of other sites. NMR titrations confirm that the third site binds LC8 even in variants that lack the other LC8-binding sites. The third site is the closest to the oligomerization domain of 53BP1, and its discovery would challenge our current understanding of the role of LC8 in 53BP1 function.
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Affiliation(s)
- Jesse Howe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Austin Weeks
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Patrick Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon.
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Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM. J Mol Biol 2022; 434:167520. [PMID: 35245498 PMCID: PMC9050902 DOI: 10.1016/j.jmb.2022.167520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 01/17/2022] [Accepted: 02/27/2022] [Indexed: 12/29/2022]
Abstract
Multivalent intrinsically disordered protein (IDP) complexes are prevalent in biology and act in regulation of diverse processes, including transcription, signaling events, and the assembly and disassembly of complex macromolecular architectures. These systems pose significant challenges to structural investigation, due to continuum dynamics imparted by the IDP and compositional heterogeneity resulting from characteristic low-affinity interactions. Here, we developed a modular pipeline for automated single-particle electron microscopy (EM) distribution analysis of common but relatively understudied semi-ordered systems: 'beads-on-a-string' assemblies, composed of IDPs bound at multivalent sites to the ubiquitous ∼20 kDa cross-linking hub protein LC8. This approach quantifies conformational geometries and compositional heterogeneity on a single-particle basis, and statistically corrects spurious observations arising from random proximity of bound and unbound LC8. The statistical correction is generically applicable to oligomer characterization and not specific to our pipeline. Following validation, the approach was applied to the nuclear pore IDP Nup159 and the transcription factor ASCIZ. This analysis unveiled significant compositional and conformational diversity in both systems that could not be obtained from ensemble single particle EM class-averaging strategies, and new insights for exploring how these architectural properties might contribute to their physiological roles in supramolecular assembly and transcriptional regulation. We expect that this approach may be adopted to many other intrinsically disordered systems that have evaded traditional methods of structural characterization.
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8
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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] [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.
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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
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Donor MT, Wilson JW, Shepherd SO, Prell JS. Lipid Head Group Adduction to Soluble Proteins Follows Gas-Phase Basicity Predictions: Dissociation Barriers and Charge Abstraction. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116670. [PMID: 34421332 PMCID: PMC8372978 DOI: 10.1016/j.ijms.2021.116670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry analysis of membrane proteins has yielded many useful insights in recent years with respect to membrane protein-lipid interactions, including identifying specific interactions and even measuring binding affinities based on observed abundances of lipid-bound ions after collision-induced dissociation (CID). However, the behavior of non-covalent complexes subjected to extensive CID can in principle be affected by numerous factors related to gas-phase chemistry, including gas-phase basicity (GB) and acidity, shared-proton bonds, and other factors. A recent report from our group showed that common lipids span a wide range of GB values. Notably, phosphatidylcholine (PC) and sphingomyelin lipids are more basic than arginine, suggesting they may strip charge upon dissociation in positive ion mode, while phosphoserine lipids are slightly less basic than arginine and may form especially strong shared-proton bonds. Here, we use CID to probe the strength of non-specific gas-phase interactions between lipid head groups and several soluble proteins, used to deliberately avoid possible physiological protein-lipid interactions. The strengths of the protein-head group interactions follow the trend predicted based solely on lipid and amino acid GBs: phosphoserine (PS) head group forms the strongest bonds with these proteins and out-competes the other head groups studied, while glycerophosphocholine (GPC) head groups form the weakest interactions and dissociate carrying away a positive charge. These results indicate that gas-phase thermochemistry can play an important role in determining which head groups remain bound to protein ions with native-like structures and charge states in positive ion mode upon extensive collisional activation.
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Affiliation(s)
- Micah T. Donor
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Jesse W. Wilson
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR 97403-1252
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10
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The role of dancing duplexes in biology and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021. [PMID: 34656330 DOI: 10.1016/bs.pmbts.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Across species, a common protein assembly arises: proteins containing structured domains separated by long intrinsically disordered regions, and dimerized through a self-association domain or through strong protein interactions. These systems are termed "IDP duplexes." These flexible dimers have roles in diverse pathologies including development of cancer, viral infections, and neurodegenerative disease. Here we discuss the role of disorder in IDP duplexes with similar domain architectures that bind hub protein, LC8. LC8-binding IDP duplexes are categorized into three groups: IDP duplexes that contain a self-association domain that is extended by LC8 binding, IDP duplexes that have no self-association domain and are dimerized through binding several copies of LC8, and multivalent LC8-binders that also have a self-association domain. Additionally, we discuss non-LC8-binding IDP duplexes with similar domain organizations, including the Nucleocapsid protein of SARS-CoV-2. We propose that IDP duplexes have structural features that are essential in many biological processes and that improved understanding of their structure function relationship will provide new therapeutic opportunities.
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11
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Aliyari E, Konermann L. Atomistic Insights into the Formation of Nonspecific Protein Complexes during Electrospray Ionization. Anal Chem 2021; 93:12748-12757. [PMID: 34494821 DOI: 10.1021/acs.analchem.1c02836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Native electrospray ionization (ESI)-mass spectrometry (MS) is widely used for the detection and characterization of multi-protein complexes. A well-known problem with this approach is the possible occurrence of nonspecific protein clustering in the ESI plume. This effect can distort the results of binding affinity measurements, and it can even generate gas-phase complexes from proteins that are strictly monomeric in bulk solution. By combining experiments and molecular dynamics (MD) simulations, the current work for the first time provides detailed insights into the ESI clustering of proteins. Using ubiquitin as a model system, we demonstrate how the entrapment of more than one protein molecule in an ESI droplet can generate nonspecific clusters (e.g., dimers or trimers) via solvent evaporation to dryness. These events are in line with earlier proposals, according to which protein clustering is associated with the charged residue model (CRM). MD simulations on cytochrome c (which carries a large intrinsic positive charge) confirmed the viability of this CRM avenue. In addition, the cytochrome c data uncovered an alternative mechanism where protein-protein contacts were formed early within ESI droplets, followed by cluster ejection from the droplet surface. This second pathway is consistent with the ion evaporation model (IEM). The observation of these IEM events for large protein clusters is unexpected because the IEM has been thought to be associated primarily with low-molecular-weight analytes. In all cases, our MD simulations produced protein clusters that were stabilized by intermolecular salt bridges. The MD-generated charge states agreed with experiments. Overall, this work reveals that ESI-induced protein clustering does not follow a tightly orchestrated pathway but can proceed along different avenues.
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Affiliation(s)
- Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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12
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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13
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Neiswender H, Goldman CH, Veeranan-Karmegam R, Gonsalvez GB. Dynein light chain-dependent dimerization of Egalitarian is essential for maintaining oocyte fate in Drosophila. Dev Biol 2021; 478:76-88. [PMID: 34181915 DOI: 10.1016/j.ydbio.2021.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/02/2021] [Accepted: 06/17/2021] [Indexed: 11/28/2022]
Abstract
Egalitarian (Egl) is an RNA adaptor for the Dynein motor and is thought to link numerous, perhaps hundreds, of mRNAs with Dynein. Dynein, in turn, is responsible for the transport and localization of these mRNAs. Studies have shown that efficient mRNA binding by Egl requires the protein to dimerize. We recently demonstrated that Dynein light chain (Dlc) is responsible for facilitating the dimerization of Egl. Mutations in Egl that fail to interact with Dlc do not dimerize, and as such, are defective for mRNA binding. Consequently, this mutant does not efficiently associate with BicaudalD (BicD), the factor responsible for linking the Egl/mRNA complex with Dynein. In this report, we tested whether artificially dimerizing this Dlc-binding mutant using a leucine zipper would restore mRNA binding and rescue mutant phenotypes in vivo. Interestingly, we found that although artificial dimerization of Egl restored BicD binding, it only partially restored mRNA binding. As a result, Egl-dependent phenotypes, such as oocyte specification and mRNA localization, were only partially rescued. We hypothesize that Dlc-mediated dimerization of Egl results in a three-dimensional conformation of the Egl dimer that is best suited for mRNA binding. Although the leucine zipper restores Egl dimerization, it likely does not enable Egl to assemble into the conformation required for maximal mRNA binding activity.
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Affiliation(s)
- Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Rajalakshmi Veeranan-Karmegam
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA.
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Eastwood EL, Jara KA, Bornelöv S, Munafò M, Frantzis V, Kneuss E, Barbar EJ, Czech B, Hannon GJ. Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila. eLife 2021; 10:e65557. [PMID: 33538693 PMCID: PMC7861614 DOI: 10.7554/elife.65557] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
In animal gonads, the PIWI-interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. In Drosophila ovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.
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Affiliation(s)
- Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Vasileios Frantzis
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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Sever AIM, Yin V, Konermann L. Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:270-280. [PMID: 33124417 DOI: 10.1021/jasms.0c00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)2, (αβ)3, and (αβ)4] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.
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Affiliation(s)
- Alexander I M Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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