1
|
Miller SA, Jeanne Dit Fouque K, Hard ER, Balana AT, Kaplan D, Voinov VG, Ridgeway ME, Park MA, Anderson GA, Pratt MR, Fernandez-Lima F. Top/Middle-Down Characterization of α-Synuclein Glycoforms. Anal Chem 2023; 95:18039-18045. [PMID: 38047498 PMCID: PMC10836061 DOI: 10.1021/acs.analchem.3c02405] [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] [Indexed: 12/05/2023]
Abstract
α-Synuclein is an intrinsically disordered protein that plays a critical role in the pathogenesis of neurodegenerative disorders, such as Parkinson's disease. Proteomics studies of human brain samples have associated the modification of the O-linked N-acetyl-glucosamine (O-GlcNAc) to several synucleinopathies; in particular, the position of the O-GlcNAc can regulate protein aggregation and subsequent cell toxicity. There is a need for site specific O-GlcNAc α-synuclein screening tools to direct better therapeutic strategies. In the present work, for the first time, the potential of fast, high-resolution trapped ion mobility spectrometry (TIMS) preseparation in tandem with mass spectrometry assisted by an electromagnetostatic (EMS) cell, capable of electron capture dissociation (ECD), and ultraviolet photodissociation (213 nm UVPD) is illustrated for the characterization of α-synuclein positional glycoforms: T72, T75, T81, and S87 modified with a single O-GlcNAc. Top-down 213 nm UVPD and ECD MS/MS experiments of the intact proteoforms showed specific product ions for each α-synuclein glycoforms associated with the O-GlcNAc position with a sequence coverage of ∼68 and ∼82%, respectively. TIMS-MS profiles of α-synuclein and the four glycoforms exhibited large structural heterogeneity and signature patterns across the 8+-15+ charge state distribution; however, while the α-synuclein positional glycoforms showed signature mobility profiles, they were only partially separated in the mobility domain. Moreover, a middle-down approach based on the Val40-Phe94 (55 residues) chymotrypsin proteolytic product using tandem TIMS-q-ECD-TOF MS/MS permitted the separation of the parent positional isomeric glycoforms. The ECD fragmentation of the ion mobility and m/z separated isomeric Val40-Phe94 proteolytic peptides with single O-GlcNAc in the T72, T75, T81, and S87 positions provided the O-GlcNAc confirmation and positional assignment with a sequence coverage of ∼80%. This method enables the high-throughput screening of positional glycoforms and further enhances the structural mass spectrometry toolbox with fast, high-resolution mobility separations and 213 nm UVPD and ECD fragmentation capabilities.
Collapse
Affiliation(s)
- Samuel A Miller
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Eldon R Hard
- Department of Chemistry and Biological Sciences, University of Southern California, Los Angeles, California 90007, United States
| | - Aaron T Balana
- Department of Chemistry and Biological Sciences, University of Southern California, Los Angeles, California 90007, United States
| | - Desmond Kaplan
- KapScience LLC, Tewksbury, Massachusetts 01876, United States
| | | | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | | | - Matthew R Pratt
- Department of Chemistry and Biological Sciences, University of Southern California, Los Angeles, California 90007, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
2
|
Saurabh S, Nadendla K, Purohit SS, Sivakumar PM, Cetinel S. Fuzzy Drug Targets: Disordered Proteins in the Drug-Discovery Realm. ACS OMEGA 2023; 8:9729-9747. [PMID: 36969402 PMCID: PMC10034788 DOI: 10.1021/acsomega.2c07708] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) form a large part of the eukaryotic proteome. Contrary to the structure-function paradigm, the disordered proteins perform a myriad of functions in vivo. Consequently, they are involved in various disease pathways and are plausible drug targets. Unlike folded proteins, that have a defined structure and well carved out drug-binding pockets that can guide lead molecule selection, the disordered proteins require alternative drug-development methodologies that are based on an acceptable picture of their conformational ensemble. In this review, we discuss various experimental and computational techniques that contribute toward understanding IDP "structure" and describe representative pursuances toward IDP-targeting drug development. We also discuss ideas on developing rational drug design protocols targeting IDPs.
Collapse
Affiliation(s)
- Suman Saurabh
- Molecular
Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Karthik Nadendla
- Center
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Lensfield
Road, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Shubh Sanket Purohit
- Department
of Clinical Haematology, Sahyadri Superspeciality
Hospital, Pune, Maharashtra 411038, India
| | - Ponnurengam Malliappan Sivakumar
- Institute
of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
- School
of Medicine and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
| | - Sibel Cetinel
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
- Faculty of
Engineering and Natural Sciences, Molecular Biology, Genetics and
Bioengineering Program, Sabanci University, Istanbul 34956, Turkey
| |
Collapse
|
3
|
Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
Collapse
Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
| |
Collapse
|
4
|
Ujma J, Jhingree J, Norgate E, Upton R, Wang X, Benoit F, Bellina B, Barran P. Protein Unfolding in Freeze Frames: Intermediate States are Revealed by Variable-Temperature Ion Mobility-Mass Spectrometry. Anal Chem 2022; 94:12248-12255. [PMID: 36001095 PMCID: PMC9453741 DOI: 10.1021/acs.analchem.2c03066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass-selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined conformational transitions that occur to the monomeric proteins: ubiquitin, lysozyme, and α-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature-dependent framework model and comparison to known conformers. Data from ubiquitin show unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme─a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in-source enables subsequent "freezing" or thermal annealing of unfolding intermediates, whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework that describes the relative occupancy of the available conformational space.
Collapse
Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jacquelyn Jhingree
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Emma Norgate
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rosie Upton
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Xudong Wang
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian Benoit
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
5
|
Jeanne Dit Fouque K, Sipe SN, Garabedian A, Mejia G, Su L, Hossen ML, Chapagain PP, Leng F, Brodbelt JS, Fernandez-Lima F. Exploring the Conformational and Binding Dynamics of HMGA2·DNA Complexes Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1103-1112. [PMID: 35687119 PMCID: PMC9280850 DOI: 10.1021/jasms.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is an intrinsically disordered DNA-binding protein expressed during embryogenesis. In the present work, the conformational and binding dynamics of HMGA2 and HMGA2 in complex with a 22-nt (DNA22) and a 50-nt (DNA50) AT-rich DNA hairpin were investigated using trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) under native starting solvent conditions (e.g., 100 mM aqueous NH4Ac) and collision-induced unfolding/dissociation (CIU/CID) as well as solution fluorescence anisotropy to assess the role of the DNA ligand when binding to the HMGA2 protein. CIU-TIMS-CID-MS/MS experiments showed a significant reduction of the conformational space and charge-state distribution accompanied by an energy stability increase of the native HMGA2 upon DNA binding. Fluorescence anisotropy experiments and CIU-TIMS-CID-MS/MS demonstrated for the first time that HMGA2 binds with high affinity to the minor groove of AT-rich DNA oligomers and with lower affinity to the major groove of AT-rich DNA oligomers (minor groove occupied by a minor groove binder Hoechst 33258). The HMGA2·DNA22 complex (18.2 kDa) 1:1 and 1:2 stoichiometry suggests that two of the AT-hook sites are accessible for DNA binding, while the other AT-hook site is probably coordinated by the C-terminal motif peptide (CTMP). The HMGA2 transition from disordered to ordered upon DNA binding is driven by the interaction of the three basic AT-hook residues with the minor and/or major grooves of AT-rich DNA oligomers.
Collapse
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - German Mejia
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Linjia Su
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Md Lokman Hossen
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
6
|
Tajiri M, Aoki H, Shintani A, Sue K, Akashi S, Furukawa Y. Metal distribution in Cu/Zn-superoxide dismutase revealed by native mass spectrometry. Free Radic Biol Med 2022; 183:60-68. [PMID: 35314356 DOI: 10.1016/j.freeradbiomed.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/09/2022] [Accepted: 03/15/2022] [Indexed: 01/09/2023]
Abstract
Cu/Zn-superoxide dismutase (SOD1) is a homodimer with two identical subunits, each of which binds a copper and zinc ion in the native state. In contrast to such a text book case, SOD1 proteins purified in vitro or even in vivo have been often reported to bind a non-stoichiometric amount of the metal ions. Nonetheless, it is difficult to probe how those metal ions are distributed in the two identical subunits. By utilizing native mass spectrometry, we showed here that addition of a sub-stoichiometric copper/zinc ion to SOD1 led to the formation of a homodimer with a stochastic combination of the subunits binding 0, 1, and even 2 metal ions. We also found that the homodimer was able to bind four copper or four zinc ions, implying the binding of a copper and zinc ion at the canonical zinc and copper site, respectively. Such ambiguity in the metal quota and selectivity could be avoided when an intra-subunit disulfide bond in SOD1 was reduced before addition of the metal ions. Apo-SOD1 in the disulfide-reduced state was monomeric and was found to bind only one zinc ion per monomer. By binding a zinc ion, the disulfide-reduced SOD1 became conformationally compact and acquired the ability to dimerize. Based upon the results in vitro, we describe the pathway in vivo enabling SOD1 to bind copper and zinc ions with high accuracy in their quota and selectivity. A failure of correct metallation in SOD1 will also be discussed in relation to amyotrophic lateral sclerosis.
Collapse
Affiliation(s)
- Michiko Tajiri
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Hiroto Aoki
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan
| | - Atsuko Shintani
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan
| | - Kaori Sue
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan.
| | - Yoshiaki Furukawa
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan.
| |
Collapse
|
7
|
Shah JS, Buckmeier BG, Griffith W, Olafson PU, Perez de Leon AA, Renthal R. Odorant-binding protein from the stable fly (Stomoxys calcitrans) has a high-histidine N-terminal extension that binds transition metals. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 141:103707. [PMID: 34979251 DOI: 10.1016/j.ibmb.2021.103707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
The role of odorant- and pheromone-binding proteins (OBPs) in olfactory function is not fully understood. We found an OBP sequence from the stable fly, Stomoxys calcitrans, ScalOBP60, that has a 25 amino acid N-terminal extension with a high content of histidine and acidic amino acids, suggesting a possible metal binding activity. A search of public databases revealed a large number of other fly OBPs with histidine-rich N-terminal extensions, as well as beetle, wasp and ant OBPs with histidine-rich C-terminal extensions. We recombinantly expressed ScalOBP60, as well as a truncated sequence which lacks the histidine-rich N-terminal region, tScalOBP60. Using fluorescence quenching and electrospray quadrupole time-of-flight mass spectrometry (ESI-QTOF), we detected two different types of metal-binding sites. Divalent copper, nickel and zinc bind to the N-terminal histidine-rich region, and divalent copper binds to an internal sequence position. Comparison of the ESI-QTOF spectra of ScalOBP60 and tScalOBP60 showed that the histidine-rich sequence is structurally disordered, but it becomes more ordered in the presence of divalent metal. When copper is bound to the internal site, binding of a hydrophobic ligand to ScalOBP60 is inhibited. The internal and N-terminal metal sites interact allosterically, possibly through a conformational equilibrium, suggesting a mechanism for metal regulation of ligand binding to ScalOBP60. Based on our studies of ScalOBP60, we propose several possible olfactory and non-olfactory functions for this OBP.
Collapse
Affiliation(s)
- Jaee Shailesh Shah
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | | | - Wendell Griffith
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Pia Untalan Olafson
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Lab, Kerrville, TX, 78028, USA
| | | | - Robert Renthal
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA; Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
| |
Collapse
|
8
|
Azegami N, Taguchi R, Suzuki N, Sakata Y, Konuma T, Akashi S. Native Mass Spectrometry of BRD4 Bromodomains Linked to a Long Disordered Region. Mass Spectrom (Tokyo) 2022; 11:A0110. [PMID: 36713808 PMCID: PMC9853951 DOI: 10.5702/massspectrometry.a0110] [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: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
The contribution of disordered regions to protein function and structure is a relatively new field of study and of particular significance as their function has been implicated in some human diseases. Our objective was to analyze various deletion mutants of the bromodomain-containing protein 4 (BRD4) using native mass spectrometry to characterize the gas-phase behavior of the disordered region connected to the folded domain. A protein with a single bromodomain but no long disordered linker displayed a narrow charge distribution at low charge states, suggesting a compact structure. In contrast, proteins containing one or two bromodomains connected to a long disordered region exhibited multimodal charge distributions, suggesting the presence of compact and elongated conformers. In the presence of a pan-BET-bromodomain inhibitor, JQ1, the protein-JQ1 complex ions had relatively small numbers of positive charges, corresponding to compact conformers. In contrast, the ions with extremely high charge states did not form a complex with JQ1. This suggests that all of the JQ1-bound BRD4 proteins in the gas phase are in a compact conformation, including the linker region, while the unbound forms are considerably elongated. Although these are gas-phase phenomena, it is possible that the long disordered linker connected to the bromodomain causes the denaturation of the folded domain, which, in turn, affects its JQ1 recognition.
Collapse
Affiliation(s)
- Nanako Azegami
- Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
| | - Rina Taguchi
- Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
| | - Noa Suzuki
- School of Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
| | - Yusuke Sakata
- Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan,School of Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan,Correspondence to: Tsuyoshi Konuma, Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan, e-mail:
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan,School of Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan,Correspondence to: Satoko Akashi, Graduate School of Medical Life Science, Yokohama City University, 1–7–29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan, e-mail:
| |
Collapse
|
9
|
Das M, Chen N, LiWang A, Wang LP. Identification and characterization of metamorphic proteins: Current and future perspectives. Biopolymers 2021; 112:e23473. [PMID: 34528703 DOI: 10.1002/bip.23473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/06/2022]
Abstract
Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.
Collapse
Affiliation(s)
- Madhurima Das
- School of Natural Sciences, University of California, Merced, California, USA
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, California, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, California, USA.,Department of Chemistry and Biochemistry, University of California, Merced, California, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, California, USA.,Health Sciences Research Institute, University of California, Merced, California, USA.,Center for Circadian Biology, University of California, San Diego, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California, USA
| |
Collapse
|
10
|
Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
Collapse
Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
11
|
Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
Collapse
Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
| |
Collapse
|
12
|
Lermyte F, Theisen A, O'Connor PB. Solution Condition-Dependent Formation of Gas-Phase Protomers of Alpha-Synuclein in Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:364-372. [PMID: 33237779 DOI: 10.1021/jasms.0c00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One of the main characteristics of biomolecular ions in mass spectrometry is their net charge, and a range of approaches exist to either increase or decrease this quantity in the gas phase. In the context of small molecules, it is well known that, in addition to the charge state, the charge site also has a profound effect on an ion's gas-phase behavior; however, this effect has been far less explored for peptides and intact proteins. Methods exist to determine charge sites of protein ions, and others have observed that the interplay of electrostatic repulsion and inherent basicity leads to different sites gaining or losing a charge depending on the total net charge. Here, we report two distinct protonation site isomers ("protomers") of α-synuclein occurring at the same charge state. The protomers showed important differences in their gas-phase fragmentation behavior and were furthermore distinguishable by ion mobility spectrometry. One protomer was produced under standard electrospray conditions, while the other was observed after addition of 10% dimethyl sulfoxide to the protein solution. Charge sites for both protomers were determined using ultraviolet photodissociation.
Collapse
Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
13
|
Prabhu GRD, Ponnusamy VK, Witek HA, Urban PL. Sample Flow Rate Scan in Electrospray Ionization Mass Spectrometry Reveals Alterations in Protein Charge State Distribution. Anal Chem 2020; 92:13042-13049. [PMID: 32893617 DOI: 10.1021/acs.analchem.0c01945] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sample flow rate is one of the parameters that influence the sensitivity of electrospray ionization (ESI) mass spectrometry. By varying the sample flow rate, initial droplets of different sizes can be generated. Protein molecules in small droplets may form gas-phase ions earlier than the ones in large droplets. Here, we have systematically studied the influence of sample flow rate on the ESI charge state distributions (CSDs) of model proteins. A dedicated programmable sample flow rate scanner was used to infuse protein samples at different flow rates into a mass spectrometer. The synergistic influence of sample flow rate and various electrolytes (ammonium acetate, ammonium bicarbonate, ammonium formate, and piperidine) was studied. Significant alterations to the CSDs with increasing flow rate were observed. For example, in the presence of ammonium acetate, at low flow rates, lower charge states of proteins showed high intensities, while at high flow rates, ions related to higher charge states of proteins dominated the spectra. On the other hand, in the presence of piperidine, a significant reduction in the ion currents of all charge states was observed during the flow rate scan. Our observations suggest that at low flow rates the protein molecules follow a charged residue model of ionization mechanism, and at high flow rates-due to structural changes in protein molecules in large ESI droplets-the charged residue and chain ejection models can possibly coexist. We propose the use of sample flow rate scan as a way to reveal the influence of flow rate on the CSDs of the studied proteins.
Collapse
Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan.,Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry & Research Center for Environmental Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan
| | - Henryk A Witek
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan.,Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| |
Collapse
|
14
|
Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins. Int J Mol Sci 2020; 21:ijms21176208. [PMID: 32867340 PMCID: PMC7503639 DOI: 10.3390/ijms21176208] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 12/20/2022] Open
Abstract
The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attempts at rationalizing the general principles underlying both conformational properties and transitions of IDPs/IDRs must consider the abundance of charged residues (Asp, Glu, Lys, and Arg) that typifies these proteins, rendering them assimilable to polyampholytes or polyelectrolytes. Their conformation strongly depends on both the charge density and distribution along the sequence (i.e., charge decoration) as highlighted by recent experimental and theoretical studies that have introduced novel descriptors. Published experimental data are revisited herein in the frame of this formalism, in a new and possibly unitary perspective. The physicochemical properties most directly affected by charge density and distribution are compaction and solubility, which can be described in a relatively simplified way by tools of polymer physics. Dissecting factors controlling such properties could contribute to better understanding complex biological phenomena, such as fibrillation and phase separation. Furthermore, this knowledge is expected to have enormous practical implications for the design, synthesis, and exploitation of bio-derived materials and the control of natural biological processes.
Collapse
|
15
|
The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation. Sci Rep 2020; 10:2068. [PMID: 32034199 PMCID: PMC7005769 DOI: 10.1038/s41598-020-58868-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions within proteins (IDRs) serve an increasingly expansive list of biological functions, including regulation of transcription and translation, protein phosphorylation, cellular signal transduction, as well as mechanical roles. The strong link between protein function and disorder motivates a deeper fundamental characterization of IDPs and IDRs for discovering new functions and relevant mechanisms. We review recent advances in experimental techniques that have improved identification of disordered regions in proteins. Yet, experimentally curated disorder information still does not currently scale to the level of experimentally determined structural information in folded protein databases, and disorder predictors rely on several different binary definitions of disorder. To link secondary structure prediction algorithms developed for folded proteins and protein disorder predictors, we conduct molecular dynamics simulations on representative proteins from the Protein Data Bank, comparing secondary structure and disorder predictions with simulation results. We find that structure predictor performance from neural networks can be leveraged for the identification of highly dynamic regions within molecules, linked to disorder. Low accuracy structure predictions suggest a lack of static structure for regions that disorder predictors fail to identify. While disorder databases continue to expand, secondary structure predictors and molecular simulations can improve disorder predictor performance, which aids discovery of novel functions of IDPs and IDRs. These observations provide a platform for the development of new, integrated structural databases and fusion of prediction tools toward protein disorder characterization in health and disease.
Collapse
|
16
|
Han JY, Choi TS, Heo CE, Son MK, Kim HI. Gas-phase conformations of intrinsically disordered proteins and their complexes with ligands: Kinetically trapped states during transfer from solution to the gas phase. MASS SPECTROMETRY REVIEWS 2019; 38:483-500. [PMID: 31021441 DOI: 10.1002/mas.21596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Flexible structures of intrinsically disordered proteins (IDPs) are crucial for versatile functions in living organisms, which involve interaction with diverse partners. Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has been widely applied for structural characterization of apo-state and ligand-associated IDPs via two-dimensional separation in the gas phase. Gas-phase IDP structures have been regarded as kinetically trapped states originated from conformational features in solution. However, an implication of the states remains elusive in the structural characterization of IDPs, because it is unclear what structural property of IDPs is preserved. Recent studies have indicated that the conformational features of IDPs in solution are not fully reproduced in the gas phase. Nevertheless, the molecular interactions captured in the gas phase amplify the structural differences between IDP conformers. Therefore, an IDP conformational change that is not observed in solution is observable in the gas-phase structures obtained by ESI-IM-MS. Herein, we have presented up-to-date researches on the key implications of kinetically trapped states in the gas phase with a brief summary of the structural dynamics of IDPs in ESI-IM-MS.
Collapse
Affiliation(s)
- Jong Yoon Han
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | - Chae Eun Heo
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Myung Kook Son
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| |
Collapse
|
17
|
Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
Collapse
Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
| |
Collapse
|
18
|
Beveridge R, Migas LG, Das RK, Pappu RV, Kriwacki RW, Barran PE. Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins. J Am Chem Soc 2019; 141:4908-4918. [PMID: 30823702 PMCID: PMC6488185 DOI: 10.1021/jacs.8b13483] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
global dimensions and amplitudes of conformational fluctuations
of intrinsically disordered proteins are governed, in part, by the
linear segregation versus clustering of oppositely charged residues
within the primary sequence. Ion mobility-mass spectrometry (IM-MS)
affords unique advantages for probing the conformational consequences
of the linear patterning of oppositely charged residues because it
measures and separates proteins electrosprayed from solution on the
basis of charge and shape. Here, we use IM-MS to measure the conformational
consequences of charge patterning on the C-terminal intrinsically
disordered region (p27 IDR) of the cell cycle inhibitory protein p27Kip1. We report the range of charge states and accompanying
collisional cross section distributions for wild-type p27 IDR and
two variants with identical amino acid compositions, κ14 and
κ56, distinguished by the extent of linear mixing versus segregation
of oppositely charged residues. Wild-type p27 IDR (κ31) and
κ14, where the oppositely charged residues are more evenly distributed,
exhibit a broad distribution of charge states. This is concordant
with high degrees of conformational heterogeneity in solution. By
contrast, κ56 with linear segregation of oppositely charged
residues leads to limited conformational heterogeneity and a narrow
distribution of charged states. Gas-phase molecular dynamics simulations
demonstrate that the interplay between chain solvation and intrachain
interactions (self-solvation) leads to conformational distributions
that are modulated by salt concentration, with the wild-type sequence
showing the most sensitivity to changes in salt concentration. These
results suggest that the charge patterning within the wild-type p27
IDR may be optimized to sample both highly solvated and self-solvated
conformational states.
Collapse
Affiliation(s)
- Rebecca Beveridge
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology , University of Manchester , Manchester M13 9PL , U.K
| | - Lukasz G Migas
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology , University of Manchester , Manchester M13 9PL , U.K
| | - Rahul K Das
- Department of Biomedical Engineering and Center for Biological Systems Engineering , Washington University in St. Louis , Campus Box 1097, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering , Washington University in St. Louis , Campus Box 1097, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Richard W Kriwacki
- Structural Biology, MS 311, Room D1024F , St. Jude Children's Research Hospital , 262 Danny Thomas Place , Memphis , Tennessee 38105-3678 , United States
| | - Perdita E Barran
- The Michael Barber Centre for Collaborative Mass Spectrometry, The School of Chemistry, Manchester Institute for Biotechnology , University of Manchester , Manchester M13 9PL , U.K
| |
Collapse
|
19
|
Jeanne Dit Fouque K, Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS OMEGA 2019; 4:3619-3626. [PMID: 30842985 PMCID: PMC6396120 DOI: 10.1021/acsomega.8b02887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/11/2019] [Indexed: 05/14/2023]
Abstract
Topoisomerases are important complex enzymes that modulate DNA topology to maintain chromosome superstructure and integrity. These enzymes are involved in many cellular processes that resolve specific DNA superstructures and intermediates. The low abundance combined with the biological heterogeneity of relevant intermediates of topoisomerases makes their structural information not readily accessible using traditional structural biology tools (e.g., NMR and X-ray crystallography). In the present work, a second-generation trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was used to study Escherichia coli topoisomerase IA (EcTopIA) and variola virus topoisomerase IB (vTopIB) as well as their complexes with a single-stranded DNA and a stem-loop DNA under native conditions. The higher trapping efficiency and extended mass range of the new, convex TIMS geometry allowed for the separation and identification of multiple conformational states for the two topoisomerases and their DNA complexes. Inspection of the conformational space of EcTopIA and vTopIB in complex with DNA showed that upon DNA binding, the number of conformational states is significantly reduced, suggesting that the DNA binding selects for a narrow range of conformers restricted by the interaction with the DNA substrate. The large microheterogeneity observed for the two DNA binding proteins suggests that they can have multiple biological functions. This work highlights the potential of TIMS-MS for the structural investigations of intrinsically disordered proteins (e.g., DNA binding proteins) as a way to gain a better understanding of the mechanisms involved in DNA substrate recognition, binding, and assembly of the catalytically active enzyme-DNA complex.
Collapse
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| |
Collapse
|
20
|
Abstract
A sizeable proportion of active protein sequences lack structural motifs making them irresolvable by NMR and crystallography. Such intrinsically disordered proteins (IDPs) or regions (IDRs) play a major role in biological mechanisms. They are often involved in cell regulation processes, and by extension can be the perpetrator or signifier of disease. In light of their importance and the shortcomings of conventional methods of biophysical analysis to identify them and to describe their conformational variance, IDPs and IDRs have been termed "the dark proteome." In this chapter we describe the use of ion mobility-mass spectrometry (IM-MS) coupled with electrospray ionization to analyze the conformational diversity of IDPs. Using the LEA protein COR15A as an exemplar system and contrasting it with the behavior of myoglobin, we outline the methods for analyzing an IDP using nanoelectrospray ionization coupled with IM-MS, covering sample preparation, purification; optimization of mass spectrometry conditions and tuning parameters; data collection and analysis. Following this, we detail the use of a "toy" model that provides a predictive framework for the study of all proteins with ESI-IM-MS.
Collapse
|
21
|
Jeanne Dit Fouque K, Salgueiro LM, Cai R, Sha W, Schally AV, Fernandez-Lima F. Structural Motif Descriptors as a Way To Elucidate the Agonistic or Antagonistic Activity of Growth Hormone-Releasing Hormone Peptide Analogues. ACS OMEGA 2018; 3:7432-7440. [PMID: 31458901 PMCID: PMC6644384 DOI: 10.1021/acsomega.8b00375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/21/2018] [Indexed: 05/05/2023]
Abstract
The synthesis of analogues of hypothalamic neuropeptide growth hormone-releasing hormone (GHRH) is an efficient strategy for designing new therapeutic agents. Several promising synthetic agonist and antagonist analogues of GHRH have been developed based on amino acid mutations of the GHRH (1-29) sequence. Because structural information on the activity of the GHRH agonists or antagonists is limited, there is a need for more effective analytical workflows capable of correlating the peptide sequence with biological activity. In the present work, three GHRH agonists-MR-356, MR-406, and MR-409-and three GHRH antagonists-MIA-602, MIA-606, and MIA-690-were investigated to assess the role of substitutions in the amino acid sequence on structural motifs and receptor binding affinities. The use of high resolution trapped ion mobility spectrometry coupled to mass spectrometry allowed the observation of a large number of peptide-specific mobility bands (or structural motif descriptors) as a function of the amino acid sequence and the starting solution environment. A direct correlation was observed between the amino acid substitutions (i.e., basic residues and d/l-amino acids), the structural motif descriptors, and the biological function (i.e., receptor binding affinities of the GHRH agonists and antagonists). The simplicity, ease, and high throughput of the proposed workflow based on the structural motif descriptors can significantly reduce the cost and time during screening of new synthetic peptide analogues.
Collapse
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry, Florida International
University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| | - Luis M. Salgueiro
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Renzhi Cai
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Wei Sha
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Andrew V. Schally
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular
Sciences Institute, Florida International
University, 11200 SW 8th Street, AHC4-211, Miami, Florida 33199, United States
- E-mail:
| |
Collapse
|
22
|
Saikusa K, Osakabe A, Kato D, Fuchigami S, Nagadoi A, Nishimura Y, Kurumizaka H, Akashi S. Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry. Anal Chem 2018; 90:8217-8226. [PMID: 29860831 DOI: 10.1021/acs.analchem.8b01649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Histone tails, which protrude from nucleosome core particles (NCPs), play crucial roles in the regulation of DNA transcription, replication, and repair. In this study, structural diversity of nucleosomes was investigated in detail by analyzing the observed charge states of nucleosomes reconstituted with various lengths of DNA using positive-mode electrospray ionization mass spectrometry (ESI-MS) and molecular dynamics (MD) simulation. Here, we show that canonical NCPs, having 147 bp DNA closely wrapped around a histone octamer, can be classified into three groups by charge state, with the least-charged group being more populated than the highly charged and intermediate groups. Ions with low charge showed small collision cross sections (CCSs), suggesting that the histone tails are generally compact in the gas phase, whereas the minor populations with higher charges appeared to have more loosened structure. Overlapping dinucleosomes, which contain 14 histone proteins closely packed with 250 bp DNA, showed similar characteristics. In contrast, mononucleosomes reconstituted with a histone octamer and longer DNA (≥250 bp), which have DNA regions uninvolved in the core-structure formation, showed only low-charge ions. This was also true for dinucleosomes with free DNA regions. These results suggest that free DNA regions affect the nucleosome structures. To investigate the possible structures of NCP observed in ESI-MS, computational structural calculations in solution and in vacuo were performed. They suggested that conformers with large CCS values have slightly loosened structure with extended tail regions, which might relate to the biological function of histone tails.
Collapse
Affiliation(s)
- Kazumi Saikusa
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.,Graduate School of Science , Hiroshima University , 1-3-1 Kagamiyama , Higashi-Hiroshima , Hiroshima 739-8526 , Japan
| | - Akihisa Osakabe
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 , Japan
| | - Daiki Kato
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 , Japan
| | - Sotaro Fuchigami
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Aritaka Nagadoi
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 , Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| |
Collapse
|
23
|
Martin EM, Kondrat FDL, Stewart AJ, Scrivens JH, Sadler PJ, Blindauer CA. Native electrospray mass spectrometry approaches to probe the interaction between zinc and an anti-angiogenic peptide from histidine-rich glycoprotein. Sci Rep 2018; 8:8646. [PMID: 29872214 PMCID: PMC5988744 DOI: 10.1038/s41598-018-26924-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
Zinc modulates the biological function of histidine-rich glycoprotein (HRG) through binding to its His-rich region (HRR). The Zn2+-binding properties of a 35 amino-acid biologically-active peptide mimic of the HRR, HRGP330, were investigated using dissociative mass spectrometry approaches in addition to travelling-wave ion mobility mass spectrometry (TWIM-MS). Native mass spectrometry confirmed zinc binding to HRGP330; however, broadening of the 1H NMR resonances upon addition of Zn2+ ions precluded the attainment of structural information. A complementary approach employing TWIM-MS indicated that HRGP330 has a more compact structure in the presence of Zn2+ ions. Top-down MS/MS data supported a metal-binding-induced conformational change, as fewer fragments were observed for Zn2+-bound HRGP330. Zn2+-bound fragments of both N-terminal and C-terminal ends of the peptide were identified from collision-induced dissociation (CID) and electron transfer dissociation/proton transfer reaction (ETD/PTR) experiments, suggesting that multiple binding sites exist within this region of HRG. The combination of mass spectrometry and NMR approaches provides new insight into the highly dynamic interaction between zinc and this His-rich peptide.
Collapse
Affiliation(s)
- Esther M Martin
- Department of Chemistry, University of Warwick, Coventry, UK
- Medimmune, Cambridge, UK
| | - Frances D L Kondrat
- School of Life Sciences, University of Warwick, Coventry, UK
- Immunocore Ltd, Abingdon, UK
| | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews, UK
| | - James H Scrivens
- School of Life Sciences, University of Warwick, Coventry, UK
- School of Science, Engineering and Design, Teeside University, Middlesbrough, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Coventry, UK
| | | |
Collapse
|
24
|
Khanal N, Gaye MM, Clemmer DE. Multiple solution structures of the disordered peptide indolicidin from IMS-MS analysis. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:52-58. [PMID: 30906201 PMCID: PMC6426319 DOI: 10.1016/j.ijms.2017.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The solution-favored conformations of the 13-residue disordered peptide, indolicidin (Ile1-Leu2-Pro3-Trp4-Lys5-Trp6-Pro7-Trp8-Trp9-Pro10-Trp11-Arg12-Arg13), are evaluated using electrospray ionization (ESI) coupled to ion mobility spectrometry-mass spectrometry (IMS-MS). The ESI-IMS-MS distributions for the dominant [M+4H]4+ ions indicate that three populations of structures coexist in a range of aqueous to non-aqueous solutions (water:dioxane, water:trifluoroethanol, and water:hexafluoroisopropanol). Conformer types and their relative abundances change in response to different solution environments suggesting that the gas phase conformers reflect on the solution populations present in different solvent environments. Collisional activation of isolated gas phase conformations with IMS-IMS-MS experiments provides additional insight about the relative stabilities of different structural types in the absence of solvent. Simulated annealing studies suggest that proline configuration may be important for the presence of multiple conformations.
Collapse
|
25
|
Stuchfield D, Barran P. Unique insights to intrinsically disordered proteins provided by ion mobility mass spectrometry. Curr Opin Chem Biol 2018; 42:177-185. [DOI: 10.1016/j.cbpa.2018.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 02/05/2023]
|
26
|
Oil Palm Phenolics Inhibit the In Vitro Aggregation of β-Amyloid Peptide into Oligomeric Complexes. Int J Alzheimers Dis 2018; 2018:7608038. [PMID: 29666700 PMCID: PMC5831689 DOI: 10.1155/2018/7608038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 01/01/2023] Open
Abstract
Alzheimer's disease is a severe neurodegenerative disease characterized by the aggregation of amyloid-β peptide (Aβ) into toxic oligomers which activate microglia and astrocytes causing acute neuroinflammation. Multiple studies show that the soluble oligomers of Aβ42 are neurotoxic and proinflammatory, whereas the monomers and insoluble fibrils are relatively nontoxic. We show that Aβ42 aggregation is inhibited in vitro by oil palm phenolics (OPP), an aqueous extract from the oil palm tree (Elaeis guineensis). The data shows that OPP inhibits stacking of β-pleated sheets, which is essential for oligomerization. We demonstrate the inhibition of Aβ42 aggregation by (1) mass spectrometry; (2) Congo Red dye binding; (3) 2D-IR spectroscopy; (4) dynamic light scattering; (5) transmission electron microscopy; and (6) transgenic yeast rescue assay. In the yeast rescue assay, OPP significantly reduces the cytotoxicity of aggregating neuropeptides in yeast genetically engineered to overexpress these peptides. The data shows that OPP inhibits (1) the aggregation of Aβ into oligomers; (2) stacking of β-pleated sheets; and (3) fibrillar growth and coalescence. These inhibitory effects prevent the formation of neurotoxic oligomers and hold potential as a means to reduce neuroinflammation and neuronal death and thereby may play some role in the prevention or treatment of Alzheimer's disease.
Collapse
|
27
|
Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol 2018; 611:137-192. [DOI: 10.1016/bs.mie.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
28
|
Li X, Tao Y, Murphy JW, Scherer AN, Lam TT, Marshall AG, Koleske AJ, Boggon TJ. The repeat region of cortactin is intrinsically disordered in solution. Sci Rep 2017; 7:16696. [PMID: 29196701 PMCID: PMC5711941 DOI: 10.1038/s41598-017-16959-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/19/2017] [Indexed: 01/14/2023] Open
Abstract
The multi-domain protein, cortactin, contains a 37-residue repeating motif that binds to actin filaments. This cortactin repeat region comprises 6½ similar copies of the motif and binds actin filaments. To better understand this region of cortactin, and its fold, we conducted extensive biophysical analysis. Size exclusion chromatography with multi-angle light scattering (SEC-MALS) reveals that neither constructs of the cortactin repeats alone or together with the adjacent helical region homo-oligomerize. Using circular dichroism (CD) we find that in solution the cortactin repeats resemble a coil-like intrinsically disordered protein. Small-angle X-ray scattering (SAXS) also indicates that the cortactin repeats are intrinsically unfolded, and the experimentally observed radius of gyration (Rg) is coincidental to that calculated by the program Flexible-Meccano for an unfolded peptide of this length. Finally, hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicates that the domain contains limited hydrophobic core regions. These experiments therefore provide evidence that in solution the cortactin repeat region of cortactin is intrinsically disordered.
Collapse
Affiliation(s)
- Xiaofeng Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yeqing Tao
- Department of Chemistry, Florida State University, 600 W., College Avenue, Tallahassee, FL, 32306, USA.,Biopharmaceutical Analytical Sciences, Biopharm R&D, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA, 19406, USA
| | - James W Murphy
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander N Scherer
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Yale MS & Proteomics Resource, Yale University, New Haven, CT, 06520, USA
| | - Alan G Marshall
- Department of Chemistry, Florida State University, 600 W., College Avenue, Tallahassee, FL, 32306, USA.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| |
Collapse
|
29
|
D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
Collapse
Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| |
Collapse
|
30
|
Heller GT, Aprile FA, Vendruscolo M. Methods of probing the interactions between small molecules and disordered proteins. Cell Mol Life Sci 2017; 74:3225-3243. [PMID: 28631009 PMCID: PMC5533867 DOI: 10.1007/s00018-017-2563-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.
Collapse
Affiliation(s)
- Gabriella T Heller
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | |
Collapse
|
31
|
Devine PWA, Fisher HC, Calabrese AN, Whelan F, Higazi DR, Potts JR, Lowe DC, Radford SE, Ashcroft AE. Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1855-1862. [PMID: 28484973 PMCID: PMC5556138 DOI: 10.1007/s13361-017-1689-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Paul W A Devine
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Henry C Fisher
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fiona Whelan
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Daniel R Higazi
- Ipsen Ltd. UK, Wrexham Industrial Estate, 9 Ash Road North, Wrexham, LL13 9UF, UK
| | | | - David C Lowe
- MedImmune, Sir Aaron Klug Building, Granta Science Park, Cambridge, CB21 6GH, UK
| | - Sheena E Radford
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
32
|
Jhingree JR, Bellina B, Pacholarz KJ, Barran PE. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1450-1461. [PMID: 28585116 PMCID: PMC5486678 DOI: 10.1007/s13361-017-1692-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 05/22/2023]
Abstract
Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Jacquelyn R Jhingree
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kamila J Pacholarz
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
33
|
Marcinko TM, Dong J, LeBlanc R, Daborowski KV, Vachet RW. Small molecule-mediated inhibition of β-2-microglobulin-based amyloid fibril formation. J Biol Chem 2017; 292:10630-10638. [PMID: 28468825 DOI: 10.1074/jbc.m116.774083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint and bone function. Recently, several small molecules have been identified as potential inhibitors of β2m amyloid formation in vitro Here we investigated whether these molecules are more broadly applicable inhibitors of β2m amyloid formation by studying their effect on Cu(II)-induced β2m amyloid formation. Using a variety of biophysical techniques, we also examined their inhibitory mechanisms. We found that two molecules, doxycycline and rifamycin SV, can inhibit β2m amyloid formation in vitro by causing the formation of amorphous, redissolvable aggregates. Rather than interfering with β2m amyloid formation at the monomer stage, we found that doxycycline and rifamycin SV exert their effect by binding to oligomeric species both in solution and in gas phase. Their binding results in a diversion of the expected Cu(II)-induced progression of oligomers toward a heterogeneous collection of oligomers, including trimers and pentamers, that ultimately matures into amorphous aggregates. Using ion mobility mass spectrometry, we show that both inhibitors promote the compaction of the initially formed β2m dimer, which causes the formation of other off-pathway and amyloid-incompetent oligomers that are isomeric with amyloid-competent oligomers in some cases. Overall, our results suggest that doxycycline and rifamycin are general inhibitors of Cu(II)-induced β2m amyloid formation. Interestingly, the putative mechanism of their activity is different depending on how amyloid formation is initiated with β2m, which underscores the complexity of how these structures assemble in vitro.
Collapse
Affiliation(s)
- Tyler M Marcinko
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Jia Dong
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Raquel LeBlanc
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kate V Daborowski
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Richard W Vachet
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| |
Collapse
|
34
|
Donor MT, Ewing SA, Zenaidee MA, Donald WA, Prell JS. Extended Protein Ions Are Formed by the Chain Ejection Model in Chemical Supercharging Electrospray Ionization. Anal Chem 2017; 89:5107-5114. [DOI: 10.1021/acs.analchem.7b00673] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Micah T. Donor
- Department
of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Simon A. Ewing
- Department
of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Muhammad A. Zenaidee
- School
of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - 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
| |
Collapse
|
35
|
Ewing SA, Donor MT, Wilson JW, Prell JS. Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:587-596. [PMID: 28194738 PMCID: PMC5634518 DOI: 10.1007/s13361-017-1594-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/09/2016] [Accepted: 12/29/2016] [Indexed: 05/19/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, native-like or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a "trajectory method" (TM) based CCS calculator, named "Collidoscope," which utilizes parallel processing and optimized trajectory sampling, and implements both He and N2 as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared with those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using X-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Simon A Ewing
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA
| | - Micah T Donor
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA
| | - Jesse W Wilson
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, OR, 97403-1253, USA.
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR, 97403-1252, USA.
| |
Collapse
|
36
|
Mandacaru SC, do Vale LHF, Vahidi S, Xiao Y, Skinner OS, Ricart CAO, Kelleher NL, de Sousa MV, Konermann L. Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools. Biochemistry 2017; 56:1645-1655. [PMID: 28252287 DOI: 10.1021/acs.biochem.7b00020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Royal jelly (RJ) triggers the development of female honeybee larvae into queens. This effect has been attributed to the presence of major royal jelly protein 1 (MRJP1) in RJ. MRJP1 isolated from royal jelly is tightly associated with apisimin, a 54-residue α-helical peptide that promotes the noncovalent assembly of MRJP1 into multimers. No high-resolution structural data are available for these complexes, and their binding stoichiometry remains uncertain. We examined MRJP1/apisimin using a range of biophysical techniques. We also investigated the behavior of deglycosylated samples, as well as samples with reduced apisimin content. Our mass spectrometry (MS) data demonstrate that the native complexes predominantly exist in a (MRJP14 apisimin4) stoichiometry. Hydrogen/deuterium exchange MS reveals that MRJP1 within these complexes is extensively disordered in the range of residues 20-265. Marginally stable secondary structure (likely antiparallel β-sheet) exists around residues 266-432. These weakly structured regions interchange with conformers that are extensively unfolded, giving rise to bimodal (EX1) isotope distributions. We propose that the native complexes have a "dimer of dimers" quaternary structure in which MRJP1 chains are bridged by apisimin. Specifically, our data suggest that apisimin acts as a linker that forms hydrophobic contacts involving the MRJP1 segment 316VLFFGLV322. Deglycosylation produces large soluble aggregates, highlighting the role of glycans as aggregation inhibitors. Samples with reduced apisimin content form dimeric complexes with a (MRJP12 apisimin1) stoichiometry. The information uncovered in this work will help pave the way toward a better understanding of the unique physiological role played by MRJP1 during queen differentiation.
Collapse
Affiliation(s)
- Samuel C Mandacaru
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7.,Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Luis H F do Vale
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil.,Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Siavash Vahidi
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| | - Yiming Xiao
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| | - Owen S Skinner
- Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Carlos A O Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Neil L Kelleher
- Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Marcelo Valle de Sousa
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Lars Konermann
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| |
Collapse
|
37
|
Natalello A, Santambrogio C, Grandori R. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:21-28. [PMID: 27730522 DOI: 10.1007/s13361-016-1490-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| |
Collapse
|
38
|
Native Mass Spectrometry for the Characterization of Structure and Interactions of Membrane Proteins. Methods Mol Biol 2017; 1635:205-232. [PMID: 28755371 DOI: 10.1007/978-1-4939-7151-0_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past years, native mass spectrometry and ion mobility have grown into techniques that are widely applicable to the study of aspects of protein structure. More recently, it has become apparent that this approach provides a very promising avenue for the investigation of integral membrane proteins in lipid or detergent environments.In this chapter, we discuss applications of native mass spectrometry and ion mobility in membrane protein research-what is important to take into consideration when working with membrane proteins, and what the requirements are for sample preparation for native mass spectrometry. Furthermore, we will discuss the types of information provided by the measurements, including the oligomeric state, subunit composition and stoichiometry, interactions with detergents or lipids, conformational transitions, and the binding and structural effect of ligands and drugs.
Collapse
|
39
|
Bastos P, Trindade F, Leite-Moreira A, Falcão-Pires I, Ferreira R, Vitorino R. Methodological approaches and insights on protein aggregation in biological systems. Expert Rev Proteomics 2016; 14:55-68. [DOI: 10.1080/14789450.2017.1264877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Paulo Bastos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Fábio Trindade
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Adelino Leite-Moreira
- Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Inês Falcão-Pires
- Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rita Ferreira
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| |
Collapse
|
40
|
cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry. Biochem J 2016; 473:3159-75. [PMID: 27444646 PMCID: PMC5095912 DOI: 10.1042/bcj20160648] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling.
Collapse
|
41
|
Abstract
A recent ion mobility spectrometry-mass spectrometry (IMS-MS) study revealed that tryptic peptide ions containing a proline residue at the second position from the N-terminus (i.e., penultimate proline) frequently adopt multiple conformations, owing to the cis-trans isomerization of Xaa(1)-Pro(2) peptide bonds [J. Am. Soc. Mass Spectrom. 2015, 26, 444]. Here, we present a statistical analysis of a neuropeptide database that illustrates penultimate proline residues are frequently found in neuropeptides. In order to probe the effect of penultimate proline on neuropeptide conformations, IMS-MS experiments were performed on two model peptides in which penultimate proline residues were known to be important for biological activity: the N-terminal region of human neuropeptide Y (NPY1-9, Tyr(1)-Pro(2)-Ser(3)-Lys(4)-Pro(5)-Asp(6)-Asn(7)-Pro(8)-Gly(9)-NH2) and a tachykinin-related peptide (CabTRP Ia, Ala(1)-Pro(2)-Ser(3)-Gly(4)-Phe(5)-Leu(6)-Gly(7)-Met(8)-Arg(9)-NH2). From these studies, it appears that penultimate prolines allow neuropeptides to populate multiple conformations arising from the cis-trans isomerization of Xaa(1)-Pro(2) peptide bonds. Although it is commonly proposed that the role of penultimate proline residues is to protect peptides from enzymatic degradation, the present results indicate that penultimate proline residues also are an important means of increasing the conformational heterogeneity of neuropeptides.
Collapse
Affiliation(s)
- Matthew S Glover
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - Earl P Bellinger
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - Predrag Radivojac
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| | - David E Clemmer
- †Department of Chemistry, ‡Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
42
|
Distinct higher-order α-synuclein oligomers induce intracellular aggregation. Biochem J 2015; 468:485-93. [DOI: 10.1042/bj20150159] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/08/2015] [Indexed: 12/12/2022]
Abstract
The cell-to-cell transmission of pathology in Parkinson's disease has been linked to soluble amyloid oligomers. Ion mobility spectrometry (IMS)–MS has been used to show that these soluble oligomers have a compact ring-like conformation.
Collapse
|
43
|
D'Urzo A, Konijnenberg A, Rossetti G, Habchi J, Li J, Carloni P, Sobott F, Longhi S, Grandori R. Molecular basis for structural heterogeneity of an intrinsically disordered protein bound to a partner by combined ESI-IM-MS and modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:472-481. [PMID: 25510932 DOI: 10.1007/s13361-014-1048-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 06/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered N(TAIL) domain and the phosphoprotein X domain (P(XD)) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire N(TAIL) domain bound to P(XD) at atomic resolution.
Collapse
Affiliation(s)
- Annalisa D'Urzo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Scarff CA, Almeida B, Fraga J, Macedo-Ribeiro S, Radford SE, Ashcroft AE. Examination of Ataxin-3 (atx-3) Aggregation by Structural Mass Spectrometry Techniques: A Rationale for Expedited Aggregation upon Polyglutamine (polyQ) Expansion. Mol Cell Proteomics 2015; 14:1241-53. [PMID: 25700012 PMCID: PMC4424396 DOI: 10.1074/mcp.m114.044610] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/13/2023] Open
Abstract
Expansion of polyglutamine stretches leads to the formation of polyglutamine-containing neuronal aggregates and neuronal death in nine diseases for which there currently are no treatments or cures. This is largely due to a lack in understanding of the mechanisms by which expanded polyglutamine regions contribute to aggregation and disease. To complicate matters further, several of the polyglutamine-disease related proteins, including ataxin-3, have a multistage aggregation mechanism in which flanking domain self-assembly precedes polyglutamine aggregation yet is influenced by polyglutamine expansion. How polyglutamine expansion influences flanking domain aggregation is poorly understood. Here, we use a combination of mass spectrometry and biophysical approaches to investigate this issue for ataxin-3. We show that the conformational dynamics of the flanking Josephin domain in ataxin-3 with an expanded polyglutamine tract are altered in comparison to those exhibited by its nonexpanded counterpart, specifically within the aggregation-prone region of the Josephin domain (amino acid residues 73–96). Expansion thus exposes this region more frequently in ataxin-3 containing an expanded polyglutamine tract, providing a molecular explanation of why aggregation is accelerated upon polyglutamine expansion. Here, harnessing the power of ion mobility spectrometry-mass spectrometry, oligomeric species formed during aggregation are characterized and a model for oligomer growth proposed. The results suggest that a conformational change occurs at the dimer level that initiates self-assembly. New insights into ataxin-3 fibril architecture are also described, revealing the region of the Josephin domain involved in protofibril formation and demonstrating that polyglutamine aggregation proceeds as a distinct second step after protofibril formation without requiring structural rearrangement of the protofibril core. Overall, the results enable the effect of polyglutamine expansion on every stage of ataxin-3 self-assembly, from monomer through to fibril, to be described and a rationale for expedited aggregation upon polyglutamine expansion to be provided.
Collapse
Affiliation(s)
- Charlotte A Scarff
- From the ‡Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Bruno Almeida
- §IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-4180 Porto, Portugal
| | - Joana Fraga
- §IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-4180 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- §IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-4180 Porto, Portugal
| | - Sheena E Radford
- From the ‡Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK;
| | - Alison E Ashcroft
- From the ‡Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK;
| |
Collapse
|
45
|
Kondrat FDL, Struwe WB, Benesch JLP. Native mass spectrometry: towards high-throughput structural proteomics. Methods Mol Biol 2015; 1261:349-371. [PMID: 25502208 DOI: 10.1007/978-1-4939-2230-7_18] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Native mass spectrometry (MS) has become a sensitive method for structural proteomics, allowing practitioners to gain insight into protein self-assembly, including stoichiometry and three-dimensional architecture, as well as complementary thermodynamic and kinetic aspects. Although MS is typically performed in vacuum, a body of literature has described how native solution-state structure is largely retained on the timescale of the experiment. Native MS offers the benefit that it requires substantially smaller quantities of a sample than traditional structural techniques such as NMR and X-ray crystallography, and is therefore well suited to high-throughput studies. Here we first describe the native MS approach and outline the structural proteomic data that it can deliver. We then provide practical details of experiments to examine the structural and dynamic properties of protein assemblies, highlighting potential pitfalls as well as principles of best practice.
Collapse
Affiliation(s)
- Frances D L Kondrat
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | | | | |
Collapse
|
46
|
Clarke DJ, Campopiano DJ. Desalting large protein complexes during native electrospray mass spectrometry by addition of amino acids to the working solution. Analyst 2015; 140:2679-86. [DOI: 10.1039/c4an02334j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A simple method for mitigating the adverse effects of salt adduction during native protein mass spectrometry by addition of amino-acids.
Collapse
Affiliation(s)
- David J. Clarke
- School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh
- UK
| | | |
Collapse
|
47
|
Phillips AS, Gomes AF, Kalapothakis JMD, Gillam JE, Gasparavicius J, Gozzo FC, Kunath T, MacPhee C, Barran PE. Conformational dynamics of α-synuclein: insights from mass spectrometry. Analyst 2015; 140:3070-81. [DOI: 10.1039/c4an02306d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Different mass spectrometry approaches are combined to investigate the conformational flexibility of α-synuclein.
Collapse
Affiliation(s)
- Ashley S. Phillips
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Alexandre F. Gomes
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | | | - Jay E. Gillam
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | | | - Fabio C. Gozzo
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine
- University of Edinburgh
- Edinburgh
- UK
| | - Cait MacPhee
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | - Perdita E. Barran
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| |
Collapse
|
48
|
Xiao C, Pérez LM, Russell DH. Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions. Analyst 2015; 140:6933-44. [DOI: 10.1039/c5an00826c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.
Collapse
Affiliation(s)
- Chunying Xiao
- Texas A&M University
- Department of Chemistry
- College Station
- USA
| | - Lisa M. Pérez
- Texas A&M University
- Department of Chemistry
- College Station
- USA
| | | |
Collapse
|
49
|
Abstract
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles. Nowadays mass spectrometry-based approaches play a pivotal role in both detection and characterization of proteins. Here we describe two applications to study insoluble proteins: (a) hydrogen/deuterium exchange combined with mass spectrometry to analyze structural properties of amyloid fibrils and (b) the screening for inhibitors of the aggregation process by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Collapse
Affiliation(s)
- Sílvia Bronsoms
- Servei de Proteòmica i Biologia Estructural, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain,
| | | |
Collapse
|
50
|
Voronina L, Rizzo TR. Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin. Phys Chem Chem Phys 2015; 17:25828-36. [DOI: 10.1039/c5cp01651g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We explore conformational space of triply protonated bradykinin. Three conformational families are mobility-separated and spectroscopically characterized. Kinetically trapped structures are identified via annealing.
Collapse
Affiliation(s)
- Liudmila Voronina
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| |
Collapse
|