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Smith JW, Carnevale LN, Das A, Chen Q. Electron videography of a lipid-protein tango. SCIENCE ADVANCES 2024; 10:eadk0217. [PMID: 38630809 PMCID: PMC11023515 DOI: 10.1126/sciadv.adk0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Lauren N. Carnevale
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Aditi Das
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Materials Research Laboratory, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
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2
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Ham D, Inoue A, Xu J, Du Y, Chung KY. Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq. Commun Biol 2024; 7:362. [PMID: 38521872 PMCID: PMC10960872 DOI: 10.1038/s42003-024-06056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.
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Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Shenzhen Futian Biomedical Innovation R&D Center, the Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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3
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Maier R, Cuevas Arenas R, Zhang F, García-Sáez A, Schreiber F. Structural Insights into Polymer-Bounded Lipid Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2450-2459. [PMID: 36724350 DOI: 10.1021/acs.langmuir.2c03412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Membrane proteins are an essential part of signaling and transport processes and are targeted by multiple drugs. To isolate and investigate them in their native state, polymer-bounded nanodiscs have become valuable tools. In this study, we investigate the lipid model system dimyristoyl-phosphocholine (DMPC) with the nanodisc-forming copolymers styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA). Using small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS), we studied the influence of polymer concentration and temperature on the nanodisc structure. In Tris buffer, the size of nanodiscs formed with SMA is smaller compared to DIBMA at the same polymer ratio. In both cases, the size decreases monotonically with increasing polymer concentration, and this effect is more pronounced when using SMA. Measurements at temperatures (T) between 5 and 30 °C in phosphate buffer showed an incomplete solubilization at high T even at polymer/lipid ratios above that required for complete lipid solubilization. For DIBMA, the nanodiscs developed at lower temperatures are stable and the net repulsion increases, while for SMA, the individual nanodiscs possess smaller sizes and are less affected by T. However, using DLS, one can observe SMA agglomerates at low T. Interestingly, for both polymers, no drastic changes of the observable parameters (radius and bilayer thickness) are seen upon cooling, which would indicate a sharp (first-order) phase transition from liquid-crystalline to gel, but only gradual changes. Hence, we conclude that the transition from a gel toward a liquid-crystalline lipid phase proceeds over a broad T-range compared to a continuous lipid bilayer. These results can pave the way toward the development of better protocols for studying membrane proteins stabilized in this type of membrane mimics.
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Affiliation(s)
- Ralph Maier
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076Tübingen, Germany
| | - Rodrigo Cuevas Arenas
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076Tübingen, Germany
- Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584CGUtrecht, Netherlands
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076Tübingen, Germany
| | - Ana García-Sáez
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076Tübingen, Germany
- Institut für Genetik, Universität zu Köln, Joseph-Stelzmann-Strasse 26, 50931Köln, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076Tübingen, Germany
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4
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Hammerschmid D, Calvaresi V, Bailey C, Russell Lewis B, Politis A, Morris M, Denbigh L, Anderson M, Reading E. Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies. Anal Chem 2023; 95:3002-3011. [PMID: 36706021 PMCID: PMC9909672 DOI: 10.1021/acs.analchem.2c04876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins due to their presence of impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Herein, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium-labeled protein-lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein-lipid nanodisc─both empty and loaded with the ∼115 kDa transmembrane protein AcrB─proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO2-coated and TiO2 beads and describe how solution conditions can be optimized to maximize not only the performance of our online but also the existing offline, delipidation workflows for HDX-MS. We envision that this HDX-MS method will significantly ease membrane protein analysis, allowing to better interrogate their dynamics in artificial lipid bilayers or even native cell membranes.
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Affiliation(s)
- Dietmar Hammerschmid
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Valeria Calvaresi
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Chloe Bailey
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | | | - Argyris Politis
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Laetitia Denbigh
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Eamonn Reading
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
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5
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Xu D, Chen X, Li Y, Chen Z, Xu W, Wang X, Lv Y, Wang Z, Wu M, Liu G, Wang J. Reconfigurable Peptide Analogs of Apolipoprotein A-I Reveal Tunable Features of Nanodisc Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1262-1276. [PMID: 36626237 DOI: 10.1021/acs.langmuir.2c03082] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nanodisc (ND)-forming membrane scaffold proteins or peptides developed from apolipoprotein A-I (apoA-I) have led to considerable promise in structural biology and therapeutic applications. However, the rationale and regularity characteristics in peptide sequence design remain inconclusive. Here, we proposed a consensus-based normalization approach through the reversed engineering of apoA-IΔ1-45 to design reconfigurable apoA-I peptide analogs (APAs) for tunable ND assembly. We present extensive morphological validations and computational simulation analyses on divergent APA-NDs that are generated by our method. Fifteen divergent APAs were generated accordingly to study the assembly machinery of NDs. We show that APA designs exhibit multifactorial influence in terms of varying APA tandem repeats, sequence composition, and lipid-to-APA ratio to form tunable diameters of NDs. There is a strong positive correlation between DMPC-to-APA ratios and ND diameters. Longer APA with more tandem repeats tends to yield higher particle size homogeneity. Our results also suggest proline is a dispensable residue for the APA-ND formation. Interestingly, proline-rich substitution not only provides an inward-bending effect in forming smaller NDs but also induces the cumulative chain flexibility that enables larger ND formation at higher lipid ratios. Additionally, proline-tryptophan residues in APAs play a dominant role in forming larger NDs. Molecular simulation shows that enriched basic and acidic residues in APAs evoke abundant hydrogen-bond and salt bridge networks to reinforce the structural stability of APA-NDs. Together, our findings provide a rational basis for understanding APA design. The proposed model could be extended to other apolipoproteins for desired ND engineering.
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Affiliation(s)
- Daiyun Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Zhidong Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Wanting Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Yonghui Lv
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen518033, China
| | - Meiying Wu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen361102, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen518107, China
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6
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Biochemical and structural basis for differential inhibitor sensitivity of EGFR with distinct exon 19 mutations. Nat Commun 2022; 13:6791. [PMID: 36357385 PMCID: PMC9649653 DOI: 10.1038/s41467-022-34398-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) are used to treat non-small cell lung cancers (NSCLC) driven by epidermal growth factor receptor (EGFR) mutations in the tyrosine kinase domain (TKD). TKI responses vary across tumors driven by the heterogeneous group of exon 19 deletions and mutations, but the molecular basis for these differences is not understood. Using purified TKDs, we compared kinetic properties of several exon 19 variants. Although unaltered for the second generation TKI afatinib, sensitivity varied significantly for both the first and third generation TKIs erlotinib and osimertinib. The most sensitive variants showed reduced ATP-binding affinity, whereas those associated with primary resistance retained wild type ATP-binding characteristics (and low KM, ATP). Through crystallographic and hydrogen-deuterium exchange mass spectrometry (HDX-MS) studies, we identify possible origins for the altered ATP-binding affinity underlying TKI sensitivity and resistance, and propose a basis for classifying uncommon exon 19 variants that may have predictive clinical value.
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7
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Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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8
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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9
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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10
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Calvaresi V, Redsted A, Norais N, Rand KD. Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Size-Exclusion Chromatography for Analysis of Complex Protein Samples. Anal Chem 2021; 93:11406-11414. [PMID: 34387074 DOI: 10.1021/acs.analchem.1c01171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The growing use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ligands, and/or highly ionizable reducing agents. Here, we describe how a short size-exclusion chromatography (SEC) column can be integrated with a conventional temperature-controlled HDX-MS setup to achieve fast and online removal of unwanted species from the HDX sample prior to chromatographic separation and MS analysis. Dual-mode valves permit labeled proteins eluting after SEC to be directed to the proteolytic and chromatographic columns, while unwanted sample components are led to waste. The SEC-coupled HDX-MS method allows analyses to be completed with lower or similar back-exchange compared to conventional experiments. We demonstrate the suitability of the method for the analysis of challenging protein samples, achieving efficient online removal of lipid components from protein-lipid systems, depletion of an antibody from an antigen during epitope mapping, and elimination of MS interfering compounds such as tris(2-carboxyethyl)phosphine (TCEP) during HDX-MS analysis of a disulfide-bonded protein. The implementation of the short SEC column to the conventional HDX-MS setup is straightforward and could be of significant general utility during the HDX-MS analysis of complex protein states.
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Affiliation(s)
- Valeria Calvaresi
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,GSK, Siena 53100, Italy
| | - Andreas Redsted
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,GSK, Siena 53100, Italy
| | | | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
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11
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Yun MW, Kim K, Park JY, Chung KY. Conformational Dynamics Analysis of MEK1 Using Hydrogen/Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2021; 28:481-488. [PMID: 33143608 DOI: 10.2174/0929866527666201103152534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/10/2020] [Accepted: 10/10/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Activation of mitogen-activated protein kinases (MAPKs) is regulated by a phosphorylation cascade comprising three kinases, MAPK kinase kinase (MAP3K), MAPK kinase (MAP2K), and MAPK. MAP2K1 and MAPK2K2, also known as MEK1 and MEK2, activate ERK1 and ERK2. The structure of the MAPK signaling cascade has been studied, but high-resolution structural studies of MAP2Ks have often focused on kinase domains or docking sites, but not on full-length proteins. OBJECTIVE To understand the conformational dynamics of MEK1. METHODS Full-length MEK1 was purified from Escherichia coli (BL21), and its conformational dynamics were analyzed using hydrogen/deuterium exchange mass spectrometry (HDX-MS). The effects of ATP binding were examined by co-incubating MEK1 and adenylyl-imidodiphosphate (AMP- PNP), a non-hydrolysable ATP analog. RESULTS MEK1 exhibited mixed EX1/EX2 HDX kinetics within the N-terminal tail through β1, αI, and the C-terminal helix. AMP-PNP binding was found to reduce conformational dynamics within the glycine-rich loop and regions near the DFG motif, along with the activation lip. CONCLUSION We report for the first time that MEK1 has regions that slowly change its folded and unfolded states (mixed EX1/EX2 kinetics) and also report the conformational effects of ATP-binding to MEK1.
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Affiliation(s)
- Min Woo Yun
- School of Pharmacy, Sungkyunkwan University, Suwon 440-746, Korea
| | - Kiae Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 440-746, Korea
| | - Ji Young Park
- School of Pharmacy, Sungkyunkwan University, Suwon 440-746, Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 440-746, Korea
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12
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Marty MT. Nanodiscs and Mass Spectrometry: Making Membranes Fly. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116436. [PMID: 33100891 PMCID: PMC7584149 DOI: 10.1016/j.ijms.2020.116436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cells are surrounded by a protective lipid bilayer membrane, and membrane proteins in the bilayer control the flow of chemicals, information, and energy across this barrier. Many therapeutics target membrane proteins, and some directly target the lipid membrane itself. However, interactions within biological membranes are challenging to study due to their heterogeneity and insolubility. Mass spectrometry (MS) has become a powerful technique for studying membrane proteins, especially how membrane proteins interact with their surrounding lipid environment. Although detergent micelles are the most common membrane mimetic, nanodiscs are emerging as a promising platform for MS. Nanodiscs, nanoscale lipid bilayers encircled by two scaffold proteins, provide a controllable lipid bilayer for solubilizing membrane proteins. This Young Scientist Perspective focuses on native MS of intact nanodiscs and highlights the unique experiments enabled by making membranes fly, including studying membrane protein-lipid interactions and exploring the specificity of fragile transmembrane peptide complexes. It will also explore current challenges and future perspectives for interfacing nanodiscs with MS.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
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13
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Nilsson O, Lindvall M, Obici L, Ekström S, Lagerstedt JO, Del Giudice R. Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux. J Lipid Res 2020; 62:100004. [PMID: 33410751 PMCID: PMC7890215 DOI: 10.1194/jlr.ra120000920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 01/17/2023] Open
Abstract
Apolipoprotein A-I (ApoA-I) of high density lipoproteins (HDLs) is essential for the transportation of cholesterol between peripheral tissues and the liver. However, specific mutations in ApoA-I of HDLs are responsible for a late-onset systemic amyloidosis, the pathological accumulation of protein fibrils in tissues and organs. Carriers of these mutations do not exhibit increased cardiovascular disease risk despite displaying reduced levels of ApoA-I/HDL cholesterol. To explain this paradox, we show that the HDL particle profiles of patients carrying either L75P or L174S ApoA-I amyloidogenic variants show a higher relative abundance of the 8.4-nm versus 9.6-nm particles and that serum from patients, as well as reconstituted 8.4- and 9.6-nm HDL particles (rHDL), possess increased capacity to catalyze cholesterol efflux from macrophages. Synchrotron radiation circular dichroism and hydrogen-deuterium exchange revealed that the variants in 8.4-nm rHDL have altered secondary structure composition and display a more flexible binding to lipids than their native counterpart. The reduced HDL cholesterol levels of patients carrying ApoA-I amyloidogenic variants are thus balanced by higher proportion of small, dense HDL particles, and better cholesterol efflux due to altered, region-specific protein structure dynamics.
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Affiliation(s)
- Oktawia Nilsson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Mikaela Lindvall
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Laura Obici
- Amyloidosis Research & Treatment Centre, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Simon Ekström
- BioMS - Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, Lund, Sweden
| | - Jens O Lagerstedt
- Department of Experimental Medical Science, Lund University, Lund, Sweden; Lund Institute of Advanced Neutron and X-ray Science (LINXS), Lund, Sweden.
| | - Rita Del Giudice
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
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14
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Sligar SG, Denisov IG. Nanodiscs: A toolkit for membrane protein science. Protein Sci 2020; 30:297-315. [PMID: 33165998 DOI: 10.1002/pro.3994] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self-assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native-like bilayer environment that maintain a target's functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.
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Affiliation(s)
- Stephen G Sligar
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ilia G Denisov
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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15
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Structural analysis of lecithin:cholesterol acyltransferase bound to high density lipoprotein particles. Commun Biol 2020; 3:28. [PMID: 31942029 PMCID: PMC6962161 DOI: 10.1038/s42003-019-0749-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Lecithin:cholesterol acyltransferase (LCAT) catalyzes a critical step of reverse cholesterol transport by esterifying cholesterol in high density lipoprotein (HDL) particles. LCAT is activated by apolipoprotein A-I (ApoA-I), which forms a double belt around HDL, however the manner in which LCAT engages its lipidic substrates and ApoA-I in HDL is poorly understood. Here, we used negative stain electron microscopy, crosslinking, and hydrogen-deuterium exchange studies to refine the molecular details of the LCAT-HDL complex. Our data are consistent with LCAT preferentially binding to the edge of discoidal HDL near the boundary between helix 5 and 6 of ApoA-I in a manner that creates a path from the lipid bilayer to the active site of LCAT. Our results provide not only an explanation why LCAT activity diminishes as HDL particles mature, but also direct support for the anti-parallel double belt model of HDL, with LCAT binding preferentially to the helix 4/6 region.
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16
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O'Brien DP, Hourdel V, Chenal A, Brier S. Hydrogen/Deuterium Exchange Mass Spectrometry for the Structural Analysis of Detergent-Solubilized Membrane Proteins. Methods Mol Biol 2020; 2127:339-358. [PMID: 32112332 DOI: 10.1007/978-1-0716-0373-4_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Integral membrane proteins are involved in numerous biological functions and represent important drug targets. Despite their abundance in the human proteome, the number of integral membrane protein structures is largely underrepresented in the Protein Data Bank. The challenges associated with the biophysical characterization of such biological systems are well known. Most structural approaches, including X-ray crystallography, SAXS, or mass spectrometry (MS), require the complete solubilization of membrane proteins in aqueous solutions. Detergents are frequently used for this task, but may interfere with the analysis, as is the case with MS. The use of "MS-friendly" detergents, such as non-ionic alkyl glycoside detergents, has greatly facilitated the analysis of detergent-solubilized membrane proteins. Here, we describe a protocol, which we have successfully implemented in our laboratory to study the structure and dynamics of detergent-solubilized integral membrane proteins by Hydrogen/Deuterium eXchange and Mass Spectrometry (HDX-MS). The procedure does not require detergent removal prior to MS analysis, instead taking advantage of the ultra-high pressure chromatographic system to separate deuterated peptides from "MS-friendly" detergents.
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Affiliation(s)
- Darragh P O'Brien
- Biochemistry of Macromolecular Interaction Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Véronique Hourdel
- Environment and Infectious Risks Unit, Department of Infection and Epidemiology, Institut Pasteur, Paris, France
| | - Alexandre Chenal
- Biochemistry of Macromolecular Interaction Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Sébastien Brier
- Biological NMR Technological Platform, Center for Technological Resources and Research, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
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17
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Schmidpeter PAM, Sukomon N, Nimigean CM. Reconstitution of Membrane Proteins into Platforms Suitable for Biophysical and Structural Analyses. Methods Mol Biol 2020; 2127:191-205. [PMID: 32112324 PMCID: PMC9288841 DOI: 10.1007/978-1-0716-0373-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Integral membrane proteins have historically been challenging targets for biophysical research due to their low solubility in aqueous solution. Their importance for chemical and electrical signaling between cells, however, makes them fascinating targets for investigators interested in the regulation of cellular and physiological processes. Since membrane proteins shunt the barrier imposed by the cell membrane, they also serve as entry points for drugs, adding pharmaceutical research and development to the interests. In recent years, detailed understanding of membrane protein function has significantly increased due to high-resolution structural information obtained from single-particle cryo-EM, X-ray crystallography, and NMR. In order to further advance our mechanistic understanding on membrane proteins as well as foster drug development, it is crucial to generate more biophysical and functional data on these proteins under defined conditions. To that end, different techniques have been developed to stabilize integral membrane proteins in native-like environments that allow both structural and biophysical investigations-amphipols, lipid bicelles, and lipid nanodiscs. In this chapter, we provide detailed protocols for the reconstitution of membrane proteins according to these three techniques. We also outline some of the possible applications of each technique and discuss their advantages and possible caveats.
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Affiliation(s)
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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18
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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19
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Möller IR, Slivacka M, Hausner J, Nielsen AK, Pospíšilová E, Merkle PS, Lišková R, Polák M, Loland CJ, Kádek A, Man P, Rand KD. Improving the Sequence Coverage of Integral Membrane Proteins during Hydrogen/Deuterium Exchange Mass Spectrometry Experiments. Anal Chem 2019; 91:10970-10978. [DOI: 10.1021/acs.analchem.9b00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ingvar R. Möller
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Marika Slivacka
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Jiří Hausner
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen N DK-2200, Denmark
| | - Eliška Pospíšilová
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Patrick S. Merkle
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Růžena Lišková
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Marek Polák
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Claus J. Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen N DK-2200, Denmark
| | - Alan Kádek
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Petr Man
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
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20
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Bolla JR, Agasid MT, Mehmood S, Robinson CV. Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry. Annu Rev Biochem 2019; 88:85-111. [PMID: 30901263 DOI: 10.1146/annurev-biochem-013118-111508] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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21
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Hydrogen-deuterium exchange mass spectrometry of membrane proteins in lipid nanodiscs. Chem Phys Lipids 2019; 220:14-22. [PMID: 30802434 DOI: 10.1016/j.chemphyslip.2019.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/31/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (H/DX MS) provides a quantitative comparison of the relative rates of exchange of amide protons for solvent deuterons. In turn, the rate of amide exchange depends on a complex combination of the stability of local secondary structure, solvent accessibility, and dynamics. H/DX MS has, therefore, been widely used to probe structure and function of soluble proteins, but its application to membrane proteins was limited previously to detergent solubilized samples. The large excess of lipids from model membranes, or from membrane fractions derived from in vivo samples, presents challenges with mass spectrometry. The lipid nanodisc platform, consisting of apolipoprotein A-derived membrane scaffold proteins, provides a native like membrane environment in which to capture analyte membrane proteins with a well defined, and low, ratio of lipid to protein. Membrane proteins in lipid nanodiscs are amenable to H/DX MS, and this is expected to lead to a rapid increase in the number of membrane proteins subjected to this analysis. Here we review the few literature examples of the application of H/DX MS to membrane proteins in nanodiscs. The incremental improvements in the experimental workflow of the H/DX MS are described and potential applications of this approach to study membrane proteins are described.
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22
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Camp T, McLean M, Kato M, Cheruzel L, Sligar S. The hydrodynamic motion of Nanodiscs. Chem Phys Lipids 2019; 220:28-35. [PMID: 30802435 DOI: 10.1016/j.chemphyslip.2019.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 02/02/2023]
Abstract
We present a fluorescence-based methodology for monitoring the rotational dynamics of Nanodiscs. Nanodiscs are nano-scale lipid bilayers surrounded by a helical membrane scaffold protein (MSP) that have found considerable use in studying the interactions between membrane proteins and their lipid bilayer environment. Using a long-lifetime Ruthenium label covalently attached to the Nanodiscs, we find that Nanodiscs of increasing diameter, made by varying the number of helical repeats in the MSP, display increasing rotational correlation times. We also model our system using both analytical equations that describe rotating spheroids and numerical calculations performed on atomic models of Nanodiscs. Using these methods, we observe a linear relationship between the experimentally determined rotational correlation times and those calculated from both analytical equations and numerical solutions. This work sets the stage for accurate, label-free quantification of protein-lipid interactions at the membrane surface.
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Affiliation(s)
- Tyler Camp
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 314F Roger Adams Laboratory (MC-712), 600 S Mathews Ave, Urbana, IL, 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 417 RAL (MC-712), 600 South Mathews Avenue, Urbana, IL, 61801, United States
| | - Mark McLean
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 417 RAL (MC-712), 600 South Mathews Avenue, Urbana, IL, 61801, United States
| | - Mallory Kato
- Department of Chemistry, San Jose State University, San Jose, CA, 95192-0101, United States
| | - Lionel Cheruzel
- Department of Chemistry, San Jose State University, San Jose, CA, 95192-0101, United States
| | - Stephen Sligar
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 314F Roger Adams Laboratory (MC-712), 600 S Mathews Ave, Urbana, IL, 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 417 RAL (MC-712), 600 South Mathews Avenue, Urbana, IL, 61801, United States.
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23
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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24
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Johansen NT, Pedersen MC, Porcar L, Martel A, Arleth L. Introducing SEC–SANS for studies of complex self-organized biological systems. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1178-1191. [DOI: 10.1107/s2059798318007180] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/14/2018] [Indexed: 01/11/2023]
Abstract
Small-angle neutron scattering (SANS) is maturing as a method for studying complex biological structures. Owing to the intrinsic ability of the technique to discern between 1H- and 2H-labelled particles, it is especially useful for contrast-variation studies of biological systems containing multiple components. SANS is complementary to small-angle X-ray scattering (SAXS), in which similar contrast variation is not easily performed but in which data with superior counting statistics are more easily obtained. Obtaining small-angle scattering (SAS) data on monodisperse complex biological structures is often challenging owing to sample degradation and/or aggregation. This problem is enhanced in the D2O-based buffers that are typically used in SANS. In SAXS, such problems are solved using an online size-exclusion chromatography (SEC) setup. In the present work, the feasibility of SEC–SANS was investigated using a series of complex and difficult samples of membrane proteins embedded in nanodisc particles that consist of both phospholipid and protein components. It is demonstrated that SEC–SANS provides data of sufficient signal-to-noise ratio for these systems, while at the same time circumventing aggregation. By combining SEC–SANS and SEC–SAXS data, an optimized basis for refining structural models of the investigated structures is obtained.
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25
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Wilson CJ, Das M, Jayaraman S, Gursky O, Engen JR. Effects of Disease-Causing Mutations on the Conformation of Human Apolipoprotein A-I in Model Lipoproteins. Biochemistry 2018; 57:4583-4596. [PMID: 30004693 DOI: 10.1021/acs.biochem.8b00538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasma high-density lipoproteins (HDLs) are protein-lipid nanoparticles that transport lipids and protect against atherosclerosis. Human apolipoprotein A-I (apoA-I) is the principal HDL protein whose mutations can cause either aberrant lipid metabolism or amyloid disease. Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) was used to study the apoA-I conformation in model discoidal lipoproteins similar in size to large plasma HDL. We examined how point mutations associated with hereditary amyloidosis (F71Y and L170P) or atherosclerosis (L159R) influence the local apoA-I conformation in model lipoproteins. Unlike other apoA-I forms, the large particles showed minimal conformational heterogeneity, suggesting a fully extended protein conformation. Mutation-induced structural perturbations in lipid-bound protein were attenuated compared to the free protein and indicated close coupling between the two belt-forming apoA-I molecules. These perturbations propagated to distant lipoprotein sites, either increasing or decreasing their protection. This HDX MS study of large model HDL, compared with previous studies of smaller particles, ascertained that apoA-I's central region helps accommodate the protein conformation to lipoproteins of various sizes. This study also reveals that the effects of mutations on lipoprotein conformational dynamics are much weaker than those in a lipid-free protein. Interestingly, the mutation-induced perturbations propagate to distant sites nearly 10 nm away and alter their protection in ways that cannot be predicted from the lipoprotein structure and stability. We propose that long-range mutational effects are mediated by both protein and lipid and can influence lipoprotein functionality.
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Affiliation(s)
- Christopher J Wilson
- Department of Chemistry and Chemical Biology , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Madhurima Das
- Department of Physiology & Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118 , United States
| | - Shobini Jayaraman
- Department of Physiology & Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118 , United States
| | - Olga Gursky
- Department of Physiology & Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118 , United States.,Amyloidosis Research Center , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - John R Engen
- Department of Chemistry and Chemical Biology , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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26
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Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR. Nat Protoc 2017; 13:79-98. [PMID: 29215632 DOI: 10.1038/nprot.2017.094] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Suitable membrane mimetics are crucial to the performance of structural and functional studies of membrane proteins. Phospholipid nanodiscs (formed when a membrane scaffold protein encircles a small portion of a lipid bilayer) have native-like membrane properties. These have been used for a variety of functional studies, but structural studies by high-resolution solution-state NMR spectroscopy of membrane proteins in commonly used nanodiscs of 10-nm diameter were limited by the high molecular weight of these particles, which caused unfavorably large NMR line widths. We have recently constructed truncated versions of the membrane scaffold protein, allowing the preparation of a range of stepwise-smaller nanodiscs (6- to 8-nm diameter) to overcome this limitation. Here, we present a protocol on the assembly of phospholipid nanodiscs of various sizes for structural studies of membrane proteins with solution-state NMR spectroscopy. We describe specific isotope-labeling schemes required for working with large membrane protein systems in nanodiscs, and provide guidelines on the setup of NMR non-uniform sampling (NUS) data acquisition and high-resolution NMR spectra reconstruction. We discuss critical points and pitfalls relating to optimization of nanodiscs for NMR spectroscopy and outline a strategy for the high-resolution structure determination and positioning of isotope-labeled membrane proteins in nanodiscs using nuclear Overhauser enhancement spectroscopy (NOESY) spectroscopy, residual dipolar couplings (RDCs) and paramagnetic relaxation enhancements (PREs). Depending on the target protein of interest, nanodisc assembly and purification can be achieved within 12-24 h. Although the focus of this protocol is on protein NMR, these nanodiscs can also be used for (cryo-) electron microscopy (EM) and small-angle X-ray and neutron-scattering studies.
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27
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Peetz O, Henrich E, Laguerre A, Löhr F, Hein C, Dötsch V, Bernhard F, Morgner N. Insights into Cotranslational Membrane Protein Insertion by Combined LILBID-Mass Spectrometry and NMR Spectroscopy. Anal Chem 2017; 89:12314-12318. [PMID: 29039652 DOI: 10.1021/acs.analchem.7b03309] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cotranslational insertion of membrane proteins into defined nanoparticle membranes has been developed as an efficient process to produce highly soluble samples in native-like environments and to study lipid-dependent effects on protein structure and function. Numerous examples of the structural and functional characterization of transporters, ion channels, or G-protein-coupled receptors in cotranslationally formed nanodisc complexes demonstrate the versatility of this approach, although the basic underlying mechanisms of membrane insertion are mainly unknown. We have revealed the first aspects of the insertion of proteins into nanodiscs by combining cell-free expression, noncovalent mass spectrometry, and NMR spectroscopy. We provide evidence of cooperative insertion of homo-oligomeric complexes and demonstrate the possibility to modulate their stoichiometry by modifying reaction conditions. Additionally, we show that significant amounts of lipid are released from the nanodiscs upon insertion of larger protein complexes.
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Affiliation(s)
- Oliver Peetz
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Erik Henrich
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Aisha Laguerre
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Frank Löhr
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Christopher Hein
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Volker Dötsch
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Frank Bernhard
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry and ‡Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University , Frankfurt am Main 60438, Germany
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Wade JH, Jones JD, Lenov IL, Riordan CM, Sligar SG, Bailey RC. Microfluidic platform for efficient Nanodisc assembly, membrane protein incorporation, and purification. LAB ON A CHIP 2017; 17:2951-2959. [PMID: 28767110 PMCID: PMC5589448 DOI: 10.1039/c7lc00601b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The characterization of integral membrane proteins presents numerous analytical challenges on account of their poor activity under non-native conditions, limited solubility in aqueous solutions, and low expression in most cell culture systems. Nanodiscs are synthetic model membrane constructs that offer many advantages for studying membrane protein function by offering a native-like phospholipid bilayer environment. The successful incorporation of membrane proteins within Nanodiscs requires experimental optimization of conditions. Standard protocols for Nanodisc formation can require large amounts of time and input material, limiting the facile screening of formation conditions. Capitalizing on the miniaturization and efficient mass transport inherent to microfluidics, we have developed a microfluidic platform for efficient Nanodisc assembly and purification, and demonstrated the ability to incorporate functional membrane proteins into the resulting Nanodiscs. In addition to working with reduced sample volumes, this platform simplifies membrane protein incorporation from a multi-stage protocol requiring several hours or days into a single platform that outputs purified Nanodiscs in less than one hour. To demonstrate the utility of this platform, we incorporated Cytochrome P450 into Nanodiscs of variable size and lipid composition, and present spectroscopic evidence for the functional active site of the membrane protein. This platform is a promising new tool for membrane protein biology and biochemistry that enables tremendous versatility for optimizing the incorporation of membrane proteins using microfluidic gradients to screen across diverse formation conditions.
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Affiliation(s)
- James H Wade
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Lipid-Mediated Regulation of Embedded Receptor Kinases via Parallel Allosteric Relays. Biophys J 2017; 112:643-654. [PMID: 28256224 DOI: 10.1016/j.bpj.2016.12.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/15/2016] [Accepted: 12/12/2016] [Indexed: 01/29/2023] Open
Abstract
Membrane-anchored receptors are essential cellular signaling elements for stimulus sensing, propagation, and transmission inside cells. However, the contributions of lipid interactions to the function and dynamics of embedded receptor kinases have not been described in detail. In this study, we used amide hydrogen/deuterium exchange mass spectrometry, a sensitive biophysical approach, to probe the dynamics of a membrane-embedded receptor kinase, EnvZ, together with functional assays to describe the role of lipids in receptor kinase function. Our results reveal that lipids play an important role in regulating receptor function through interactions with transmembrane segments, as well as through peripheral interactions with nonembedded domains. Specifically, the lipid membrane allosterically modulates the activity of the embedded kinase by altering the dynamics of a glycine-rich motif that is critical for phosphotransfer from ATP. This allostery in EnvZ is independent of membrane composition and involves direct interactions with transmembrane and periplasmic segments, as well as peripheral interactions with nonembedded domains of the protein. In the absence of the membrane-spanning regions, lipid allostery is propagated entirely through peripheral interactions. Whereas lipid allostery impacts the phosphotransferase function of the kinase, extracellular stimulus recognition is mediated via a four-helix bundle subdomain located in the cytoplasm, which functions as the osmosensing core through osmolality-dependent helical stabilization. Our findings emphasize the functional modularity in a membrane-embedded kinase, separated into membrane association, phosphotransferase function, and stimulus recognition. These components are integrated through long-range communication relays, with lipids playing an essential role in regulation.
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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31
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Vadas O, Jenkins ML, Dornan GL, Burke JE. Using Hydrogen-Deuterium Exchange Mass Spectrometry to Examine Protein-Membrane Interactions. Methods Enzymol 2016; 583:143-172. [PMID: 28063489 DOI: 10.1016/bs.mie.2016.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS experiments measure protein conformational dynamics in their native state, based on the rate of exchange of amide hydrogens with solvent. This review discusses the use of HDX-MS as a tool to identify the interfaces of proteins with membranes and membrane-associated proteins, as well as define conformational changes elicited by membrane recruitment. Specific examples will focus on the use of HDX-MS to examine how large macromolecular protein complexes are recruited and activated on membranes, and how both posttranslational modifications and cancer-linked oncogenic mutations affect these processes.
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Affiliation(s)
- O Vadas
- Pharmaceutical Sciences Section, University of Geneva, Geneva, Switzerland
| | | | - G L Dornan
- University of Victoria, Victoria BC, Canada
| | - J E Burke
- University of Victoria, Victoria BC, Canada.
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Lu Y, Zhang H, Niedzwiedzki DM, Jiang J, Blankenship RE, Gross ML. Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc. Anal Chem 2016; 88:8827-34. [PMID: 27500903 PMCID: PMC5201186 DOI: 10.1021/acs.analchem.6b01945] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although membrane proteins are crucial participants in photosynthesis and other biological processes, many lack high-resolution structures. Prior to achieving a high-resolution structure, we are investigating whether MS-based footprinting can provide coarse-grained protein structure by following structural changes that occur upon ligand binding, pH change, and membrane binding. Our platform probes topology and conformation of membrane proteins by combining MS-based footprinting, specifically fast photochemical oxidation of proteins (FPOP), and lipid Nanodiscs, which are more similar to the native membrane environment than are the widely used detergent micelles. We describe here results that show a protein's outer membrane regions are more heavily footprinted by OH radicals whereas the regions spanning the lipid bilayer remain inert to the labeling. Nanodiscs generally exhibit more protection of membrane proteins compared to detergent micelles and less shielding to those protein residues that exist outside the membrane. The combination of immobilizing the protein in Nanodiscs and footprinting with FPOP is a feasible approach to map extra-membrane protein surfaces, even at the amino-acid level, and to illuminate intrinsic membrane protein topology.
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Affiliation(s)
- Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Dariusz M. Niedzwiedzki
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jing Jiang
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E. Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Harrison RA, Engen JR. Conformational insight into multi-protein signaling assemblies by hydrogen-deuterium exchange mass spectrometry. Curr Opin Struct Biol 2016; 41:187-193. [PMID: 27552080 DOI: 10.1016/j.sbi.2016.08.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/08/2016] [Accepted: 08/08/2016] [Indexed: 01/14/2023]
Abstract
Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) can provide information about proteins that can be challenging to obtain by other means. Structure/function relationships, binding interactions, and the effects of modification have all been measured with HDX MS for a diverse and growing array of signaling proteins and multiprotein signaling complexes. As a result of hardware and software improvements, receptors and complexes involved in cellular signaling-including those associated with membranes-can now be studied. The growing body of HDX MS studies of signaling complexes at membranes is particularly exciting. Recent examples are presented to illustrate what can be learned about signaling proteins with this technique.
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Affiliation(s)
- Rane A Harrison
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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34
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Zeno WF, Rystov A, Sasaki DY, Risbud SH, Longo ML. Crowding-Induced Mixing Behavior of Lipid Bilayers: Examination of Mixing Energy, Phase, Packing Geometry, and Reversibility. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4688-4697. [PMID: 27096947 PMCID: PMC5519306 DOI: 10.1021/acs.langmuir.6b00831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In an effort to develop a general thermodynamic model from first-principles to describe the mixing behavior of lipid membranes, we examined lipid mixing induced by targeted binding of small (Green Fluorescent Protein (GFP)) and large (nanolipoprotein particles (NLPs)) structures to specific phases of phase-separated lipid bilayers. Phases were targeted by incorporation of phase-partitioning iminodiacetic acid (IDA)-functionalized lipids into ternary lipid mixtures consisting of DPPC, DOPC, and cholesterol. GFP and NLPs, containing histidine tags, bound the IDA portion of these lipids via a metal, Cu(2+), chelating mechanism. In giant unilamellar vesicles (GUVs), GFP and NLPs bound to the Lo domains of bilayers containing DPIDA, and bound to the Ld region of bilayers containing DOIDA. At sufficiently large concentrations of DPIDA or DOIDA, lipid mixing was induced by bound GFP and NLPs. The validity of the thermodynamic model was confirmed when it was found that the statistical mixing distribution as a function of crowding energy for smaller GFP and larger NLPs collapsed to the same trend line for each GUV composition. Moreover, results of this analysis show that the free energy of mixing for a ternary lipid bilayer consisting of DOPC, DPPC, and cholesterol varied from 7.9 × 10(-22) to 1.5 × 10(-20) J/lipid at the compositions observed, decreasing as the relative cholesterol concentration was increased. It was discovered that there appears to be a maximum packing density, and associated maximum crowding pressure, of the NLPs, suggestive of circular packing. A similarity in mixing induced by NLP1 and NLP3 despite large difference in projected areas was analytically consistent with monovalent (one histidine tag) versus divalent (two histidine tags) surface interactions, respectively. In addition to GUVs, binding and induced mixing behavior of NLPs was also observed on planar, supported lipid multibilayers. The mixing process was reversible, with Lo domains reappearing after addition of EDTA for NLP removal.
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Affiliation(s)
| | | | - Darryl Y Sasaki
- Sandia National Laboratories , P.O. Box 969, Livermore, California 94551, United States
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35
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36
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Das M, Wilson CJ, Mei X, Wales TE, Engen JR, Gursky O. Structural Stability and Local Dynamics in Disease-Causing Mutants of Human Apolipoprotein A-I: What Makes the Protein Amyloidogenic? J Mol Biol 2015; 428:449-62. [PMID: 26562506 DOI: 10.1016/j.jmb.2015.10.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 01/27/2023]
Abstract
ApoA-I, the major protein of plasma high-density lipoprotein, removes cellular cholesterol and protects against atherosclerosis. ApoA-I mutations can cause familial amyloidosis, a life-threatening disease wherein N-terminal protein fragments form fibrils in vital organs. To unveil the protein misfolding mechanism and to understand why some mutations cause amyloidosis while others do not, we analyzed the structure, stability, and lipid-binding properties of naturally occurring mutants of full-length human apoA-I causing either amyloidosis (G26R, W50R, F71Y, and L170P) or aberrant lipid metabolism (L159R). Global and local protein conformation and dynamics in solution were assessed by circular dichroism, fluorescence, and hydrogen-deuterium exchange mass spectrometry. All mutants showed increased deuteration in residues 14-22, supporting our hypothesis that decreased protection of this major amyloid "hot spot" can trigger protein misfolding. In addition, L159R showed local helical unfolding near the mutation site, consistent with cleavage of this mutant in plasma to generate the labile 1-159 fragment. Together, the results suggest that reduced protection of the major amyloid "hot spot", combined with the structural integrity of the native helix bundle conformation, shifts the balance from protein clearance to β-aggregation. A delicate balance between the overall structural integrity of a globular protein and the local destabilization of its amyloidogenic segments may be a fundamental determinant of this and other amyloid diseases. Furthermore, mutation-induced conformational changes observed in the helix bundle, which comprises the N-terminal 75% of apoA-I, and its flexible C-terminal tail suggest the propagation of structural perturbations to distant sites via an unexpected template-induced ensemble-based mechanism, challenging the classical structure-based view.
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Affiliation(s)
- Madhurima Das
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
| | - Christopher J Wilson
- Department of Chemistry & Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Xiaohu Mei
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
| | - Thomas E Wales
- Department of Chemistry & Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Olga Gursky
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
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37
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Affiliation(s)
- Iwona Siuda
- Department of Biological
Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
| | - D. Peter Tieleman
- Department of Biological
Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
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38
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Trabjerg E, Jakobsen RU, Mysling S, Christensen S, Jørgensen TJD, Rand KD. Conformational analysis of large and highly disulfide-stabilized proteins by integrating online electrochemical reduction into an optimized H/D exchange mass spectrometry workflow. Anal Chem 2015; 87:8880-8. [PMID: 26249042 DOI: 10.1021/acs.analchem.5b01996] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of disulfide-bonded proteins by hydrogen/deuterium exchange mass spectrometry (HDX-MS) requires effective and rapid reduction of disulfide bonds before enzymatic digestion in order to increase sequence coverage. In a conventional HDX-MS workflow, disulfide bonds are reduced chemically by addition of a reducing agent to the quench solution (e.g., tris(2-carboxyethyl)phosphine (TCEP)). The chemical reduction, however, is severely limited under quenched conditions due to a narrow time window as well as low pH and temperature. Here, we demonstrate the real-world applicability of integrating electrochemical reduction into an online HDX-MS workflow. We have optimized the electrochemical reduction efficiency during HDX-MS analysis of two particularly challenging disulfide stabilized proteins: a therapeutic IgG1-antibody and nerve growth factor-β (NGF). Several different parameters (flow rate and applied square wave potential, as well as the type of labeling and quench buffer) were investigated, and the optimized workflow increased the sequence coverage of NGF from 46% with chemical reduction to 99%, when electrochemical reduction was applied. Additionally, the optimized workflow also enabled a similar high sequence coverage of 96% and 87% for the heavy and light chain of the IgG1-antibody, respectively. The presented results demonstrate the successful electrochemical reduction during HDX-MS analysis of both a small exceptional tightly disulfide-bonded protein (NGF) as well as the largest protein attempted to date (IgG1-antibody). We envision that online electrochemical reduction is poised to decrease the complexity of sample handling and increase the versatility of the HDX-MS technique.
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Affiliation(s)
- Esben Trabjerg
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, Copenhagen E, DK-2100, Denmark.,Department of Biologics, H. Lundbeck A/S , Ottiliavej 9, Valby, DK-2500, Denmark
| | - Rasmus U Jakobsen
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, Copenhagen E, DK-2100, Denmark
| | - Simon Mysling
- Finsen Laboratory, Rigshospitalet and Biotech Research and Innovation Centre (BRIC), Copenhagen Biocenter , Ole Maaløes vej 5, Copenhagen N, DK-2200, Denmark
| | - Søren Christensen
- Department of Biologics, H. Lundbeck A/S , Ottiliavej 9, Valby, DK-2500, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campuvej 55, Odense, DK-5230, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, Copenhagen E, DK-2100, Denmark
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39
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Pirrone GF, Vernon BC, Kent MS, Engen JR. Hydrogen Exchange Mass Spectrometry of Proteins at Langmuir Monolayers. Anal Chem 2015; 87:7022-9. [PMID: 26134943 DOI: 10.1021/acs.analchem.5b01724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hydrogen exchange (HX) mass spectrometry (MS) is valuable for providing conformational information for proteins/peptides that are very difficult to analyze with other methods such as peripheral membrane proteins and peptides that interact with membranes. We developed a new type of HX MS measurement that integrates Langmuir monolayers. A lipid monolayer was generated, a peptide or protein associated with it, and then the monolayer-associated peptide or protein was exposed to deuterium. The deuterated species was recovered from the monolayer, digested, and deuterium incorporation monitored by MS. Test peptides showed that deuterium recovery in an optimized protocol was equivalent to deuterium recovery in conventional solution HX MS. The reproducibility of the measurements was high, despite the requirement of generating a new monolayer for each deuterium labeling time. We validated that known conformational changes in the presence of a monolayer/membrane could be observed with the peptide melittin and the myristoylated protein Arf-1. Results in an accompanying paper show that the method can reveal details of conformational changes in a protein (HIV-1 Nef), which adopts a different conformation, depending on whether or not it is able to insert into the lipid layer. Overall, the HX MS Langmuir monolayer method provided new and meaningful conformational information for proteins that associate with lipid layers. The combination of HX MS results with neutron or X-ray reflection of the same proteins in Langmuir monolayers can be more informative than the isolated use of either method.
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Affiliation(s)
- Gregory F Pirrone
- †Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115-5000, United States
| | - Briana C Vernon
- ‡Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Michael S Kent
- ‡Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - John R Engen
- †Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115-5000, United States
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40
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Zeno WF, Hilt S, Risbud SH, Voss JC, Longo ML. Spectroscopic Characterization of Structural Changes in Membrane Scaffold Proteins Entrapped within Mesoporous Silica Gel Monoliths. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8640-8649. [PMID: 25849085 PMCID: PMC5522711 DOI: 10.1021/acsami.5b00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The changes in the orientation and conformation of three different membrane scaffold proteins (MSPs) upon entrapment in sol-gel-derived mesoporous silica monoliths were investigated. MSPs were examined in either a lipid-free or a lipid-bound conformation, where the proteins were associated with lipids to form nanolipoprotein particles (NLPs). NLPs are water-soluble, disk-shaped patches of a lipid bilayer that have amphiphilic MSPs shielding the hydrophobic lipid tails. The NLPs in this work had an average thickness of 5 nm and diameters of 9.2, 9.7, and 14.8 nm. We have previously demonstrated that NLPs are more suitable lipid-based structures for silica gel entrapment than liposomes because of their size compatibility with the mesoporous network (2-50 nm) and minimally altered structure after encapsulation. Here we further elaborate on that work by using a variety of spectroscopic techniques to elucidate whether or not different MSPs maintain their protein-lipid interactions after encapsulation. Fluorescence spectroscopy and quenching of the tryptophan residues with acrylamide, 5-DOXYL-stearic acid, and 16-DOXYL-stearic acid were used to determine the MSP orientation. We also utilized fluorescence anisotropy of tryptophans to measure the relative size of the NLPs and MSP aggregates after entrapment. Finally, circular dichroism spectroscopy was used to examine the secondary structure of the MSPs. Our results showed that, after entrapment, all of the lipid-bound MSPs maintained orientations that were minimally changed and indicative of association with lipids in NLPs. The tryptophan residues appeared to remain buried within the hydrophobic core of the lipid tails in the NLPs and appropriately spaced from the bilayer center. Also, after entrapment, lipid-bound MSPs maintained a high degree of α-helical content, a secondary structure associated with protein-lipid interactions. These findings demonstrate that NLPs are capable of serving as viable hosts for functional integral membrane proteins in the synthesis of sol-gel-derived bioinorganic hybrid nanomaterials.
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Affiliation(s)
- Wade F. Zeno
- Department of Chemical Engineering and Materials Science, University of California Davis, Davis, California, 95616
| | - Silvia Hilt
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, 95616
| | - Subhash H. Risbud
- Department of Chemical Engineering and Materials Science, University of California Davis, Davis, California, 95616
| | - John C. Voss
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, 95616
| | - Marjorie L. Longo
- Department of Chemical Engineering and Materials Science, University of California Davis, Davis, California, 95616
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41
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Arndt JR, Brown RJ, Burke KA, Legleiter J, Valentine SJ. Lysine residues in the N-terminal huntingtin amphipathic α-helix play a key role in peptide aggregation. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:117-126. [PMID: 25601683 DOI: 10.1002/jms.3504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
Huntington's disease is a genetic neurodegenerative disorder caused by an expansion in a polyglutamine domain near the N-terminus of the huntingtin (htt) protein that results in the formation of protein aggregates. Here, htt aggregate structure has been examined using hydrogen-deuterium exchange techniques coupled with tandem mass spectrometry. The focus of the study is on the 17-residue N-terminal flanking region of the peptide that has been shown to alter htt aggregation kinetics and morphology. A top-down sequencing strategy employing electron transfer dissociation is utilized to determine the location of accessible and protected hydrogens. In these experiments, peptides aggregate in a deuterium-rich solvent at neutral pH and are subsequently subjected to deuterium-hydrogen back-exchange followed by rapid quenching, disaggregation, and tandem mass spectrometry analysis. Electrospray ionization of the peptide solution produces the [M + 5H](5+) to [M + 10H](10+) charge states and reveals the presence of multiple peptide sequences differing by single glutamine residues. The [M + 7H](7+) to [M + 9](9+) charge states corresponding to the full peptide are used in the electron transfer dissociation analyses. Evidence for protected residues is observed in the 17-residue N-terminal tract and specifically points to lysine residues as potentially playing a significant role in htt aggregation.
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Affiliation(s)
- James R Arndt
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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42
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Ikeda K, Nakano M. Self-reproduction of nanoparticles through synergistic self-assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:17-21. [PMID: 25541673 DOI: 10.1021/la503491p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe a self-reproduction mechanism of nanometer-sized particles (i.e., nanodiscs) through chemical ligation of the precursors and self-assembly of the building blocks. The ligation reaction was accelerated on lipid bilayer surfaces, and the products spontaneously assembled into nanodiscs with lipid molecules. With the increase in the number of nanodiscs, a rapid proliferation of the nanodiscs occurred through the spatial rearrangements of the molecules between the pre-existing nanodiscs and the unreacted materials, rather than template- or complex-enhanced ligation of the precursors. The subsequent process of surface-enhanced ligation of integrated precursors matured the nanoparticles into identical copies of the pre-existing assembly. Our study showed that the synergistic self-assembly mechanism probably underlie the self-replication principles for heterogeneous multimolecular systems.
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Affiliation(s)
- Keisuke Ikeda
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama , Toyama 930-0194, Japan
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43
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Kacprzyk-Stokowiec A, Kulma M, Traczyk G, Kwiatkowska K, Sobota A, Dadlez M. Crucial role of perfringolysin O D1 domain in orchestrating structural transitions leading to membrane-perforating pores: a hydrogen-deuterium exchange study. J Biol Chem 2014; 289:28738-52. [PMID: 25164812 DOI: 10.1074/jbc.m114.577981] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Perfringolysin O (PFO) is a toxic protein that binds to cholesterol-containing membranes, oligomerizes, and forms a β-barrel transmembrane pore, leading to cell lysis. Previous studies have uncovered the sequence of events in this multistage structural transition to a considerable detail, but the underlying molecular mechanisms are not yet fully understood. By measuring hydrogen-deuterium exchange patterns of peptide bond amide protons monitored by mass spectrometry (MS), we have mapped structural changes in PFO and its variant bearing a point mutation during incorporation to the lipid environment. We have defined all regions that undergo structural changes caused by the interaction with the lipid environment both in wild-type PFO, thus providing new experimental constraints for molecular modeling of the pore formation process, and in a point mutant, W165T, for which the pore formation process is known to be inefficient. We have demonstrated that point mutation W165T causes destabilization of protein solution structure, strongest for domain D1, which interrupts the pathway of structural transitions in other domains necessary for proper oligomerization in the membrane. In PFO, the strongest changes accompanying binding to the membrane focus in D1; the C-terminal part of D4; and strands β1, β4, and β5 of D3. These changes were much weaker for PFO(W165T) lipo where substantial stabilization was observed only in D4 domain. In this study, the application of hydrogen-deuterium exchange analysis monitored by MS provided new insight into conformational changes of PFO associated with the membrane binding, oligomerization, and lytic pore formation.
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Affiliation(s)
- Aleksandra Kacprzyk-Stokowiec
- From the Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego St., 02-106 Warsaw, Poland
| | - Magdalena Kulma
- From the Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego St., 02-106 Warsaw, Poland
| | - Gabriela Traczyk
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland, and
| | - Katarzyna Kwiatkowska
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland, and
| | - Andrzej Sobota
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland, and
| | - Michał Dadlez
- From the Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego St., 02-106 Warsaw, Poland, Department of Biology, Institute of Genetics and Biotechnology, Warsaw University, 1 Miecznikowa Street, 02-185 Warsaw, Poland
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44
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Zeno WF, Hilt S, Aravagiri K, Risbud SH, Voss JC, Parikh AN, Longo ML. Analysis of lipid phase behavior and protein conformational changes in nanolipoprotein particles upon entrapment in sol-gel-derived silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:9780-9788. [PMID: 25062385 PMCID: PMC4140539 DOI: 10.1021/la5025058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/24/2014] [Indexed: 06/02/2023]
Abstract
The entrapment of nanolipoprotein particles (NLPs) and liposomes in transparent, nanoporous silica gel derived from the precursor tetramethylorthosilicate was investigated. NLPs are discoidal patches of lipid bilayer that are belted by amphiphilic scaffold proteins and have an average thickness of 5 nm. The NLPs in this work had a diameter of roughly 15 nm and utilized membrane scaffold protein (MSP), a genetically altered variant of apolipoprotein A-I. Liposomes have previously been examined inside of silica sol-gels and have been shown to exhibit instability. This is attributed to their size (∼150 nm) and altered structure and constrained lipid dynamics upon entrapment within the nanometer-scale pores (5-50 nm) of the silica gel. By contrast, the dimensional match of NLPs with the intrinsic pore sizes of silica gel opens the possibility for their entrapment without disruption. Here we demonstrate that NLPs are more compatible with the nanometer-scale size of the porous environment by analysis of lipid phase behavior via fluorescence anisotropy and analysis of scaffold protein secondary structure via circular dichroism spectroscopy. Our results showed that the lipid phase behavior of NLPs entrapped inside of silica gel display closer resemblance to its solution behavior, more so than liposomes, and that the MSP in the NLPs maintain the high degree of α-helix secondary structure associated with functional protein-lipid interactions after entrapment. We also examined the effects of residual methanol on lipid phase behavior and the size of NLPs and found that it exerts different influences in solution and in silica gel; unlike in free solution, silica entrapment may be inhibiting NLP size increase and/or aggregation. These findings set precedence for a bioinorganic hybrid nanomaterial that could incorporate functional integral membrane proteins.
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Affiliation(s)
- Wade F. Zeno
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
| | - Silvia Hilt
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
| | - Kannan
K. Aravagiri
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
| | - Subhash H. Risbud
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
| | - John C. Voss
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
| | - Atul N. Parikh
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
| | - Marjorie L. Longo
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Medicine, University
of California Davis, Davis, California 95616, United States
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45
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Bereszczak JZ, Watts NR, Wingfield PT, Steven AC, Heck AJR. Assessment of differences in the conformational flexibility of hepatitis B virus core-antigen and e-antigen by hydrogen deuterium exchange-mass spectrometry. Protein Sci 2014; 23:884-96. [PMID: 24715628 DOI: 10.1002/pro.2470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 01/17/2023]
Abstract
Hepatitis B virus core-antigen (capsid protein) and e-antigen (an immune regulator) have almost complete sequence identity, yet the dimeric proteins (termed Cp149d and Cp(-10)149d , respectively) adopt quite distinct quaternary structures. Here we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) to study their structural properties. We detect many regions that differ substantially in their HDX dynamics. Significantly, whilst all regions in Cp(-10)149d exchange by EX2-type kinetics, a number of regions in Cp149d were shown to exhibit a mixture of EX2- and EX1-type kinetics, hinting at conformational heterogeneity in these regions. Comparison of the HDX of the free Cp149d with that in assembled capsids (Cp149c ) indicated increased resistance to exchange at the C-terminus where the inter-dimer contacts occur. Furthermore, evidence of mixed exchange kinetics were not observed in Cp149c , implying a reduction in flexibility upon capsid formation. Cp(-10)149d undergoes a drastic structural change when the intermolecular disulphide bridge is reduced, adopting a Cp149d -like structure, as evidenced by the detected HDX dynamics being more consistent with Cp149d in many, albeit not all, regions. These results demonstrate the highly dynamic nature of these similar proteins. To probe the effect of these structural differences on the resulting antigenicity, we investigated binding of the antibody fragment (Fab E1) that is known to bind a conformational epitope on the four-helix bundle. Whilst Fab E1 binds to Cp149c and Cp149d , it does not bind non-reduced and reduced Cp(-10)149d , despite unhindered access to the epitope. These results imply a remarkable sensitivity of this epitope to its structural context.
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Affiliation(s)
- Jessica Z Bereszczak
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Netherlands Proteomics Centre, The Netherlands
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46
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Parker CH, Morgan C, Rand KD, Engen JR, Jorgenson J, Stafford DW. A conformational investigation of propeptide binding to the integral membrane protein γ-glutamyl carboxylase using nanodisc hydrogen exchange mass spectrometry. Biochemistry 2014; 53:1511-20. [PMID: 24512177 PMCID: PMC3970815 DOI: 10.1021/bi401536m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/07/2014] [Indexed: 01/16/2023]
Abstract
Gamma (γ)-glutamyl carboxylase (GGCX) is an integral membrane protein responsible for the post-translational catalytic conversion of select glutamic acid (Glu) residues to γ-carboxy glutamic acid (Gla) in vitamin K-dependent (VKD) proteins. Understanding the mechanism of carboxylation and the role of GGCX in the vitamin K cycle is of biological interest in the development of therapeutics for blood coagulation disorders. Historically, biophysical investigations and structural characterizations of GGCX have been limited due to complexities involving the availability of an appropriate model membrane system. In previous work, a hydrogen exchange mass spectrometry (HX MS) platform was developed to study the structural configuration of GGCX in a near-native nanodisc phospholipid environment. Here we have applied the nanodisc-HX MS approach to characterize specific domains of GGCX that exhibit structural rearrangements upon binding the high-affinity consensus propeptide (pCon; AVFLSREQANQVLQRRRR). pCon binding was shown to be specific for monomeric GGCX-nanodiscs and promoted enhanced structural stability to the nanodisc-integrated complex while maintaining catalytic activity in the presence of carboxylation co-substrates. Noteworthy modifications in HX of GGCX were prominently observed in GGCX peptides 491-507 and 395-401 upon pCon association, consistent with regions previously identified as sites for propeptide and glutamate binding. Several additional protein regions exhibited minor gains in solvent protection upon propeptide incorporation, providing evidence for a structural reorientation of the GGCX complex in association with VKD carboxylation. The results herein demonstrate that nanodisc-HX MS can be utilized to study molecular interactions of membrane-bound enzymes in the absence of a complete three-dimensional structure and to map dynamic rearrangements induced upon ligand binding.
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Affiliation(s)
- Christine H. Parker
- Department of Chemistry and Department of
Biology, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher
R. Morgan
- Department
of Chemistry & Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Kasper D. Rand
- Department
of Chemistry & Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - John R. Engen
- Department
of Chemistry & Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - James
W. Jorgenson
- Department of Chemistry and Department of
Biology, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Darrel W. Stafford
- Department of Chemistry and Department of
Biology, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
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47
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Schmidt C, Robinson CV. Dynamic protein ligand interactions--insights from MS. FEBS J 2014; 281:1950-64. [PMID: 24393119 PMCID: PMC4154455 DOI: 10.1111/febs.12707] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/19/2013] [Accepted: 12/30/2013] [Indexed: 12/31/2022]
Abstract
Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine‐tuned for different cellular actions. The study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. During the last two decades MS, and its associated techniques, has become accepted as a method for the study of protein–ligand interactions, not only for covalent complexes, where the use of MS is well established, but also, and significantly for protein–ligand interactions, for noncovalent assemblies. In this review, we employ a broad definition of a ligand to encompass protein subunits, drug molecules, oligonucleotides, carbohydrates, and lipids. Under the appropriate conditions, MS can reveal the composition, heterogeneity and dynamics of these protein–ligand interactions, and in some cases their structural arrangements and binding affinities. Herein, we highlight MS approaches for studying protein–ligand complexes, including those containing integral membrane subunits, and showcase examples from recent literature. Specifically, we tabulate the myriad of methodologies, including hydrogen exchange, proteomics, hydroxyl radical footprinting, intact complexes, and crosslinking, which, when combined with MS, provide insights into conformational changes and subtle modifications in response to ligand‐binding interactions.
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48
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Koshy SS, Eyles SJ, Weis RM, Thompson LK. Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes. Biochemistry 2013; 52:8833-42. [PMID: 24274333 DOI: 10.1021/bi401261b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.
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Affiliation(s)
- Seena S Koshy
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Program in Molecular and Cellular Biology, University of Massachusetts , Amherst, Massachusetts 01003, United States
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Mass spectrometry coupled experiments and protein structure modeling methods. Int J Mol Sci 2013; 14:20635-57. [PMID: 24132151 PMCID: PMC3821635 DOI: 10.3390/ijms141020635] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 01/02/2023] Open
Abstract
With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identified as a critical factor in its function. Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change the overall structure. Also, predicted structures are inherently static and do not provide information about structural change over time. It is challenging to address the sensitivity and the dynamics by computational structure predictions alone. However, with the fast development of diverse mass spectrometry coupled experiments, low-resolution but fast and sensitive structural information can be obtained. This information can then be integrated into the structure prediction process to further improve the sensitivity and address the dynamics of the protein structures. For this purpose, this article focuses on reviewing two aspects: the types of mass spectrometry coupled experiments and structural data that are obtainable through those experiments; and the structure prediction methods that can utilize these data as constraints. Also, short review of current efforts in integrating experimental data in the structural modeling is provided.
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50
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Collier TS, Diraviyam K, Monsey J, Shen W, Sept D, Bose R. Carboxyl group footprinting mass spectrometry and molecular dynamics identify key interactions in the HER2-HER3 receptor tyrosine kinase interface. J Biol Chem 2013; 288:25254-25264. [PMID: 23843458 DOI: 10.1074/jbc.m113.474882] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The HER2 receptor tyrosine kinase is a driver oncogene in many human cancers, including breast and gastric cancer. Under physiologic levels of expression, HER2 heterodimerizes with other members of the EGF receptor/HER/ErbB family, and the HER2-HER3 dimer forms one of the most potent oncogenic receptor pairs. Previous structural biology studies have individually crystallized the kinase domains of HER2 and HER3, but the HER2-HER3 kinase domain heterodimer structure has yet to be solved. Using a reconstituted membrane system to form HER2-HER3 kinase domain heterodimers and carboxyl group footprinting mass spectrometry, we observed that HER2 and HER3 kinase domains preferentially form asymmetric heterodimers with HER3 and HER2 monomers occupying the donor and acceptor kinase positions, respectively. Conformational changes in the HER2 activation loop, as measured by changes in carboxyl group labeling, required both dimerization and nucleotide binding but did not require activation loop phosphorylation at Tyr-877. Molecular dynamics simulations on HER2-HER3 kinase dimers identify specific inter- and intramolecular interactions and were in good agreement with MS measurements. Specifically, several intermolecular ionic interactions between HER2 Lys-716-HER3 Glu-909, HER2 Glu-717-HER3 Lys-907, and HER2 Asp-871-HER3 Arg-948 were identified by molecular dynamics. We also evaluated the effect of the cancer-associated mutations HER2 D769H/D769Y, HER3 E909G, and HER3 R948K (also numbered HER3 E928G and R967K) on kinase activity in the context of this new structural model. This study provides valuable insights into the EGF receptor/HER/ErbB kinase structure and interactions, which can guide the design of future therapies.
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Affiliation(s)
| | - Karthikeyan Diraviyam
- the Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109
| | - John Monsey
- From the Division of Oncology, Department of Medicine, and
| | - Wei Shen
- From the Division of Oncology, Department of Medicine, and
| | - David Sept
- the Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109
| | - Ron Bose
- From the Division of Oncology, Department of Medicine, and; the Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110 and.
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