1
|
Hydrogen/deuterium exchange-mass spectrometry of integral membrane proteins in native-like environments: current scenario and the way forward. Essays Biochem 2023; 67:187-200. [PMID: 36876893 PMCID: PMC10070480 DOI: 10.1042/ebc20220173] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 03/07/2023]
Abstract
Integral membrane proteins (IMPs) perform a range of diverse functions and their dysfunction underlies numerous pathological conditions. Consequently, IMPs constitute most drug targets, and the elucidation of their mechanism of action has become an intense field of research. Historically, IMP studies have relied on their extraction from membranes using detergents, which have the potential to perturbate their structure and dynamics. To circumnavigate this issue, an array of membrane mimetics has been developed that aim to reconstitute IMPs into native-like lipid environments that more accurately represent the biological membrane. Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a versatile tool for probing protein dynamics in solution. The continued development of HDX-MS methodology has allowed practitioners to investigate IMPs using increasingly native-like membrane mimetics, and even pushing the study of IMPs into the in vivo cellular environment. Consequently, HDX-MS has come of age and is playing an ever-increasingly important role in the IMP structural biologist toolkit. In the present mini-review, we discuss the evolution of membrane mimetics in the HDX-MS context, focusing on seminal publications and recent innovations that have led to this point. We also discuss state-of-the-art methodological and instrumental advancements that are likely to play a significant role in the generation of high-quality HDX-MS data of IMPs in the future.
Collapse
|
2
|
Tupertsev B, Osipenko S, Kireev A, Nikolaev E, Kostyukevich Y. Simple In Vitro 18O Labeling for Improved Mass Spectrometry-Based Drug Metabolites Identification: Deep Drug Metabolism Study. Int J Mol Sci 2023; 24:ijms24054569. [PMID: 36902002 PMCID: PMC10002766 DOI: 10.3390/ijms24054569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
The identification of drug metabolites formed with different in vitro systems by HPLC-MS is a standard step in preclinical research. In vitro systems allow modeling of real metabolic pathways of a drug candidate. Despite the emergence of various software and databases, identification of compounds is still a complex task. Measurement of the accurate mass, correlation of chromatographic retention times and fragmentation spectra are often insufficient for identification of compounds especially in the absence of reference materials. Metabolites can "slip under the nose", since it is often not possible to reliably confirm that a signal belongs to a metabolite and not to other compounds in complex systems. Isotope labeling has proved to be a tool that aids in small molecule identification. The introduction of heavy isotopes is done with isotope exchange reactions or with complicated synthetic schemes. Here, we present an approach based on the biocatalytic insertion of oxygen-18 isotope under the action of liver microsomes enzymes in the presence of 18O2. Using the local anesthetic bupivacaine as an example, more than 20 previously unknown metabolites were reliably discovered and annotated in the absence of the reference materials. In combination with high-resolution mass spectrometry and modern methods of mass spectrometric metabolism data processing, we demonstrated the ability of the proposed approach to increase the degree of confidence in interpretating metabolism data.
Collapse
Affiliation(s)
- Boris Tupertsev
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
- Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, Institutskiy per., 9, Dolgoprudny, 141701 Moscow, Russia
| | - Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Albert Kireev
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Yury Kostyukevich
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
- Correspondence:
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Möller IR, Merkle PS, Calugareanu D, Comamala G, Schmidt SG, Loland CJ, Rand KD. Probing the conformational impact of detergents on the integral membrane protein LeuT by global HDX-MS. J Proteomics 2020; 225:103845. [PMID: 32480080 DOI: 10.1016/j.jprot.2020.103845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/17/2020] [Accepted: 05/24/2020] [Indexed: 01/11/2023]
Abstract
Neurotransmitter:sodium symporters (NSS) are integral membrane proteins (IMP), responsible for reuptake of neurotransmitters from the synaptic cleft. Due to challenges in production of mammalian NSS in their active form, the prokaryotic hydrophobic amino acid transporter, LeuT, served here as a steadfast model for elucidation of structure-function relationship. As NSS proteins reside within phospholipid bilayer, they require stabilization by artificial membrane systems upon their extraction. Right choice of artificial membrane system is crucial as suboptimal detergent and/or lipids can lead to destabilization or non-native stabilization. Here we study the effect of related detergents, dodecyl maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG), on the conformational dynamics of LeuT by global HDX-MS, in the presence of functionally relevant ligands. We observed that LeuT is more dynamic when solubilized in DDM compared to LMNG. Moreover, LeuT exhibited increased HDX in the presence of K+ compared to Na+, indicating a more dynamic conformation in the presence of K+. Upon addition of leucine, LeuT underwent additional stabilization relative to the Na+-bound state. Finally, peak broadening was observed, suggesting that LeuT undergoes slow unfolding/refolding dynamics in detergent solution. These slow dynamics were verified by local HDX, also proving that detergents modulate the rate of these dynamics. SIGNIFICANCE: Overall, we show the efficacy of global HDX-MS to evaluate the effect of artificial membrane systems on integral membrane proteins and the importance of carefully selecting compatible detergent (and/or lipid) for the solubilization of this class of proteins.
Collapse
Affiliation(s)
- Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Patrick S Merkle
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Dionisie Calugareanu
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Solveig Gaarde Schmidt
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark.
| |
Collapse
|
5
|
Brielle ES, Arkin IT. Site-Specific Hydrogen Exchange in a Membrane Environment Analyzed by Infrared Spectroscopy. J Phys Chem Lett 2018; 9:4059-4065. [PMID: 29957958 DOI: 10.1021/acs.jpclett.8b01675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hydrogen exchange is a powerful method to examine macromolecules. In membrane proteins, exchange can distinguish between solvent-accessible and -inaccessible residues due to shielding by the hydrophobic environment of the lipid bilayer. Herein, rather than examining which residues undergo hydrogen exchange, we employ a protocol that enables the full deuteration of all polar hydrogens in a membrane protein. We then measure the impact of hydrogen exchange on the shift of the amide I vibrational mode of individually labeled sites. The results enable us to correlate polarity with vibrational shifts, thereby providing a powerful tool to examine specific locations within a membrane protein in its native membrane environment.
Collapse
Affiliation(s)
- Esther S Brielle
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Jerusalem 91904 , Israel
| | - Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Jerusalem 91904 , Israel
| |
Collapse
|
6
|
Donnarumma D, Maestri C, Giammarinaro PI, Capriotti L, Bartolini E, Veggi D, Petracca R, Scarselli M, Norais N. Native State Organization of Outer Membrane Porins Unraveled by HDx-MS. J Proteome Res 2018; 17:1794-1800. [PMID: 29619829 DOI: 10.1021/acs.jproteome.7b00830] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Hydrogen-deuterium exchange (HDx) associated with mass spectrometry (MS) is emerging as a powerful tool to provide conformational information about membrane proteins. Unfortunately, as for X-ray diffraction and NMR, HDx performed on reconstituted in vitro systems might not always reflect the in vivo environment. Outer-membrane vesicles naturally released by Escherichia coli were used to carry out analysis of native OmpF through HDx-MS. A new protocol compatible with HDx analysis that avoids hindrance from the lipid contents was setup. The extent of deuterium incorporation was in good agreement with the X-ray diffraction data of OmpF as the buried β-barrels incorporated a low amount of deuterium, whereas the internal loop L3 and the external loops incorporated a higher amount of deuterium. Moreover, the kinetics of incorporation clearly highlights that peptides segregate well in two distinct groups based exclusively on a trimeric organization of OmpF in the membrane: peptides presenting fast kinetics of labeling are facing the complex surrounding environment, whereas those presenting slow kinetics are located in the buried core of the trimer. The data show that HDx-MS applied to a complex biological system is able to reveal solvent accessibility and spatial arrangement of an integral outer-membrane protein complex.
Collapse
|
7
|
Tzitzoglaki C, Wright A, Freudenberger K, Hoffmann A, Tietjen I, Stylianakis I, Kolarov F, Fedida D, Schmidtke M, Gauglitz G, Cross TA, Kolocouris A. Binding and Proton Blockage by Amantadine Variants of the Influenza M2WT and M2S31N Explained. J Med Chem 2017; 60:1716-1733. [DOI: 10.1021/acs.jmedchem.6b01115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christina Tzitzoglaki
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Anna Wright
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Anja Hoffmann
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Ian Tietjen
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ioannis Stylianakis
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - David Fedida
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michaela Schmidtke
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Timothy A. Cross
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
- Department
of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Antonios Kolocouris
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Ioannidis H, Drakopoulos A, Tzitzoglaki C, Homeyer N, Kolarov F, Gkeka P, Freudenberger K, Liolios C, Gauglitz G, Cournia Z, Gohlke H, Kolocouris A. Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J Chem Inf Model 2016; 56:862-76. [DOI: 10.1021/acs.jcim.6b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harris Ioannidis
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Drakopoulos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Christina Tzitzoglaki
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Nadine Homeyer
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Paraskevi Gkeka
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Christos Liolios
- Demokritos, National Center for Scientific Research, 15310 Athens, Greece
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antonios Kolocouris
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Lee SJC, Lee JW, Choi TS, Jin KS, Lee S, Ban C, Kim HI. Probing Conformational Change of Intrinsically Disordered α-Synuclein to Helical Structures by Distinctive Regional Interactions with Lipid Membranes. Anal Chem 2014; 86:1909-16. [DOI: 10.1021/ac404132g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shin Jung C. Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Jong Wha Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Tae Su Choi
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Kyeong Sik Jin
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Seonghwan Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Changill Ban
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Hugh I. Kim
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| |
Collapse
|
12
|
Dunkelberger EB, Woys AM, Zanni MT. 2D IR cross peaks reveal hydrogen-deuterium exchange with single residue specificity. J Phys Chem B 2013; 117:15297-305. [PMID: 23659731 PMCID: PMC3812256 DOI: 10.1021/jp402942s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A form of chemical exchange, hydrogen-deuterium exchange (HDX), has long been used as a method for studying the secondary and tertiary structure of peptides and proteins using mass spectrometry and NMR spectroscopy. Using two-dimensional infrared (2D IR) spectroscopy, we resolve cross peaks between the amide II band and a (13)C(18)O isotope-labeled amide I band, which we show measures HDX with site-specific resolution. By rapidly scanning 2D IR spectra using mid-IR pulse shaping, we monitor the kinetics of HDX exchange on-the-fly. For the antimicrobial peptide ovispirin bound to membrane bilayers, we find that the amide II peak decays with a biexponential with rate constants of 0.54 ± 0.02 and 0.12 ± 0.01 min(-1), which is a measure of the overall HDX in the peptide. The cross peaks between Ile-10-labeled ovispirin and the amide II mode, which specifically monitor HDX kinetics at Ile-10, decay with a single rate constant of 0.36 ± 0.1 min(-1). Comparing this exchange rate to theoretically determined exchange rates of Ile-10 for ovispirin in a solution random coil configuration, the exchange rate at Ile-10 is at least 100 times slower, consistent with the known α-helix structure of ovispirin in bilayers. Because backbone isotope labels produce only a very small shift of the amide II band, site-specific HDX cannot be measured with FTIR spectroscopy, which is why 2D IR spectroscopy is needed for these measurements.
Collapse
Affiliation(s)
| | - Ann Marie Woys
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
| |
Collapse
|
13
|
Hebling CM, Morgan CR, Stafford DW, Jorgenson JW, Rand KD, Engen JR. Conformational analysis of membrane proteins in phospholipid bilayer nanodiscs by hydrogen exchange mass spectrometry. Anal Chem 2010; 82:5415-9. [PMID: 20518534 DOI: 10.1021/ac100962c] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The study of membrane protein structure and enzymology has traditionally been hampered by the inherent insolubility of membrane proteins in aqueous environments and experimental challenges in emulating an in vivo lipid environment. Phospholipid bilayer nanodiscs have recently been shown to be of great use for the study of membrane proteins since they offer a controllable, stable, and monodisperse model membrane with a nativelike lipid bilayer. Here we report the integration of nanodiscs with hydrogen exchange (HX) mass spectrometry (MS) experiments, thereby allowing for analysis of the native conformation of membrane proteins. gamma-Glutamyl carboxylase (GGCX), an approximately 94 kDa transmembrane protein, was inserted into nanodiscs and labeled with deuterium oxide under native conditions. Analytical parameters including sample-handling and chromatographic separation were optimized to measure the incorporation of deuterium into GGCX. Coupling nanodisc technology with HX MS offers an effective approach for investigating the conformation and dynamics of membrane proteins in their native environment and is therefore capable of providing much needed insight into the function of membrane proteins.
Collapse
Affiliation(s)
- Christine M Hebling
- Department of Chemistry, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | | | | | | | | | |
Collapse
|
14
|
Chitta RK, Rempel DL, Gross ML. The gramicidin dimer shows both EX1 and EX2 mechanisms of H/D exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1813-1820. [PMID: 19631556 PMCID: PMC2767204 DOI: 10.1016/j.jasms.2009.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 05/08/2009] [Accepted: 05/28/2009] [Indexed: 05/28/2023]
Abstract
We describe the use of H/D amide exchange and electrospray ionization mass spectrometry to study, in organic solvents, the pentadecapeptide gramicidin as a model for protein self association. In methanol-OD, all active H's in the peptide exchange for D within 5 min, indicating a monomer/dimer equilibrium that is shifted towards the fast-exchanging monomer. H/D exchange in n-propanol-OD, however, showed a partially protected gramicidin that slowly converts to a second species that exchanges nearly all the active hydrogens, indicating EX1 kinetics for the H/D exchange. We propose that this behavior is the result of the slower rate of unfolding in n-propanol compared with that in methanol. The rate constant for the unfolding of the dimer is the rate of disappearance of the partially protected species, and it agrees within a factor of two with a value reported in literature. The rate constant of dimer refolding can be determined from the ratio of the rate constant for unfolding and the affinity constant for the dimer, which we determined in an earlier study. The unfolding activation energy is 20 kcal mol(-1), determined by performing the exchange experiments as a function of temperature. To study gramicidin in an even more hydrophobic medium than n-propanol, we measured its H/D exchange kinetics in a phospholipids vesicle and found a different H/D amide exchange behavior. Gramicidin is an unusual peptide dimer that can exhibit both EX1 and EX2 mechanisms for its H/D exchange, depending on the solvent.
Collapse
Affiliation(s)
- Raghu K Chitta
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | | | | |
Collapse
|
15
|
Langosch D, Arkin IT. Interaction and conformational dynamics of membrane-spanning protein helices. Protein Sci 2009; 18:1343-58. [PMID: 19530249 PMCID: PMC2775205 DOI: 10.1002/pro.154] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/19/2009] [Accepted: 04/20/2009] [Indexed: 12/23/2022]
Abstract
Within 1 or 2 decades, the reputation of membrane-spanning alpha-helices has changed dramatically. Once mostly regarded as dull membrane anchors, transmembrane domains are now recognized as major instigators of protein-protein interaction. These interactions may be of exquisite specificity in mediating assembly of stable membrane protein complexes from cognate subunits. Further, they can be reversible and regulatable by external factors to allow for dynamic changes of protein conformation in biological function. Finally, these helices are increasingly regarded as dynamic domains. These domains can move relative to each other in different functional protein conformations. In addition, small-scale backbone fluctuations may affect their function and their impact on surrounding lipid shells. Elucidating the ways by which these intricate structural features are encoded by the amino acid sequences will be a fascinating subject of research for years to come.
Collapse
Affiliation(s)
- Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.
| | | |
Collapse
|
16
|
Monson de Souza B, Palma MS. Monitoring the positioning of short polycationic peptides in model lipid bilayers by combining hydrogen/deuterium exchange and electrospray ionization mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2797-805. [DOI: 10.1016/j.bbamem.2008.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 09/11/2008] [Accepted: 09/12/2008] [Indexed: 11/16/2022]
|
17
|
Hansen RK, Zhai S, Skepper JN, Johnston MD, Alpar HO, Slater NKH. Mechanisms of Inactivation of HSV-2 during Storage in Frozen and Lyophilized Forms. Biotechnol Prog 2008; 21:911-7. [PMID: 15932273 DOI: 10.1021/bp049601a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural integrity of herpes simplex virus 2 (HSV-2) during freezing, thawing, and lyophilization has been studied using scanning and transmission electron microscopy. Viral particles should be thawed quickly from -80 to 37 degrees C to avoid artifacts of thawing. To avoid freezing damage, the virus should be rapidly frozen (>20 K s(-1)) rather than slowly frozen as occurs on the shelf of a lyophilizer (<1 K s(-1)). Fast freezing and thawing allows six cycles of freeze thaw with no loss of viral titer TCID50. Viral particles were characterized using immunogold labeling methods. Freshly thawed virus had 19 +/- 4 polyclonal immunogold particles virus(-1); virus stored at -80 degrees C for at least 4 months had 17 +/- 3 particles virus(-1); virus stored for 1 week at 4 degrees C had 8 +/- 4 particles virus(-1). By bulk lyophilization the number of particles was 4 +/- 4, but by fast freezing and lyophilization the number of gold particles improved to 12 +/- 5. The loss of viral membrane was directly observed, and the in vitro loss was demonstrated to occur through three possible pathways, including (i) simultaneous release of tegument and membrane, (ii) sequential release of membrane and then tegument, and (iii) release like by in vivo infection. The capsids were not further degraded as indicated by the lack of free DNA, which was only released by boiling the viral samples with 1% SDS, followed by a dilution to 0.001% w/v SDS for the real-time PCR reaction.
Collapse
Affiliation(s)
- Raino K Hansen
- Department of Chemical Engineering, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | | | | | | | | | | |
Collapse
|
18
|
Yano Y, Ogura M, Matsuzaki K. Measurement of thermodynamic parameters for hydrophobic mismatch 2: intermembrane transfer of a transmembrane helix. Biochemistry 2006; 45:3379-85. [PMID: 16519532 DOI: 10.1021/bi052286w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic matching between proteins and lipids is essential for the thermodynamic stability of integral membrane proteins. However, there is no direct thermodynamic information available about the intermembrane transfer of proteins between membranes with different hydrophobic thicknesses, which is crucial for understanding hydrophobic mismatch. This article reports the complete set of thermodynamic parameters (DeltaG, DeltaH, DeltaS, and DeltaC(p)) for the intermembrane transfer of the inert hydrophobic model transmembrane helix NBD-(AALALAA)(3)-NH(2) (NBD: 7-nitro-2-1,3-benzoxadiazol-4-yl), which is exchangeable between vesicles, from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) to dimonounsaturated-phosphocholine lipid bilayers with different hydrophobic thicknesses (C14-C22) at 37-58 degrees C. The transfer free energies were calculated from equilibrium values of the extent of helix transfer from donor to acceptor lipid vesicles, as monitored by a decrease in fluorescence resonance energy transfer from the NBD group to a lipid-labeled Rhodamine in the donor upon transfer to the quencher-free acceptor. Under hydrophobic mismatch conditions up to approximately 7 A, the helix partitioning became unfavorable up to +7 kJ mol(-)(1), hampered by an increase in entropic (up to +20 kJ mol(-)(1)) and enthalpic (up to +66 kJ mol(-)(1)) terms in thinner and thicker membranes, respectively. Together with the results that H/D exchange at the membrane interface was accelerated in thinner membranes the obtained thermodynamic parameters were reasonably explained assuming that hydrophobic mismatch induces aqueous exposure or membrane burial of the helix termini, resulting in excess energies originating from the hydration of terminal hydrophobic residues or the unfavorable Born energy of terminal partial charges of the helix macrodipole.
Collapse
Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | | | | |
Collapse
|
19
|
Busenlehner LS, Armstrong RN. Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch Biochem Biophys 2005; 433:34-46. [PMID: 15581564 DOI: 10.1016/j.abb.2004.09.002] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 09/02/2004] [Indexed: 11/25/2022]
Abstract
Conformational changes and protein dynamics play an important role in the catalytic efficiency of enzymes. Amide H/D exchange mass spectrometry (H/D exchange MS) is emerging as an efficient technique to study the local and global changes in protein structure and dynamics due to ligand binding, protein activation-inactivation by modification, and protein-protein interactions. By monitoring the selective exchange of hydrogen for deuterium along a peptide backbone, this sensitive technique probes protein motions and structural elements that may be relevant to allostery and function. In this report, several applications of H/D exchange MS are presented which demonstrate the unique capability of amide hydrogen/deuterium exchange mass spectrometry for examining dynamic and structural changes associated with enzyme catalysis.
Collapse
Affiliation(s)
- Laura S Busenlehner
- Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0416, USA.
| | | |
Collapse
|
20
|
Kolocouris A, Hansen RK, Broadhurst RW. Interaction between an amantadine analogue and the transmembrane portion of the influenza A M2 protein in liposomes probed by 1H NMR spectroscopy of the ligand. J Med Chem 2004; 47:4975-8. [PMID: 15369403 DOI: 10.1021/jm0496685] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1H NMR spectroscopy of a fluoroamantadine ligand was used to probe the pH dependence of binding to the transmembrane peptide fragment of the influenza A M2 proton channel (M2TM) incorporated into 1,2-dimyristoyl-sn-glycero-3-phosphocholine liposomes. Above pH 7.5, when M2TM bound the ligand, fluoroamantadine resonances became too broad to be detected. Fluoroamantadine interacted weakly with the liposomes, indicating it may first bind to the bilayer and then block target channels after diffusion across the membrane surface.
Collapse
Affiliation(s)
- Antonios Kolocouris
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimioupolis, Zografou, Athens 15 771, Greece
| | | | | |
Collapse
|
21
|
Williams DH, O'Brien DP, Sandercock AM, Stephens E. Order Changes within Receptor Systems upon Ligand Binding: Receptor Tightening/Oligomerisation and the Interpretation of Binding Parameters. J Mol Biol 2004; 340:373-83. [PMID: 15201058 DOI: 10.1016/j.jmb.2004.04.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Revised: 04/23/2004] [Accepted: 04/23/2004] [Indexed: 10/26/2022]
Abstract
Recent hydrogen-deuterium exchange experiments have highlighted tightening and loosening of protein structures upon ligand binding, with changes in bonding (DeltaH) and order (DeltaS) which contribute to the overall thermodynamics of ligand binding. Tightening and loosening show that ligand binding respectively stabilises or destabilises the internal structure of the protein, i.e. it shows positive or negative cooperativity between ligand binding and the receptor structure. In the case of membrane-bound receptors, such as G protein-coupled receptors (GPCRs) and ligand gated ion channel receptors (LGICRs), most binding studies have focussed on association/dissociation constants. Where these have been broken down into enthalpic and entropic contributions, the phenomenon of "thermodynamic discrimination" between antagonists and agonists has often been noted; e.g. for a receptor where agonist binding is predominantly enthalpy driven, antagonist binding is predominantly entropy driven and vice versa. These data have not previously been considered in terms of the tightening, or loosening, of receptor structures that respectively occurs upon positively, or negatively, cooperative binding of ligand. Nor have they been considered in light of the homo- and hetero-oligomerisation of GPCRs and the possibility of ligand-induced changes in oligomerisation. Here, we argue that analysis of the DeltaH and DeltaS of ligand binding may give useful information on ligand-induced changes in membrane-bound receptor oligomers, relevant to the differing effects of agonists and antagonists.
Collapse
Affiliation(s)
- Dudley H Williams
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | | | | | | |
Collapse
|
22
|
Garcia RA, Pantazatos D, Villarreal FJ. Hydrogen/Deuterium Exchange Mass Spectrometry for Investigating Protein-Ligand Interactions. Assay Drug Dev Technol 2004; 2:81-91. [PMID: 15090213 DOI: 10.1089/154065804322966342] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Amide hydrogen/deuterium exchange mass spectrometry is rapidly becoming a powerful method for high-resolution analyses of protein dynamics, structure, and function. Hydrogen/deuterium exchange approaches can provide information that greatly augments and refines information derived from high-resolution structural studies, and can provide detailed information on native protein structure when structural information is unavailable. Application of this method for rapid analyses of protein-ligand complexes could prove useful for studies of important disease-related protein complexes. The following review covers fundamentals of hydrogen/deuterium exchange and its applications to the study of protein-ligand complexes. In addition, hydrogen/deuterium exchange mass spectrometry studies on a protein-inhibitor complex are presented.
Collapse
Affiliation(s)
- Ricardo A Garcia
- Department of Medicine, University of California, San Diego, CA 92093-0613, USA.
| | | | | |
Collapse
|
23
|
Leite JF, Dougherty DA, Lester HA, Shahgholi M. Investigation of apparent mass deviations in electrospray ionization tandem mass spectrometry of a benzophenone-labeled peptide. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1677-1684. [PMID: 12872270 DOI: 10.1002/rcm.1103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In a previous study utilizing benzophenone-based topological probes to study conformationally dependent changes in mouse muscle nicotinic acetylcholine receptor (nAChR) topology, electrospray ionization tandem mass spectrometric (ESI-MS/MS) analysis led to a consistent -2.0 Da mass deviation from expected values. In the present study a synthetic peptide, corresponding to nAChR alpha1 subunit residues 130-139, was photolabeled. MS/MS analysis of this peptide using an ion trap confirmed the previously observed mass deviation, associated only with fragment ions that contain the incorporated benzophenone moiety. Analysis of peak profiles for the photolabeled ions does not indicate the typical 'peak fronting' that produces a mass shift when labile ions are prematurely ejected from the ion trap. Rather, hydrogen/deuterium (H/D) exchange experiments support the hypothesis that a chemical rearrangement involving phenyl migration and ketone formation has formed an unexpected oxidized peptide, with molecular mass 2 Da less than that expected, that is isolated for collision-induced dissociation in the ion trap together with the predicted precursor due to the broad ion isolation window specified.
Collapse
Affiliation(s)
- John F Leite
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
| | | | | | | |
Collapse
|