1
|
Xiao P, Drewniak P, Dingwell DA, Brown LS, Ladizhansky V. Probing the energy barriers and stages of membrane protein unfolding using solid-state NMR spectroscopy. SCIENCE ADVANCES 2024; 10:eadm7907. [PMID: 38758787 DOI: 10.1126/sciadv.adm7907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.
Collapse
Affiliation(s)
- Peng Xiao
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Philip Drewniak
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Dylan Archer Dingwell
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| |
Collapse
|
2
|
Xu G, Cheng K, Liu M, Li C. Studying protein stability in crowded environments by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2024; 140-141:42-48. [PMID: 38705635 DOI: 10.1016/j.pnmrs.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/07/2024]
Abstract
Most proteins perform their functions in crowded and complex cellular environments where weak interactions are ubiquitous between biomolecules. These complex environments can modulate the protein folding energy landscape and hence affect protein stability. NMR is a nondestructive and effective method to quantify the kinetics and equilibrium thermodynamic stability of proteins at an atomic level within crowded environments and living cells. Here, we review NMR methods that can be used to measure protein stability, as well as findings of studies on protein stability in crowded environments mimicked by polymer and protein crowders and in living cells. The important effects of chemical interactions on protein stability are highlighted and compared to spatial excluded volume effects.
Collapse
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Luebbers A, Gonzalez-Hernandez AJ, Zhou M, Eyles SJ, Levitz J, Garcia-Marcos M. Dissecting the molecular basis for the modulation of neurotransmitter GPCR signaling by GINIP. Structure 2024; 32:47-59.e7. [PMID: 37989308 PMCID: PMC10872408 DOI: 10.1016/j.str.2023.10.010] [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: 05/04/2023] [Revised: 09/23/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023]
Abstract
It is well established that G-protein-coupled receptors (GPCRs) stimulated by neurotransmitters are critical for neuromodulation. Much less is known about how heterotrimeric G-protein (Gαβγ) regulation after receptor-mediated activation contributes to neuromodulation. Recent evidence indicates that the neuronal protein GINIP shapes GPCR inhibitory neuromodulation via a unique mechanism of G-protein regulation that controls pain and seizure susceptibility. However, the molecular basis of this mechanism remains ill-defined because the structural determinants of GINIP responsible for binding and regulating G proteins are not known. Here, we combined hydrogen-deuterium exchange mass spectrometry, computational structure predictions, biochemistry, and cell-based biophysical assays to demonstrate an effector-like binding mode of GINIP to Gαi. Specific amino acids of GINIP's PHD domain first loop are essential for G-protein binding and subsequent regulation of Gαi-GTP and Gβγ signaling upon neurotransmitter GPCR stimulation. In summary, these findings shed light onto the molecular basis for a post-receptor mechanism of G-protein regulation that fine-tunes inhibitory neuromodulation.
Collapse
Affiliation(s)
- Alex Luebbers
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | | | - Myles Zhou
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10064, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mikel Garcia-Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02115, USA.
| |
Collapse
|
5
|
Largy E, Ranz M, Gabelica V. A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA. J Am Chem Soc 2023; 145:26843-26857. [PMID: 38044563 DOI: 10.1021/jacs.3c09365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging, because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize the G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in the inner and outer tetrads. We also established relationships among exchange rates, numbers of tetrads and bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.
Collapse
Affiliation(s)
- Eric Largy
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Matthieu Ranz
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
6
|
Jethva PN, Gross ML. Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1118749. [PMID: 37746528 PMCID: PMC10512744 DOI: 10.3389/frans.2023.1118749] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.
Collapse
Affiliation(s)
- Prashant N. Jethva
- Department of Chemistry, 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
| |
Collapse
|
7
|
Luebbers A, Zhou M, Eyles SJ, Garcia-Marcos M. Dissecting the molecular basis for the modulation of neurotransmitter GPCR signaling by GINIP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537566. [PMID: 37131787 PMCID: PMC10153262 DOI: 10.1101/2023.04.20.537566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is well-established that activation of heterotrimeric G-proteins (Gαβγ) by G-protein-coupled receptors (GPCRs) stimulated by neurotransmitters is a key mechanism underlying neuromodulation. Much less is known about how G-protein regulation after receptor-mediated activation contributes to neuromodulation. Recent evidence indicates that the neuronal protein GINIP shapes GPCR inhibitory neuromodulation via a unique mechanism of G-protein regulation that controls neurological processes like pain and seizure susceptibility. However, the molecular basis of this mechanism remains ill-defined because the structural determinants of GINIP responsible for binding Gαi subunits and regulating G-protein signaling are not known. Here, we combined hydrogen-deuterium exchange mass-spectrometry, protein folding predictions, bioluminescence resonance energy transfer assays, and biochemical experiments to identify the first loop of the PHD domain of GINIP as an obligatory requirement for Gαi binding. Surprisingly, our results support a model in which GINIP undergoes a long-range conformational change to accommodate Gαi binding to this loop. Using cell-based assays, we demonstrate that specific amino acids in the first loop of the PHD domain are essential for the regulation of Gαi-GTP and free Gβγ signaling upon neurotransmitter GPCR stimulation. In summary, these findings shed light onto the molecular basis for a post-receptor mechanism of G-protein regulation that fine-tunes inhibitory neuromodulation.
Collapse
Affiliation(s)
- Alex Luebbers
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Myles Zhou
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Mikel Garcia-Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02115, USA
| |
Collapse
|
8
|
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
|
9
|
Pastore A, Temussi PA. Crowding revisited: Open questions and future perspectives. Trends Biochem Sci 2022; 47:1048-1058. [PMID: 35691783 DOI: 10.1016/j.tibs.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/12/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Although biophysical studies have traditionally been performed in diluted solutions, it was pointed out in the late 1990s that the cellular milieu contains several other macromolecules, creating a condition of molecular crowding. How crowding affects protein stability is an important question heatedly discussed over the past 20 years. Theoretical estimations have suggested a 5-20°C effect of fold stabilisation. This estimate, however, is at variance with what has been verified experimentally that proposes only a limited increase of stability, opening the question whether some of the assumptions taken for granted should be reconsidered. The present review critically analyses the causes of this discrepancy and discusses the limitations and implications of the current concept of crowding.
Collapse
Affiliation(s)
- Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| |
Collapse
|
10
|
Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
Collapse
Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
| |
Collapse
|
11
|
Kampmeyer C, Larsen-Ledet S, Wagnkilde MR, Michelsen M, Iversen HKM, Nielsen SV, Lindemose S, Caregnato A, Ravid T, Stein A, Teilum K, Lindorff-Larsen K, Hartmann-Petersen R. Disease-linked mutations cause exposure of a protein quality control degron. Structure 2022; 30:1245-1253.e5. [PMID: 35700725 DOI: 10.1016/j.str.2022.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/08/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
More than half of disease-causing missense variants are thought to lead to protein degradation, but the molecular mechanism of how these variants are recognized by the cell remains enigmatic. Degrons are stretches of amino acids that help mediate recognition by E3 ligases and thus confer protein degradation via the ubiquitin-proteasome system. While degrons that mediate controlled degradation of, for example, signaling components and cell-cycle regulators are well described, so-called protein-quality-control degrons that mediate the degradation of destabilized proteins are poorly understood. Here, we show that disease-linked dihydrofolate reductase (DHFR) missense variants are structurally destabilized and chaperone-dependent proteasome targets. We find two regions in DHFR that act as degrons, and the proteasomal turnover of one of these was dependent on the molecular chaperone Hsp70. Structural analyses by nuclear magnetic resonance (NMR) and hydrogen/deuterium exchange revealed that this degron is buried in wild-type DHFR but becomes transiently exposed in the disease-linked missense variants.
Collapse
Affiliation(s)
- Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Sven Larsen-Ledet
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Morten Rose Wagnkilde
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mathias Michelsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Henriette K M Iversen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Søren Lindemose
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Alberto Caregnato
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, 91904 Jerusalem, Israel
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Kaare Teilum
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| |
Collapse
|
12
|
Gamage CLD, Weis DD, Walters BT. Identification of Agitation-induced Unfolding Events Causing Aggregation of Monoclonal Antibodies Using Hydrogen Exchange-Mass Spectrometry. J Pharm Sci 2022; 111:2210-2216. [DOI: 10.1016/j.xphs.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
|
13
|
Native State Hydrogen Exchange-Mass Spectrometry Methods to Probe Protein Folding and Unfolding. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2376:143-159. [PMID: 34845608 DOI: 10.1007/978-1-0716-1716-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Native state hydrogen exchange (HX) methods provide high-resolution structural data on the rare and transient opening motions in proteins under native conditions. Mass spectrometry-based HX methods (HX-MS) have gained popularity because of their ability to delineate population distributions, which allow a direct determination of the mechanism of inter conversion of the partially folded states under native conditions. Various technological advancements have provided further impetus to the development of HX-MS-based experiments to study protein folding. Classical HX-MS studies use proteolytic digestion to produce fragments of the protein subsequent to HX in solution, in order to obtain structural data. New chemical fragmentation methods, which achieve the same result as proteolysis and cause minimal change to the HX pattern in the protein, provide an attractive alternative to proteolysis. Moreover, when used in conjunction with proteolysis, chemical fragmentation methods have significantly increased the structural resolution afforded by HX-MS studies, even bringing them at par with the single amino acid resolution observed in NMR-based measurements. Experiments based on one such chemical fragmentation method, electron transfer dissociation (ETD), are described in this chapter. The ETD HX-MS method is introduced using data from a protein which is inherently resistant to proteolytic digestion as example of how such an experiment can provide high-resolution structural data on the folding-unfolding transitions of the protein under native conditions.
Collapse
|
14
|
Using hydrogen-deuterium exchange mass spectrometry to characterize Mtr4 interactions with RNA. Methods Enzymol 2022; 673:475-516. [PMID: 35965017 DOI: 10.1016/bs.mie.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) is a valuable technique to investigate the dynamics of protein systems. The approach compares the deuterium uptake of protein backbone amides under multiple conditions to characterize protein conformation and interaction. HDX-MS is versatile and can be applied to diverse ligands, however, challenges remain when it comes to exploring complexes containing nucleic acids. In this chapter, we present procedures for the optimization and application of HDX-MS to studying RNA-binding proteins and use the RNA helicase Mtr4 as a demonstrative example. We highlight considerations in designing on-exchange, bottom-up, comparative studies on proteins with RNA. Our protocol details preliminary testing and optimization of experimental parameters. Difficulties arising from the inclusion of RNA, such as signal repression and sample carryover, are addressed. We discuss how chromatography parameters can be adjusted depending on the issues presented by the RNA, emphasizing reproducible peptide recovery in the absence and presence of RNA. Methods for visualization of HDX data integrated with statistical analysis are also reviewed with examples. These protocols can be applied to future studies of various RNA-protein complexes.
Collapse
|
15
|
Hamuro Y. Quantitative Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2711-2727. [PMID: 34749499 DOI: 10.1021/jasms.1c00216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This Account describes considerations for the data generation, data analysis, and data interpretation of a hydrogen/deuterium exchange-mass spectrometry (HDX-MS) experiment to have a quantitative argument. Although HDX-MS has gained its popularity as a biophysical tool, the argument from its data often remains qualitative. To generate HDX-MS data that are more suitable for a quantitative argument, the sequence coverage and sequence resolution should be optimized during the feasibility stage, and the time window coverage and time window resolution should be improved during the HDX stage. To extract biophysically meaningful values for a certain perturbation from medium-resolution HDX-MS data, there are two major ways: (i) estimating the area between the two deuterium buildup curves using centroid values with and without the perturbation when plotted against log time scale and (ii) dissecting into multiple single-exponential curves using the isotope envelopes. To have more accurate arguments for an HDX-MS perturbation study, (i) false negatives due to sequence coverage, (ii) false negatives due to time window coverage, (iii) false positives due to sequence resolution, and (iv) false positives due to allosteric effects should be carefully examined.
Collapse
Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
| |
Collapse
|
16
|
Plessa E, Chu LP, Chan SHS, Thomas OL, Cassaignau AME, Waudby CA, Christodoulou J, Cabrita LD. Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein. Nat Commun 2021; 12:6447. [PMID: 34750347 PMCID: PMC8576036 DOI: 10.1038/s41467-021-26531-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/01/2021] [Indexed: 01/16/2023] Open
Abstract
During biosynthesis, proteins can begin folding co-translationally to acquire their biologically-active structures. Folding, however, is an imperfect process and in many cases misfolding results in disease. Less is understood of how misfolding begins during biosynthesis. The human protein, alpha-1-antitrypsin (AAT) folds under kinetic control via a folding intermediate; its pathological variants readily form self-associated polymers at the site of synthesis, leading to alpha-1-antitrypsin deficiency. We observe that AAT nascent polypeptides stall during their biosynthesis, resulting in full-length nascent chains that remain bound to ribosome, forming a persistent ribosome-nascent chain complex (RNC) prior to release. We analyse the structure of these RNCs, which reveals compacted, partially-folded co-translational folding intermediates possessing molten-globule characteristics. We find that the highly-polymerogenic mutant, Z AAT, forms a distinct co-translational folding intermediate relative to wild-type. Its very modest structural differences suggests that the ribosome uniquely tempers the impact of deleterious mutations during nascent chain emergence. Following nascent chain release however, these co-translational folding intermediates guide post-translational folding outcomes thus suggesting that Z's misfolding is initiated from co-translational structure. Our findings demonstrate that co-translational folding intermediates drive how some proteins fold under kinetic control, and may thus also serve as tractable therapeutic targets for human disease.
Collapse
Affiliation(s)
- Elena Plessa
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Lien P Chu
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Oliver L Thomas
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. .,School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
17
|
Scrosati PM, Yin V, Konermann L. Hydrogen/Deuterium Exchange Measurements May Provide an Incomplete View of Protein Dynamics: a Case Study on Cytochrome c. Anal Chem 2021; 93:14121-14129. [PMID: 34644496 DOI: 10.1021/acs.analchem.1c02471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many aspects of protein function rely on conformational fluctuations. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) provides a window into these dynamics. Despite the widespread use of HDX-MS, it remains unclear whether this technique provides a truly comprehensive view of protein dynamics. HDX is mediated by H-bond-opening/closing events, implying that HDX methods provide an H-bond-centric view. This raises the question if there could be fluctuations that leave the H-bond network unaffected, thereby rendering them undetectable by HDX-MS. We explore this issue in experiments on cytochrome c (cyt c). Compared to the Fe(II) protein, Fe(III) cyt c shows enhanced deuteration on both the distal and proximal sides of the heme. Previous studies have attributed the enhanced dynamics of Fe(III) cyt c to the facile and reversible rupture of the distal M80-Fe(III) bond. Using molecular dynamics (MD) simulations, we conducted a detailed analysis of various cyt c conformers. Our MD data confirm that rupture of the M80-Fe(III) contact triggers major reorientation of the distal Ω loop. Surprisingly, this event takes place with only miniscule H-bonding alterations. In other words, the distal loop dynamics are almost "HDX-silent". Moreover, distal loop movements cannot account for enhanced dynamics on the opposite (proximal) side of the heme. Instead, enhanced deuteration of Fe(III) cyt c is attributed to sparsely populated conformers where both the distal (M80) and proximal (H18) coordination bonds have been ruptured, along with opening of numerous H-bonds on both sides of the heme. We conclude that there can be major structural fluctuations that are only weakly coupled to changes in H-bonding, making them virtually impossible to track by HDX-MS. In such cases, HDX-MS may provide an incomplete view of protein dynamics.
Collapse
Affiliation(s)
- Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
18
|
Crilly CJ, Eicher JE, Warmuth O, Atkin JM, Pielak GJ. Water's Variable Role in Protein Stability Uncovered by Liquid-Observed Vapor Exchange NMR. Biochemistry 2021; 60:3041-3045. [PMID: 34596383 DOI: 10.1021/acs.biochem.1c00552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is essential to protein structure and stability, yet our understanding of how water shapes proteins is far from thorough. Our incomplete knowledge of protein-water interactions is due in part to a long-standing technological inability to assess experimentally how water removal impacts local protein structure. It is now possible to obtain residue-level information on dehydrated protein structures via liquid-observed vapor exchange (LOVE) NMR, a solution NMR technique that quantifies the extent of hydrogen-deuterium exchange between unprotected amide protons of a dehydrated protein and D2O vapor. Here, we apply LOVE NMR, Fourier transform infrared spectroscopy, and solution hydrogen-deuterium exchange to globular proteins GB1, CI2, and two variants thereof to link mutation-induced changes in the dehydrated protein structure to changes in solution structure and stability. We find that a mutation that destabilizes GB1 in solution does not affect its dehydrated structure, whereas a mutation that stabilizes CI2 in solution makes several regions of the protein more susceptible to dehydration-induced unfolding, suggesting that water is primarily responsible for the destabilization of the GB1 variant but plays a stabilizing role in the CI2 variant. Our results indicate that changes in dehydrated protein structure cannot be predicted from changes in solution stability alone and demonstrate the ability of LOVE NMR to uncover the variable role of water in protein stability. Further application of LOVE NMR to other proteins and their variants will improve the ability to predict and modulate protein structure and stability in both the hydrated and dehydrated states for applications in medicine and biotechnology.
Collapse
Affiliation(s)
- Candice J Crilly
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina 27599-3290, United States
| | - Jonathan E Eicher
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina 27599-3290, United States
| | - Owen Warmuth
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina 27599-3290, United States
| | - Joanna M Atkin
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina 27599-3290, United States
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina 27599-3290, United States.,Department of Biochemistry & Biophysics, UNC-CH, Chapel Hill, North Carolina 27599, United States.,Lineberger Cancer Center, UNC-CH, Chapel Hill, North Carolina 27599, United States.,Integrative Program for Biological and Genome Sciences, UNC-CH, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
19
|
Smit JH, Krishnamurthy S, Srinivasu BY, Parakra R, Karamanou S, Economou A. Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal Chem 2021; 93:12840-12847. [PMID: 34523340 DOI: 10.1021/acs.analchem.1c02155] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allosteric networks. However, identification, interpretation, and visualization of such events from HDX-MS data sets is challenging as these data sets consist of many individual data points collected across peptides, time points, and experimental conditions. Here, we present PyHDX, an open-source Python package and webserver, that allows the user to batch extract the universal quantity Gibbs free energy at residue levels over multiple protein conditions and homologues. The output is directly visualized on a linear map or 3D structures or is exported as .csv files or PyMOL scripts.
Collapse
Affiliation(s)
- Jochem H Smit
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Bindu Y Srinivasu
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Rinky Parakra
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
20
|
Politou AS, Pastore A, Temussi PA. An "Onion-like" Model of Protein Unfolding: Collective versus Site Specific Approaches. Chemphyschem 2021; 23:e202100520. [PMID: 34549492 DOI: 10.1002/cphc.202100520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/09/2021] [Indexed: 11/10/2022]
Abstract
Approximating protein unfolding by an all-or-none cooperative event is a convenient assumption that can provide precious global information on protein stability. It is however quickly emerging that the scenario is far more complex and that global denaturation curves often hide a rich heterogeneity of states that are largely probe dependent. In this review, we revisit the importance of gaining site-specific information on the unfolding process. We focus on nuclear magnetic resonance, as this is the main technique able to provide site-specific information. We review historical and most modern approaches that have allowed an appreciable advancement of the field of protein folding. We also demonstrate how unfolding is a reporter dependent event, suggesting the outmost importance of selecting the reporter carefully.
Collapse
Affiliation(s)
- Anastasia S Politou
- Faculty of Medicine, University of Ioannina.,Institute of Molecular Biology and Biotechnology-FORTH, Ioannina, Greece
| | - Annalisa Pastore
- UK Dementia Research Institute at the, Maurice Wohl Institute of King's College London, 5 Cutcombe Rd, London, SE5 9RT, United Kingdom
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the, Maurice Wohl Institute of King's College London, 5 Cutcombe Rd, London, SE5 9RT, United Kingdom
| |
Collapse
|
21
|
Rumfeldt J, Kurttila M, Takala H, Ihalainen JA. The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study. Photochem Photobiol Sci 2021; 20:1173-1181. [PMID: 34460093 DOI: 10.1007/s43630-021-00090-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
Solvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation state of the biliverdin chromophore from Deinococcus radiodurans bacteriophytchrome, and thus, the pH of the surrounding solution, is determined. The observed absorbance changes are related to the solvent access of the chromophore binding pocket, gated by the hairpin extension. We therefore propose a model with an "open" (solvent-exposed, deprotonation-active on a (sub)second time-scale) state and a "closed" (solvent-gated, deprotonation inactive) state, where the hairpin fluctuates slowly between these conformations thereby controlling the deprotonation process of the chromophore on a minute time scale. When the connection between the hairpin and the biliverdin surroundings is destabilized by a point mutation, the amplitude of the deprotonation phase increases considerably. In the absence of the extension, the chromophore deprotonates essentially without any "gating". Hence, we introduce a straightforward method to study the stability and fluctuation of the phytochrome hairpin in its photostationary state. This approach can be extended to other chromophore-protein systems where absorption changes reflect dynamic processes of the protein.
Collapse
Affiliation(s)
- Jessica Rumfeldt
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Moona Kurttila
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Heikki Takala
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
| |
Collapse
|
22
|
Dass R, Corlianò E, Mulder FAA. The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophys J 2021; 120:4107-4114. [PMID: 34370996 PMCID: PMC8510857 DOI: 10.1016/j.bpj.2021.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/20/2021] [Accepted: 08/03/2021] [Indexed: 12/03/2022] Open
Abstract
Although electrostatics have long been recognized to play an important role in hydrogen exchange (HX) with solvent, the quantitative assessment of its magnitude in the unfolded state has hitherto been lacking. This limits the utility of HX as a quantitative method to study protein stability, folding, and dynamics. Using the intrinsically disordered human protein α-synuclein as a proxy for the unfolded state, we show that a hybrid mean-field approach can effectively compute the electrostatic potential at all backbone amide positions along the chain. From the electrochemical potential, a fourfold reduction in hydroxide concentration near the protein backbone is predicted for the C-terminal domain, a prognosis that is in direct agreement with experimentally derived protection factors from NMR spectroscopy. Thus, impeded HX for the C-terminal region of α-synuclein is not the result of intramolecular hydrogen bonding and/or structure formation.
Collapse
Affiliation(s)
- Rupashree Dass
- Department of Chemistry and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Enrico Corlianò
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
23
|
Otzen DE, Pedersen JN, Somavarapu AK, Clement A, Ji M, Petersen EH, Pedersen JS, Urban S, Schafer NP. Cys-labeling kinetics of membrane protein GlpG: a role for specific SDS binding and micelle changes? Biophys J 2021; 120:4115-4128. [PMID: 34370995 DOI: 10.1016/j.bpj.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/20/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
Empirically, α-helical membrane protein folding stability in surfactant micelles can be tuned by varying the mole fraction MFSDS of anionic (sodium dodecyl sulfate (SDS)) relative to nonionic (e.g., dodecyl maltoside (DDM)) surfactant, but we lack a satisfying physical explanation of this phenomenon. Cysteine labeling (CL) has thus far only been used to study the topology of membrane proteins, not their stability or folding behavior. Here, we use CL to investigate membrane protein folding in mixed DDM-SDS micelles. Labeling kinetics of the intramembrane protease GlpG are consistent with simple two-state unfolding-and-exchange rates for seven single-Cys GlpG variants over most of the explored MFSDS range, along with exchange from the native state at low MFSDS (which inconveniently precludes measurement of unfolding kinetics under native conditions). However, for two mutants, labeling rates decline with MFSDS at 0-0.2 MFSDS (i.e., native conditions). Thus, an increase in MFSDS seems to be a protective factor for these two positions, but not for the five others. We propose different scenarios to explain this and find the most plausible ones to involve preferential binding of SDS monomers to the site of CL (based on computational simulations) along with changes in size and shape of the mixed micelle with changing MFSDS (based on SAXS studies). These nonlinear impacts on protein stability highlights a multifaceted role for SDS in membrane protein denaturation, involving both direct interactions of monomeric SDS and changes in micelle size and shape along with the general effects on protein stability of changes in micelle composition.
Collapse
Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Arun Kumar Somavarapu
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Anders Clement
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Ming Ji
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emil Hartvig Petersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark; Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Sinisa Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus C, Denmark
| |
Collapse
|
24
|
Sivaraman T. A Review on Computational Approaches for Analyzing Hydrogen- Deuterium (H/D) Exchange of Proteins. Protein Pept Lett 2021; 28:372-381. [PMID: 33006533 DOI: 10.2174/0929866527666201002145859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 11/22/2022]
Abstract
Native state Hydrogen-Deuterium (H/D) exchange method has been used to study the structures and the unfolding pathways for quite a number of proteins. The H/D exchange method is generally monitored using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) techniques. NMR-assisted H/D exchange methods primarily monitor the residue level fluctuation of proteins, whereas MS-assisted H/D exchange methods analyze multifold ensemble conformations of proteins. In this connection, quite a large number of computational tools and algorithms have been developed for processing and analyzing huge amount of the H/D exchange data generated from these techniques. In this review, most of the freely available computational tools associated with the H/D exchange of proteins have been comprehensively reviewed and scopes to improve/ develop novel computational approaches for analyzing the H/D exchange data of proteins have also been brought into fore.
Collapse
Affiliation(s)
- Thirunavukkarasu Sivaraman
- Drug Design and Discovery Lab, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore - 641021, Tamil Nadu, India
| |
Collapse
|
25
|
Dörner S, Schwob L, Atak K, Schubert K, Boll R, Schlathölter T, Timm M, Bülow C, Zamudio-Bayer V, von Issendorff B, Lau JT, Techert S, Bari S. Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:670-684. [PMID: 33573373 DOI: 10.1021/jasms.0c00390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]+) and methionine enkephalin ([MetEnk+H]+) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur-aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]+. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]+.
Collapse
Affiliation(s)
- Simon Dörner
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kaan Atak
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kaja Schubert
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Rebecca Boll
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Martin Timm
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Christine Bülow
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Vicente Zamudio-Bayer
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Bernd von Issendorff
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - J Tobias Lau
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Simone Techert
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| |
Collapse
|
26
|
Kaur K, Xiong J, Sawant N, Agarwal S, Hickey JM, Holland DA, Mukhopadhyay TK, Brady JR, Dalvie NC, Tracey MK, Love KR, Love JC, Weis DD, Joshi SB, Volkin DB. Mechanism of Thimerosal-Induced Structural Destabilization of a Recombinant Rotavirus P[4] Protein Antigen Formulated as a Multi-Dose Vaccine. J Pharm Sci 2021; 110:1054-1066. [PMID: 33278412 PMCID: PMC7884053 DOI: 10.1016/j.xphs.2020.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022]
Abstract
In a companion paper, a two-step developability assessment is presented to rapidly evaluate low-cost formulations (multi-dose, aluminum-adjuvanted) for new subunit vaccine candidates. As a case study, a non-replicating rotavirus (NRRV) recombinant protein antigen P[4] was found to be destabilized by the vaccine preservative thimerosal, and this effect was mitigated by modification of the free cysteine (C173S). In this work, the mechanism(s) of thimerosal-P[4] protein interactions, along with subsequent effects on the P[4] protein's structural integrity, are determined. Reversible complexation of ethylmercury, a thimerosal degradation byproduct, with the single cysteine residue of P[4] protein is demonstrated by intact protein mass analysis and biophysical studies. A working mechanism involving a reversible S-Hg coordinate bond is presented based on the literature. This reaction increased the local backbone flexibility of P[4] within the helical region surrounding the cysteine residue and then caused more global destabilization, both as detected by HX-MS. These effects correlate with changes in antibody-P[4] binding parameters and alterations in P[4] conformational stability due to C173S modification. Epitope mapping by HX-MS demonstrated involvement of the same cysteine-containing helical region of P[4] in antibody-antigen binding. Future formulation challenges to develop low-cost, multi-dose formulations for new recombinant protein vaccine candidates are discussed.
Collapse
Affiliation(s)
- Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Jian Xiong
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Nishant Sawant
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Sanjeev Agarwal
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - John M Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - David A Holland
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Tarit K Mukhopadhyay
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, UK
| | - Joseph R Brady
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Neil C Dalvie
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mary Kate Tracey
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kerry R Love
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - J Christopher Love
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David D Weis
- Department of Chemistry and R.N. Adams Institute of Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047.
| |
Collapse
|
27
|
Chen J, Dai Y, Gong X, Zhang G. Cation-amino acid interactions: Implications for protein destabilization. Biochem Biophys Res Commun 2021; 548:47-52. [PMID: 33631673 DOI: 10.1016/j.bbrc.2021.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/04/2021] [Indexed: 11/28/2022]
Abstract
The mechanism for protein stabilization or destabilization has long been an open quest. In the present study, we have studied the interactions between amino acids and guanidinium (Gdm+)/ammonium (NH4+) ions by using low field nuclear magnetic resonance (LF-NMR), where Gdm+ and NH4+ are denaturant and stabilizer for proteins, respectively. It shows that Gdm+ favors to bind to the thiol group or the hydroxyl group on the side chain but weakly interacts with the α-carboxyl group. In contrast, NH4+ prefers to bind to the α-carboxyl group but slightly interacts with the thiol group or the hydroxyl group on the side chain of amino acids. 1HNMR reveals the hydrogen bonding between NH4+ and the α-carboxyl group, which is not involved in the interactions between Gdm+ and cysteine. Our study demonstrates that the strong interactions between the denaturant and the sulfur atom or the disulfide bond promote the direct binding of the denaturant toward proteins, leading to the destabilization.
Collapse
Affiliation(s)
- Jiantao Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Yingkang Dai
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Xiangjun Gong
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China; Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, PR China.
| | - Guangzhao Zhang
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| |
Collapse
|
28
|
Kumar M, Dhaka N, Raza T, Dadhwal P, Atreya HS, Mukherjee SP. Domain Stability Regulated through the Dimer Interface Controls the Formation Kinetics of a Specific NF-κB Dimer. Biochemistry 2021; 60:513-523. [PMID: 33555182 DOI: 10.1021/acs.biochem.0c00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NF-κB family of transcription factors is a key regulator of the immune response in the vertebrates. The family comprises five proteins that function as dimers formed in various combinations among the members, with the RelA-p50 dimer being physiologically the most abundant. While most of the 15 possible dimers are scarcely present in the cell with some remaining experimentally undetected to date, there are specific gene sets that are only activated by certain sparsely populated NF-κB dimers. The mechanism of transcription activation of such specific genes that are activated only by specific NF-κB dimers remains unclear. Here we show that the dimer interfacial residues control the stabilization of the global hydrogen bond network of the NF-κB dimerization domain, which, in turn, controls the thermodynamic stabilization of different NF-κB dimers. The relatively low thermodynamic stability of the RelA-RelA homodimer is critical as it facilitates the formation of the more stable RelA-p50 heterodimer. Through the modulation of the thermodynamic stability of the RelA-RelA homodimer, the kinetics of the RelA-p50 heterodimer formation can be regulated. This phenomenon provides an insight into the mechanism of RelA-RelA specific target gene regulation in physiology.
Collapse
Affiliation(s)
- Manish Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Nitin Dhaka
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Tahseen Raza
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Prikshat Dadhwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sulakshana P Mukherjee
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| |
Collapse
|
29
|
Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res 2021; 20:1133-1152. [PMID: 33464917 PMCID: PMC7839417 DOI: 10.1021/acs.jproteome.0c00764] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 12/17/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administration, but there are no effective drugs to treat COVID-19, and pandemic mitigation efforts like physical distancing have had acute social and economic consequences. In this perspective, we discuss how the proteomic research community can leverage technologies and expertise to address the pandemic by investigating four key areas of study in SARS-CoV-2 biology. Specifically, we discuss how (1) mass spectrometry-based structural techniques can overcome limitations and complement traditional structural approaches to inform the dynamic structure of SARS-CoV-2 proteins, complexes, and virions; (2) virus-host protein-protein interaction mapping can identify the cellular machinery required for SARS-CoV-2 replication; (3) global protein abundance and post-translational modification profiling can characterize signaling pathways that are rewired during infection; and (4) proteomic technologies can aid in biomarker identification, diagnostics, and drug development in order to monitor COVID-19 pathology and investigate treatment strategies. Systems-level high-throughput capabilities of proteomic technologies can yield important insights into SARS-CoV-2 biology that are urgently needed during the pandemic, and more broadly, can inform coronavirus virology and host biology.
Collapse
Affiliation(s)
- Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robyn M. Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
30
|
Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:613-628. [PMID: 33534058 PMCID: PMC8189984 DOI: 10.1007/s00249-021-01502-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/11/2022]
Abstract
FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.
Collapse
|
31
|
Hamuro Y. Tutorial: Chemistry of Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:133-151. [PMID: 33227208 DOI: 10.1021/jasms.0c00260] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chemistry related to hydrogen/deuterium exchange-mass spectrometry (HDX-MS) for the analysis of proteins is described. First, the HDX rates of various functional groups in proteins are explained by reviewing the observed rates described in the literature, followed by estimating rates of all types of heteroatom hydrogens in proteins using proton transfer theory and the pKa values. The estimated HDX rates match well with the respective observed rates for most functional groups, with the exception of indole and amide groups. The discrepancies between the observed and estimated HDX rates for these groups are explained by the reaction mechanisms. Second, the factors that affect the HDX rates of backbone amide hydrogen, including side chain, N- and C-terminals, pH, temperature, organic solvent, and isotopes, are discussed. These factors are important for the proper design of exchange reactions and downstream process as well as the analysis and interpretation of HDX-MS data.
Collapse
Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
| |
Collapse
|
32
|
Crilly CJ, Brom JA, Kowalewski ME, Piszkiewicz S, Pielak GJ. Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR. Biochemistry 2021; 60:152-159. [PMID: 33400518 DOI: 10.1021/acs.biochem.0c00863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Water is key to protein structure and stability, yet the relationship between protein-water interactions and structure is poorly understood, in part because there are few techniques that permit the study of dehydrated protein structure at high resolution. Here, we describe liquid-observed vapor exchange (LOVE) NMR, a solution NMR-based method that provides residue-level information about the structure of dehydrated proteins. Using the model protein GB1, we show that LOVE NMR measurements reflect the fraction of the dried protein population trapped in a conformation where a given residue is protected from exchange with D2O vapor. Comparisons to solution hydrogen-deuterium exchange data affirm that the dried protein structure is strongly influenced by local solution stability and that the mechanism of dehydration protection exerted by the widely used protectant trehalose differs from its mechanism of stabilization in solution. Our results highlight the need for refined models of cosolute-mediated dehydration protection and demonstrate the ability of LOVE NMR to inform such models.
Collapse
Affiliation(s)
- Candice J Crilly
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Julia A Brom
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Mark E Kowalewski
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Samantha Piszkiewicz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Gary J Pielak
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Integrative Program for Biological & Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7100, United States
| |
Collapse
|
33
|
Abstract
The reversibility of solid-state hydrogen-deuterium exchange (ssHDX) and the effects of prehydration on the rate and extent of deuterium incorporation were evaluated using poly-d,l-alanine (PDLA) peptides colyophilized with various excipients. In prehydration studies, samples were equilibrated at a controlled relative humidity (6% or 11% RH) for 12 h and then transferred to corresponding D2O humidity conditions (6% or 11% RD) for deuterium labeling. In amorphous samples, the rate and extent of deuterium incorporation were similar in prehydrated samples and controls not subjected to prehydration. In reversibility studies, PDLA samples were maximally deuterated in controlled D2O humidity conditions (6% or 11% RD) and then transferred to corresponding H2O relative humidity (0%, 6%, 11%, or 43% RH). Hysteresis in deuterium removal was observed when compared with the deuterium incorporation kinetics for all formulations and conditions, confirming that the reaction is reversible in the solid state and that the forward and reverse processes differ. The extent of deuterium loss reached a plateau that depended on the delabeling relative humidity. Reverse reaction rate constants were quantified using a first-order kinetic model, a limiting case of the reversible first-order model applicable under sink conditions. For other conditions, plateau (steady-state) deuteration levels were related to forward and reverse rate constants in a reversible first-order kinetic model. The results support a mechanistic interpretation of ssHDX kinetics as a reversible first-order process, in which the forward (deuteration) rate depends on the activity of the deuterium donor.
Collapse
Affiliation(s)
- Rajashekar Kammari
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States.,National Institute for Bioprocessing Research and Training, Belfield, Blackrock, Co., Dublin A94 X099, Ireland
| |
Collapse
|
34
|
Evaluation of Predictors of Protein Relative Stability Obtained by Solid-State Hydrogen/Deuterium Exchange Monitored by FTIR. Pharm Res 2020; 37:168. [PMID: 32794130 DOI: 10.1007/s11095-020-02897-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/28/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE Hydrogen/deuterium (H/D) exchange over a range of temperatures suggests a protein structural/mobility transition in the solid state below the system glass transition temperature (Tg). The purpose of this study was to determine whether solid-state protein stability correlates with the difference between storage temperature and apparent Td where an abrupt change in mobility occurs, or alternatively, the extent of H/D exchange at a single temperature correlates directly to protein stability in lyophilized solids. METHODS Solid-state H/D exchange was monitored by FTIR spectroscopy to study the extent of exchange and the apparent transition temperature in both pure recombinant human serum albumin (rHSA) and rHSA formulated with sucrose or trehalose. H/D exchange of freeze-dried formulations at 11% RH and temperatures from 30 to 80°C was monitored. Protein stability against aggregation at 40°C/11% RH for 6 months was assessed by size exclusion chromatography (SEC). RESULTS Both sucrose and trehalose showed equivalent protection of protein secondary structure by FTIR. The rHSA:sucrose formulation showed superior long-term stability at 40°C by SEC over the trehalose formulation, but the apparent Td determined from H/D exchange was much higher in the trehalose formulation. Instead, the extent of H/D exchange (X∞) was lower in the sucrose formulation at the temperature of the stability studies (40°C) than found for the trehalose formulation, which was consistent with better stability in the sucrose formulation. CONCLUSIONS While apparent Td did not correlate with protein stability for rHSA, the extent of H/D exchange, X∞, did.
Collapse
|
35
|
Narang D, Lento C, J. Wilson D. HDX-MS: An Analytical Tool to Capture Protein Motion in Action. Biomedicines 2020; 8:biomedicines8070224. [PMID: 32709043 PMCID: PMC7399943 DOI: 10.3390/biomedicines8070224] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/07/2023] Open
Abstract
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites.
Collapse
Affiliation(s)
- Dominic Narang
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
- Centre for Research of Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto, ON M3J 1P3, Canada
- Correspondence:
| |
Collapse
|
36
|
Kammari R, Topp EM. Effects of Secondary Structure on Solid-State Hydrogen–Deuterium Exchange in Model α-Helix and β-Sheet Peptides. Mol Pharm 2020; 17:3501-3512. [DOI: 10.1021/acs.molpharmaceut.0c00521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajashekar Kammari
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Elizabeth M. Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- National Institute for Bioprocessing Research and Training, Belfield, Blackrock, Co., Dublin A94 X099, Ireland
| |
Collapse
|
37
|
Xu S, Kennedy MA. Structural dynamics of pentapeptide repeat proteins. Proteins 2020; 88:1493-1512. [PMID: 32548861 DOI: 10.1002/prot.25969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/19/2020] [Accepted: 06/06/2020] [Indexed: 12/14/2022]
Abstract
Pentapeptide repeat proteins (PRPs) represent a large superfamily with more than 38 000 sequences in nearly 3500 species, the majority belonging to cyanobacteria but represented among all branches of life. PRPs contain at least eight consecutive pentapeptide repeats with the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K). PRPs fold into right-handed quadrilateral β helices, also known as repeat-five-residue (Rfr)-folds, with four consecutive pentapeptide repeats comprising a single coil, the ~90° change in polypeptide direction in square-shaped coils achieved by type I, II and IV β turns, and hydrogen bonds between coils establishing β ladders on each Rfr-fold face. PRPs are broadly categorized into group 1 and 2 involved in antibiotic resistance and group 3 currently having unknown functions. Motivated by their intriguing structures, we are investigating PRP biophysical characteristics, including Rfr-fold thermal stability, β turn and β ladder hydrogen bond amide exchange rates and backbone dynamics. Here, we present analysis of 20 ns molecular dynamics (MD) simulations and all atom normal mode analysis (aaNMA) calculations for four group 1 and group 2 and four group 3 PRPs whose structures have been determined by X-ray crystallography. The MD cross-correlation matrices and aaNMA indicated strong correlated motion between adjacent coils and weak coupled motion between coils separated by one or more intervening coils. Slow anticorrelated motions were detected between adjacent coils in aaNMA modes that we hypothesize are requisite to access exchange-competent states necessary to permit solvent exchange of amide hydrogens involved in β-ladder and β-turns hydrogen bonds, which can have lifetimes on the order of months.
Collapse
Affiliation(s)
- Shenyuan Xu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| |
Collapse
|
38
|
Tajoddin NN, Konermann L. Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments. Anal Chem 2020; 92:10058-10067. [DOI: 10.1021/acs.analchem.0c01828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
39
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
40
|
Szekely O, Olsen GL, Novakovic M, Rosenzweig R, Frydman L. Assessing Site-Specific Enhancements Imparted by Hyperpolarized Water in Folded and Unfolded Proteins by 2D HMQC NMR. J Am Chem Soc 2020; 142:9267-9284. [PMID: 32338002 PMCID: PMC7304870 DOI: 10.1021/jacs.0c00807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Hyperpolarized water
can be a valuable aid in protein NMR, leading
to amide group 1H polarizations that are orders of magnitude
larger than their thermal counterparts. Suitable procedures can exploit
this to deliver 2D 1H–15N correlations
with good resolution and enhanced sensitivity. These enhancements
depend on the exchange rates between the amides and the water, thereby
yielding diagnostic information about solvent accessibility. This
study applied this “HyperW” method to four proteins
exhibiting a gamut of exchange behaviors: PhoA(350–471), an unfolded 122-residue fragment; barstar, a fully folded ribonuclease
inhibitor; R17, a 13.3 kDa system possessing folded and unfolded forms
under slow interconversion; and drkN SH3, a protein domain whose folded
and unfolded forms interchange rapidly and with temperature-dependent
population ratios. For PhoA4(350–471) HyperW sensitivity
enhancements were ≥300×, as expected for an unfolded protein
sequence. Though fully folded, barstar also exhibited substantial
enhancements; these, however, were not uniform and, according to CLEANEX
experiments, reflected the solvent-exposed residues. R17 showed the
expected superposition of ≥100-fold enhancements for its unfolded
form, coexisting with more modest enhancements for their folded counterparts.
Unexpected, however, was the behavior of drkN SH3, for which HyperW
enhanced the unfolded but, surprisingly, enhanced even more certain folded protein sites. These preferential enhancements were
repeatedly and reproducibly observed. A number of explanations—including
three-site exchange magnetization transfers between water and the
unfolded and folded states; cross-correlated relaxation processes
from hyperpolarized “structural” waters and labile side-chain
protons; and the possibility that faster solvent exchange rates characterize
certain folded sites over their unfolded counterparts—are considered
to account for them.
Collapse
|
41
|
Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
Collapse
|
42
|
Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020; 118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.
Collapse
Affiliation(s)
- Richard T Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
| |
Collapse
|
43
|
Eggertson MJ, Fadgen K, Engen JR, Wales TE. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data. Methods Mol Biol 2020; 2051:407-435. [PMID: 31552640 DOI: 10.1007/978-1-4939-9744-2_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A major component of a hydrogen exchange mass spectrometry experiment is the analysis of protein and peptide mass spectra to yield information about deuterium incorporation. The processing of data that are produced includes the identification of each peptic peptide to create a master table/array of peptide identity that typically includes sequence, retention time and retention time range, mass range, and undeuterated mass. The amount of deuterium incorporated into each of the peptides in this array must then be determined. Various software platforms have been developed in order to perform this specific type of data analysis. We describe the fundamental parameters to be considered at each step along the way and how data processing, either by an individual or by software, must approach the analysis.
Collapse
Affiliation(s)
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
| |
Collapse
|
44
|
Pedersen MC, Wang Y, Tidemand FG, Martel A, Lindorff-Larsen K, Arleth L. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719012469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Recent developments in neutron scattering instrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. The experiments are typically conducted in D2O-based buffers to emphasize or diminish scattering from a particular component or to minimize background noise in the experiment. To extract most information from such experiments it is thus desirable to determine accurate estimates of how and when closely bound hydrogen atoms from the biomolecule exchange with the deuterium in the solvent. This article introduces and documents software, PSX, for exploring the effect of hydrogen–deuterium exchange for proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effects of both heterogenous exchange rates throughout the protein structure and varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scattering on biological macromolecules in solution. The analysis presented here suggests that the common assumption of 90% exchange is in many cases an overestimate with the rapid sample handling systems currently available, which leads to fitting and calibration issues when analysing the data. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing licence.
Collapse
|
45
|
Zheng J, Strutzenberg T, Pascal BD, Griffin PR. Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry. Curr Opin Struct Biol 2019; 58:305-313. [DOI: 10.1016/j.sbi.2019.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 06/15/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022]
|
46
|
Abstract
Although many proteins possess a distinct folded structure lying at a minimum in a funneled free energy landscape, thermal energy causes any protein to continuously access lowly populated excited states. The existence of excited states is an integral part of biological function. Although transitions into the excited states may lead to protein misfolding and aggregation, little structural information is currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species to light. As pressure acts to favor states with lower partial molar volume, NMR follows the ensuing change in the equilibrium spectroscopically, with residue-specific resolution. For T4 lysozyme L99A, relaxation dispersion NMR was used to follow the increase in population of a previously identified "invisible" folded state with pressure, as this is driven by the reduction in cavity volume by the flipping-in of a surface aromatic group. Furthermore, multiple partly disordered excited states were detected at equilibrium using pressure-dependent H/D exchange NMR spectroscopy. Here, unfolding reduced partial molar volume by the removal of empty internal cavities and packing imperfections through subglobal and global unfolding. A close correspondence was found for the distinct pressure sensitivities of various parts of the protein and the amount of internal cavity volume that was lost in each unfolding event. The free energies and populations of excited states allowed us to determine the energetic penalty of empty internal protein cavities to be 36 cal⋅Å-3.
Collapse
|
47
|
Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
Collapse
Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
48
|
Kammari R, Topp EM. Solid-State Hydrogen–Deuterium Exchange Mass Spectrometry (ssHDX-MS) of Lyophilized Poly-d,l-Alanine. Mol Pharm 2019; 16:2935-2946. [PMID: 31244225 DOI: 10.1021/acs.molpharmaceut.9b00162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajashekar Kammari
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth M. Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
49
|
Investigating the Conformational Response of the Sortilin Receptor upon Binding Endogenous Peptide- and Protein Ligands by HDX-MS. Structure 2019; 27:1103-1113.e3. [PMID: 31104815 DOI: 10.1016/j.str.2019.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 11/20/2022]
Abstract
Sortilin is a multifunctional neuronal receptor involved in sorting of neurotrophic factors and apoptosis signaling. So far, structural characterization of sortilin and its endogenous ligands has been limited to crystallographic studies of sortilin in complex with the neuropeptide neurotensin. Here, we use hydrogen/deuterium exchange mass spectrometry to investigate the conformational response of sortilin to binding biological ligands including the peptides neurotensin and the sortilin propeptide and the proteins progranulin and pro-nerve growth factor-β. The results show that the ligands use two binding sites inside the cavity of the β-propeller of sortilin. However, ligands have distinct differences in their conformational impact on the receptor. Interestingly, the protein ligands induce conformational stabilization in a remote membrane-proximal domain, hinting at an unknown conformational link between the ligand binding region and this membrane-proximal region of sortilin. Our findings improve our structural understanding of sortilin and how it mediates diverse ligand-dependent functions important in neurobiology.
Collapse
|
50
|
Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem 2019; 91:7336-7345. [PMID: 31045344 DOI: 10.1021/acs.analchem.9b01100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ sLab⟩ ≤ (0.15 ± 0.01) Da (1σx̅). All laboratories achieved ⟨sLab⟩ ≤ 0.4 Da. For immersions of protein at THDX = (3.6 to 25) °C and for D2O exchange times of tHDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σreproducibility15 Laboratories( tHDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at THDX = 25 °C exhibited reproducibility of σreproducibility25C cohort( tHDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.
Collapse
Affiliation(s)
- Jeffrey W Hudgens
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Elyssia S Gallagher
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Ioannis Karageorgos
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Kyle W Anderson
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - James J Filliben
- Statistical Engineering Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - George M Bou-Assaf
- Analytical Development , Biogen Inc. , 225 Binney Street , Cambridge , Massachusetts 02142 , United States
| | - Alfonso Espada
- Centro de Investigación Lilly S.A. , 28108 Alcobendas , Spain
| | - Michael J Chalmers
- Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | - Hui-Min Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Benjamin T Walters
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jennifer Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - John Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States.,Joint Center for Structural Genomics , La Jolla , California 92037 , United States
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Xiaojun Lu
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Ratnesh Pandey
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Arun Chandramohan
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Sasidhar N Nirudodhi
- Vaccine R&D , Pfizer Inc. , 401 N Middletown Rd , Pearl River, New York 10965 , United States
| | - Justin B Sperry
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Jason C Rouse
- Analytical R&D , Pfizer Inc. , 1 Burtt Road , Andover , Massachusetts 01810 , United States
| | - James A Carroll
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Ulrike Leurs
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - David D Weis
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Mohammed A Al-Naqshabandi
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States.,Department of General Science , Soran University , Kawa Street , Soran , Kurdistan Region, Iraq
| | - Tyler S Hageman
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Malvina Papanastasiou
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - Sheng Li
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Sarah Urata
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| |
Collapse
|