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Grifnée E, Kune C, Delvaux C, Tilmant T, Quinton L, Matagne A, Mazzucchelli G, Far J, De Pauw E. Investigation of Structure-Stabilizing Elements in Proteins by Ion Mobility Mass Spectrometry and Collision-Induced Unfolding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1076-1088. [PMID: 38660944 DOI: 10.1021/jasms.3c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A recently developed proteolytic reactor, designed for protein structural investigation, was coupled to ion mobility mass spectrometry to monitor collisional cross section (CCS) evolution of model proteins undergoing trypsin-mediated mono enzymatic digestion. As peptides are released during digestion, the CCS of the remaining protein structure may deviate from the classical 2/3 power of the CCS-mass relationship for spherical structures. The classical relationship between CCS and mass (CCS = A × M2/3) for spherical structures, assuming a globular shape in the gas phase, may deviate as stabilizing elements are lost during digestion. In addition, collision-induced unfolding (CIU) experiments on partially digested proteins provided insights into the CCS resilience in the gas phase to ion activation, potentially due to the presence of stabilizing elements. The study initially investigated a model peptide ModBea (3 kDa), assessing the impact of disulfide bridges on CCS resilience in both reduced and oxidized forms. Subsequently, β-lactoglobulin (2 disulfide bridges), calmodulin (Ca2+ coordination cation), and cytochrome c (heme) were selected to investigate the influence of common structuring elements on CCS resilience. CIU experiments probed the unfolding process, evaluating the effect of losing specific peptides on the energy landscapes of partially digested proteins. Comparisons of the TWCCSN2→He to trend curves describing the CCS/mass relationship revealed that proteins with structure-stabilizing elements consistently exhibit TWCCSN2→He and greater resilience toward CIU compared to proteins lacking these elements. The integration of online digestion, ion mobility, and CIU provides a valuable tool for identifying structuring elements in biopolymers in the gas phase.
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Affiliation(s)
- Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Thomas Tilmant
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Center for Protein Engineering, InBioS Research Unit, University of Liège, B-4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
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2
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Luan M, Hou Z, Zhang B, Ma L, Yuan S, Liu Y, Huang G. Inter-Domain Repulsion of Dumbbell-Shaped Calmodulin during Electrospray Ionization Revealed by Molecular Dynamics Simulations. Anal Chem 2023; 95:8798-8806. [PMID: 37309130 DOI: 10.1021/acs.analchem.2c05630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The mechanisms whereby protein ions are released from nanodroplets at the liquid-gas interface have continued to be controversial since electrospray ionization (ESI) mass spectrometry was widely applied in biomolecular structure analysis in solution. Several viable pathways have been proposed and verified for single-domain proteins. However, the ESI mechanism of multi-domain proteins with more complicated and flexible structures remains unclear. Herein, dumbbell-shaped calmodulin was chosen as a multi-domain protein model to perform molecular dynamics simulations to investigate the structural evolution during the ESI process. For [Ca4CAM], the protein followed the classical charge residue model. As the inter-domain electrostatic repulsion increased, the droplet was found to split into two sub-droplets, while stronger-repulsive apo-calmodulin unfolded during the early evaporation stage. We designated this novel ESI mechanism as the domain repulsion model, which provides new mechanistic insights into further exploration of proteins containing more domains. Our results suggest that greater attention should be paid to the effect of domain-domain interactions on structure retention during liquid-gas interface transfer when mass spectrometry is used as the developing technique in gas phase structural biology.
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Affiliation(s)
- Moujun Luan
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Zhuanghao Hou
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Buchun Zhang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Likun Ma
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Siming Yuan
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Yangzhong Liu
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Guangming Huang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
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3
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Kim C, Kim Y, Lee SJ, Yun SR, Choi J, Kim SO, Yang Y, Ihee H. Visualizing Heterogeneous Protein Conformations with Multi-Tilt Nanoparticle-Aided Cryo-Electron Microscopy Sampling. NANO LETTERS 2023; 23:3334-3343. [PMID: 37068052 PMCID: PMC10141564 DOI: 10.1021/acs.nanolett.3c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Obtaining the heterogeneous conformation of small proteins is important for understanding their biological role, but it is still challenging. Here, we developed a multi-tilt nanoparticle-aided cryo-electron microscopy sampling (MT-NACS) technique that enables the observation of heterogeneous conformations of small proteins and applied it to calmodulin. By imaging the proteins labeled by two gold nanoparticles at multiple tilt angles and analyzing the projected positions of the nanoparticles, the distributions of 3D interparticle distances were obtained. From the measured distance distributions, the conformational changes associated with Ca2+ binding and salt concentration were determined. MT-NACS was also used to track the structural change accompanied by the interaction between amyloid-beta and calmodulin, which has never been observed experimentally. This work offers an alternative platform for studying the functional flexibility of small proteins.
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Affiliation(s)
- Changin Kim
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yeeun Kim
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
| | - Sang Jin Lee
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jungkweon Choi
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seong Ok Kim
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yongsoo Yang
- Department
of Physics, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Y.Y.:
email, ; tel, +82-42-350-7303
| | - Hyotcherl Ihee
- Department
of Chemistry, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KI
for the BioCentury, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Republic
of Korea
- Center
for Advanced Reaction Dynamics, Institute
for Basic Science (IBS), Daejeon 34141, Republic of Korea
- H.I.: email, ; tel, +82-42-350-2844
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4
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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5
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Byrd E, Wilkinson M, Radford SE, Sobott F. Taking Charge: Metal Ions Accelerate Amyloid Aggregation in Sequence Variants of α-Synuclein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:493-504. [PMID: 36794792 PMCID: PMC9983014 DOI: 10.1021/jasms.2c00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Αlpha-synuclein (αS) is an intrinsically disordered protein which exhibits a high degree of conformational heterogeneity. In vivo, αS experiences various environments which cause adaptation of its structural ensemble. Divalent metal ions are prominent in synaptic terminals where αS is located and are thought to bind to the αS C-terminal region. Herein, we used native nanoelectrospray ionization ion mobility-mass spectrometry to investigate changes in the charge state distribution and collision cross sections of wild-type N-terminally acetylated (NTA) αS, along with a deletion variant (ΔΔNTA) which inhibits amyloid formation and a C-terminal truncated variant (119NTA) which increases the rate of amyloid formation. We also examine the effect of the addition of divalent metal ions, Ca2+, Mn2+, and Zn2+, and correlate the conformational properties of the αS monomer with the ability to aggregate into amyloid, measured using Thioflavin T fluorescence and negative stain transmission electron microscopy. We find a correlation between the population of species with a low collision cross section and accelerated amyloid assembly kinetics, with the presence of metal ions resulting in protein compaction and causing ΔΔ to regain its ability to form an amyloid. The results portray how the αS conformational ensemble is governed by specific intramolecular interactions that influence its amyloidogenic behavior.
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Affiliation(s)
- Emily
J. Byrd
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Frank Sobott
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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6
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Sipe SN, Sanders JD, Reinecke T, Clowers BH, Brodbelt JS. Separation and Collision Cross Section Measurements of Protein Complexes Afforded by a Modular Drift Tube Coupled to an Orbitrap Mass Spectrometer. Anal Chem 2022; 94:9434-9441. [PMID: 35736993 PMCID: PMC9302900 DOI: 10.1021/acs.analchem.2c01653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
New developments in analytical technologies and biophysical methods have advanced the characterization of increasingly complex biomolecular assemblies using native mass spectrometry (MS). Ion mobility methods, in particular, have enabled a new dimension of structural information and analysis of proteins, allowing separation of conformations and providing size and shape insights based on collision cross sections (CCSs). Based on the concepts of absorption-mode Fourier transform (aFT) multiplexing ion mobility spectrometry (IMS), here, a modular drift tube design proves capable of separating native-like proteins up to 148 kDa with resolution up to 45. Coupled with high-resolution Orbitrap MS, binding of small ligands and cofactors can be resolved in the mass domain and correlated to changes in structural heterogeneity observed in the ion-neutral CCS distributions. We also demonstrate the ability to rapidly determine accurate CCSs for proteins with 1-min aFT-IMS-MS sweeps without the need for calibrants or correction factors.
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Affiliation(s)
- Sarah N. Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D. Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tobias Reinecke
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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7
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Schmidt T, Wang D, Jeon J, Schwieters CD, Clore GM. Quantitative Agreement between Conformational Substates of Holo Calcium-Loaded Calmodulin Detected by Double Electron-Electron Resonance EPR and Predicted by Molecular Dynamics Simulations. J Am Chem Soc 2022; 144:12043-12051. [PMID: 35759799 DOI: 10.1021/jacs.2c02201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Calcium-loaded calmodulin (CaM/4Ca2+) comprises two domains that undergo rigid body reorientation from a predominantly extended conformation to a compact one upon binding target peptides. A recent replica-exchange molecular dynamics (MD) simulation on holo CaM/4Ca2+ suggested the existence of distinct structural clusters (substates) along the path from extended to compact conformers in the absence of substrates. Here, we experimentally demonstrate the existence of CaM/4Ca2+ substates trapped in local minima by three freezing/annealing regimes (slow, 40 s; intermediate, 1.5 s; fast, 0.5 ms) using pulsed Q-band double electron-electron resonance (DEER) EPR spectroscopy to measure interdomain distances between nitroxide spin-labels positioned at A17C and A128C in the N- and C-terminal domains, respectively. The DEER echo curves were directly fit to population-optimized P(r) pairwise distance distributions calculated from the coordinates of the MD clusters and compact crystal structure. DEER data on fully deuterated CaM/4Ca2+ were acquired at multiple values of the second echo period (10-35 μs) and analyzed globally to eliminate instrumental and overfitting artifacts and ensure accurate populations, peak positions, and widths. The DEER data for all three freezing regimes are quantitatively accounted for within experimental error by 5-6 distinct conformers comprising a predominantly populated extended form (60-75%) and progressively more compact states whose populations decrease as the degree of compactness increases. The shortest interdomain separation is found in the compact crystal structure, which has an occupancy of 4-6%. Thus, CaM/4Ca2+ samples high energy local minima comprising a few discrete substates of increasing compactness in a rugged energy landscape.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - David Wang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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8
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Liu FC, Ridgeway ME, Park MA, Bleiholder C. Tandem-trapped ion mobility spectrometry/mass spectrometry ( tTIMS/MS): a promising analytical method for investigating heterogenous samples. Analyst 2022; 147:2317-2337. [PMID: 35521797 PMCID: PMC9914546 DOI: 10.1039/d2an00335j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ion mobility spectrometry/mass spectrometry (IMS/MS) is widely used to study various levels of protein structure. Here, we review the current state of affairs in tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS). Two different tTIMS/MS instruments are discussed in detail: the first tTIMS/MS instrument, constructed from coaxially aligning two TIMS devices; and an orthogonal tTIMS/MS configuration that comprises an ion trap for irradiation of ions with UV photons. We discuss the various workflows the two tTIMS/MS setups offer and how these can be used to study primary, tertiary, and quaternary structures of protein systems. We also discuss, from a more fundamental perspective, the processes that lead to denaturation of protein systems in tTIMS/MS and how to soften the measurement so that biologically meaningful structures can be characterised with tTIMS/MS. We emphasize the concepts underlying tTIMS/MS to underscore the opportunities tandem-ion mobility spectrometry methods offer for investigating heterogeneous samples.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | | | | | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA. .,Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
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9
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Lin Y, Gross ML. Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies. Biomolecules 2022; 12:135. [PMID: 35053283 PMCID: PMC8773722 DOI: 10.3390/biom12010135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), "fast photochemical oxidation of proteins" (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including "protein-ligand interactions by mass spectrometry, titration and HD exchange" (PLIMSTEX) and "ligand titration, fast photochemical oxidation of proteins and mass spectrometry" (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.
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Affiliation(s)
- Yanchun Lin
- 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
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10
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Huang S, Wang J, Sun H, Fu Y, Wang Y. Probing Changes in Ca 2+-Induced Interaction Forces between Calmodulin and Melittin by Atomic Force Microscopy. MICROMACHINES 2020; 11:E906. [PMID: 33007824 PMCID: PMC7601158 DOI: 10.3390/mi11100906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 11/16/2022]
Abstract
Mechanobiology studies the means by which physical forces and mechanical properties change intra- or inter- biological macromolecules. Calmodulin (CaM) is involved in physiological activities and various metabolic processes in eukaryotic cells. Although the configuration changes in the interaction between calmodulin and melittin have been studied, the biomechanical relationship of their interaction has rarely been explored. Here, we measured the adhesion forces between calmodulin and melittin in solutions of gradient concentration of calcium ions using atomic force microscopy (AFM). We found that the specific (Fi) and nonspecific (F0) adhesion forces between single melittin and calmodulin in a PBS solution were 69.4 ± 5.0 and 29.3 ± 8.9 pN, respectively. In the presence of 10-7 to 10-3 M Ca2+ PBS solution, the Fi increased significantly to 93.8 ± 5.0, 139.9 ± 9.0, 140.4 ± 9.7, 171.5 ± 9.0, and 213.3 ± 17.8 pN, indicating that the unbinding force between melittin and calmodulin increased in the presence of Ca2+ in a concentration-dependent manner. These findings demonstrated that biomechanical studies based on AFM could help us better understand the melittin/calmodulin-binding processes in the presence of calcium and help us design and screen peptide drugs based on calmodulin.
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Affiliation(s)
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education College of Bioengineering, Chongqing University, Chongqing 400044, China; (S.H.); (H.S.); (Y.F.); (Y.W.)
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11
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Wang S, Liao L, Huang Y, Wang M, Zhou H, Chen D, Liu F, Ji D, Xia X, Jiang B, Huang J, Xiong K. Pin1 Is Regulated by CaMKII Activation in Glutamate-Induced Retinal Neuronal Regulated Necrosis. Front Cell Neurosci 2019; 13:276. [PMID: 31293391 PMCID: PMC6603237 DOI: 10.3389/fncel.2019.00276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
In our previous study, we reported that peptidyl-prolyl isomerase 1 (Pin1)-modulated regulated necrosis (RN) occurred in cultured retinal neurons after glutamate injury. In the current study, we investigated the role of calcium/calmodulin-dependent protein kinase II (CaMKII) in Pin1-modulated RN in cultured rat retinal neurons, and in an animal in vivo model. We first demonstrated that glutamate might lead to calcium overloading mainly through ionotropic glutamate receptors activation. Furthermore, CaMKII activation induced by overloaded calcium leads to Pin1 activation and subsequent RN. Inactivation of CaMKII by KN-93 (KN, i.e., a specific CaMKII inhibitor) application can decrease the glutamate-induced retinal neuronal RN. Finally, by using an animal in vivo model, we also demonstrated the important role of CaMKII in glutamate-induced RN in rat retina. In addition, flash electroretinogram results provided evidence that the impaired visual function induced by glutamate can recover after CaMKII inhibition. In conclusion, CaMKII is an up-regulator of Pin1 and responsible for the RN induced by glutamate. This study provides further understanding of the regulatory pathway of RN and is a complementary mechanism for Pin1 activation mediated necrosis. This finding will provide a potential target to protect neurons from necrosis in neurodegenerative diseases, such as glaucoma, diabetic retinopathy, and even central nervous system diseases.
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Affiliation(s)
- Shuchao Wang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China.,Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lvshuang Liao
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yanxia Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Mi Wang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hongkang Zhou
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Dan Chen
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Fengxia Liu
- Department of Human Anatomy, School of Basic Medical Science, Xinjiang Medical University, Ürümqi, China
| | - Dan Ji
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Xia
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - Bing Jiang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jufang Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
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12
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Kondalaji SG, Khakinejad M, Valentine SJ. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to Gas-Phase Structures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1665-1677. [PMID: 29858839 PMCID: PMC6525623 DOI: 10.1007/s13361-018-1996-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 05/16/2023]
Abstract
Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. Graphical Abstract ᅟ.
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Affiliation(s)
- Samaneh Ghassabi Kondalaji
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Mahdiar Khakinejad
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Stephen J Valentine
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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13
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How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions? Methods 2018; 144:3-13. [PMID: 29704661 DOI: 10.1016/j.ymeth.2018.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/03/2018] [Accepted: 04/21/2018] [Indexed: 01/16/2023] Open
Abstract
Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology and dynamics, complementing conventional biophysical techniques. Despite the maturation of native MS and greatly expanded range of applications in recent decades, further dissemination is needed to make the community aware of such a technique. In this review, we attempt to provide an overview of the current body of knowledge regarding major aspects of native MS and explain how such technique contributes to the characterization of biomacromolecular higher-order structure and interactions.
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14
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Hoffmann W, Folmert K, Moschner J, Huang X, von Berlepsch H, Koksch B, Bowers MT, von Helden G, Pagel K. NFGAIL Amyloid Oligomers: The Onset of Beta-Sheet Formation and the Mechanism for Fibril Formation. J Am Chem Soc 2017; 140:244-249. [PMID: 29235867 DOI: 10.1021/jacs.7b09510] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The hexapeptide NFGAIL is a highly amyloidogenic peptide, derived from the human islet amyloid polypeptide (hIAPP). Recent investigations indicate that presumably soluble hIAPP oligomers are one of the cytotoxic species in type II diabetes. Here we use thioflavin T staining, transmission electron microscopy, as well as ion mobility-mass spectrometry coupled to infrared (IR) spectroscopy to study the amyloid formation mechanism and the quaternary and secondary structure of soluble NFGAIL oligomers. Our data reveal that at neutral pH NFGAIL follows a nucleation dependent mechanism to form amyloid fibrils. During the lag phase, highly polydisperse, polymorph, and compact oligomers (oligomer number n = 2-13) as well as extended intermediates (n = 4-11) are present. IR secondary structural analysis reveals that compact conformations adopt turn-like structures, whereas extended oligomers exhibit a significant amount of β-sheet content. This agrees well with previous molecular dynamic simulations and provides direct experimental evidence that unordered off-pathway NFGAIL aggregates up to the size of at least the 13-mer as well as partially folded β-sheet containing oligomers are coexisting.
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Affiliation(s)
- Waldemar Hoffmann
- Freie Universität Berlin , Institute of Chemistry and Biochemistry - Organic Chemistry, Takustr. 3, 14195 Berlin, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Kristin Folmert
- Freie Universität Berlin , Institute of Chemistry and Biochemistry - Organic Chemistry, Takustr. 3, 14195 Berlin, Germany
| | - Johann Moschner
- Freie Universität Berlin , Institute of Chemistry and Biochemistry - Organic Chemistry, Takustr. 3, 14195 Berlin, Germany
| | - Xing Huang
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Hans von Berlepsch
- Freie Universität Berlin , Institute of Chemistry and Biochemistry - Organic Chemistry, Takustr. 3, 14195 Berlin, Germany
| | - Beate Koksch
- Freie Universität Berlin , Institute of Chemistry and Biochemistry - Organic Chemistry, Takustr. 3, 14195 Berlin, Germany
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara , Santa Barbara, California 93106, United States
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Freie Universität Berlin , Institute of Chemistry and Biochemistry - Organic Chemistry, Takustr. 3, 14195 Berlin, Germany
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15
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Dilger JM, Glover MS, Clemmer DE. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1293-1303. [PMID: 28357817 DOI: 10.1007/s13361-016-1592-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/17/2016] [Accepted: 12/18/2016] [Indexed: 05/18/2023]
Abstract
Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
- Spectrum Warfare Systems Department, Naval Surface Warfare Center, Crane Division, Crane, IN, 47522, USA.
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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16
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Eschweiler JD, Kerr R, Rabuck-Gibbons J, Ruotolo BT. Sizing Up Protein-Ligand Complexes: The Rise of Structural Mass Spectrometry Approaches in the Pharmaceutical Sciences. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:25-44. [PMID: 28301749 DOI: 10.1146/annurev-anchem-061516-045414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies.
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Affiliation(s)
| | - Richard Kerr
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| | | | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
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17
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Göth M, Pagel K. Ion mobility–mass spectrometry as a tool to investigate protein–ligand interactions. Anal Bioanal Chem 2017; 409:4305-4310. [DOI: 10.1007/s00216-017-0384-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/13/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023]
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18
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Lipstein N, Göth M, Piotrowski C, Pagel K, Sinz A, Jahn O. Presynaptic Calmodulin targets: lessons from structural proteomics. Expert Rev Proteomics 2017; 14:223-242. [DOI: 10.1080/14789450.2017.1275966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Noa Lipstein
- Department of Molecular Neurobiology, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Melanie Göth
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin & Fritz Haber Institute of the Max-Planck-Society, Berlin, Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin & Fritz Haber Institute of the Max-Planck-Society, Berlin, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
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19
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Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
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20
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Bartman CE, Metwally H, Konermann L. Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations. Anal Chem 2016; 88:6905-13. [DOI: 10.1021/acs.analchem.6b01627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Claire E. Bartman
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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21
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Liko I, Hopper JTS, Allison TM, Benesch JLP, Robinson CV. Negative Ions Enhance Survival of Membrane Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1099-104. [PMID: 27106602 PMCID: PMC4869745 DOI: 10.1007/s13361-016-1381-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 05/08/2023]
Abstract
Membrane protein complexes are commonly introduced to the mass spectrometer solubilized in detergent micelles. The collisional activation used to remove the detergent, however, often causes protein unfolding and dissociation. As in the case for soluble proteins, electrospray in the positive ion mode is most commonly used for the study of membrane proteins. Here we show several distinct advantages of employing the negative ion mode. Negative polarity can yield lower average charge states for membrane proteins solubilized in saccharide detergents, with enhanced peak resolution and reduced adduct formation. Most importantly, we demonstrate that negative ion mode electrospray ionization (ESI) minimizes subunit dissociation in the gas phase, allowing access to biologically relevant oligomeric states. Together, these properties mean that intact membrane protein ions can be generated in a greater range of solubilizing detergents. The formation of negative ions, therefore, greatly expands the possibilities of using mass spectrometry on this intractable class of protein. Graphical Abstract ᅟ.
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Affiliation(s)
- Idlir Liko
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Jonathan T S Hopper
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Timothy M Allison
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK.
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22
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Liu FC, Kirk SR, Bleiholder C. On the structural denaturation of biological analytes in trapped ion mobility spectrometry – mass spectrometry. Analyst 2016; 141:3722-30. [DOI: 10.1039/c5an02399h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trapped ion mobility spectra recorded for ubiquitin are consistent with structures reported for the native state by NMR.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Samuel R. Kirk
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Institute of Molecular Biophysics
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23
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Scott D, Layfield R, Oldham NJ. Ion mobility-mass spectrometry reveals conformational flexibility in the deubiquitinating enzyme USP5. Proteomics 2015; 15:2835-41. [PMID: 25641936 DOI: 10.1002/pmic.201400457] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/23/2014] [Accepted: 01/14/2015] [Indexed: 11/05/2022]
Abstract
Many proteins exhibit conformation flexibility as part of their biological function, whether through the presence of a series of well-defined states or by the existence of intrinsic disorder. Ion mobility spectrometry, in combination with MS (IM-MS), offers a rapid and sensitive means of probing ensembles of protein structures through measurement of gas-phase collisional cross sections. We have applied IM-MS analysis to the multidomain deubiquitinating enzyme ubiquitin specific protease 5 (USP5), which is believed to exhibit significant conformational flexibility. Native ESI-MS measurement of the 94-kDa USP5 revealed two distinct charge-state distributions: [M + 17H](+) to [M + 21H](+) and [M + 24H](+) to [M + 29H](+). The collisional cross sections of these ions revealed clear groupings of 52 ± 4 nm(2) for the lower charges and 66 ± 6 nm(2) for the higher charges. Molecular dynamics simulation of a compact form of USP5, based on a crystal structure, produced structures of 53-54 nm(2) following 2 ns in the gas phase, while simulation of an extended form (based on small-angle X-ray scattering data) led to structures of 64 nm(2). These data demonstrate that IM-MS is a valuable tool in studying proteins with different discrete conformational states.
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Affiliation(s)
- Daniel Scott
- School of Chemistry, University of Nottingham, Nottingham, UK.,School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Robert Layfield
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, Nottingham, UK
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24
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Calabrese AN, Bowie JH, Pukala TL. Structural analysis of calmodulin binding by nNOS inhibitory amphibian peptides. Biochemistry 2014; 54:567-76. [PMID: 25436860 DOI: 10.1021/bi5004124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Calmodulin (CaM) is a ubiquitous protein in nature and plays a regulatory role in numerous biological processes, including the upregulation of nitric oxide (NO) synthesis in vivo. Several peptides that prevent NO production by interacting with CaM have been isolated in the cutaneous secretions of Australian amphibians, and are thought to serve as a defense mechanism against predators. In this work, we probe the mechanism by which three of these peptides, namely, caerin 1.8, dahlein 5.6, and a synthetic modification of citropin 1.1, interact with CaM to inhibit NO signaling. Isothermal titration calorimetry was used to determine thermodynamic parameters of the binding interactions and revealed that all the peptides bind to CaM in a similar fashion, with the peptide encapsulated between the two lobes of CaM. Ion mobility-mass spectrometry was used to investigate the changes in collision cross section that occur as a result of complexation, providing additional evidence for this binding mode. Finally, nuclear magnetic resonance spectroscopy was used to track chemical shift changes upon binding. The results obtained confirm that these complexes adopt canonical collapsed structures and demonstrate the strength of the interaction between the peptides and CaM. An understanding of these molecular recognition events provides insights into the underlying mechanism of the amphibian host-defense system.
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Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide , Adelaide, SA Australia 5005
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25
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Lanucara F, Holman SW, Gray CJ, Eyers CE. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat Chem 2014; 6:281-94. [DOI: 10.1038/nchem.1889] [Citation(s) in RCA: 655] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 02/11/2014] [Indexed: 02/07/2023]
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26
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Flick TG, Merenbloom SI, Williams ER. Effects of metal ion adduction on the gas-phase conformations of protein ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1654-62. [PMID: 23733259 PMCID: PMC3795793 DOI: 10.1007/s13361-013-0664-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/10/2013] [Accepted: 05/03/2013] [Indexed: 05/16/2023]
Abstract
Changes in protein ion conformation as a result of nonspecific adduction of metal ions to the protein during electrospray ionization (ESI) from aqueous solutions were investigated using traveling wave ion mobility spectrometry (TWIMS). For all proteins examined, protein cations (and in most cases anions) with nonspecific metal ion adducts are more compact than the fully protonated (or deprotonated) ions with the same charge state. Compaction of protein cations upon nonspecific metal ion binding is most significant for intermediate charge state ions, and there is a greater reduction in collisional cross section with increasing number of metal ion adducts and increasing ion valency, consistent with an electrostatic interaction between the ions and the protein. Protein cations with the greatest number of adducted metal ions are no more compact than the lowest protonated ions formed from aqueous solutions. These results show that smaller collisional cross sections for metal-attached protein ions are not a good indicator of a specific metal-protein interaction in solution because nonspecific metal ion adduction also results in smaller gaseous protein cation cross sections. In contrast, the collisional cross section of α-lactalbumin, which specifically binds one Ca(2+), is larger for the holo-form compared with the apo-form, in agreement with solution-phase measurements. Because compaction of protein cations occurs when metal ion adduction is nonspecific, elongation of a protein cation may be a more reliable indicator that a specific metal ion-protein interaction occurs in solution.
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Affiliation(s)
| | | | - Evan R. Williams
- Address reprint requests to Prof. Evan R. Williams: Department of Chemistry University of California, Berkeley Latimer Hall #1460 Berkeley, CA 94620-1460 Phone: (510) 643-7161 Fax: (510) 542-7714
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27
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Niu S, Rabuck JN, Ruotolo BT. Ion mobility-mass spectrometry of intact protein–ligand complexes for pharmaceutical drug discovery and development. Curr Opin Chem Biol 2013; 17:809-17. [DOI: 10.1016/j.cbpa.2013.06.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/17/2013] [Accepted: 06/18/2013] [Indexed: 11/30/2022]
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28
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Rabuck JN, Hyung SJ, Ko KS, Fox CC, Soellner MB, Ruotolo BT. Activation state-selective kinase inhibitor assay based on ion mobility-mass spectrometry. Anal Chem 2013; 85:6995-7002. [PMID: 23845095 DOI: 10.1021/ac4012655] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The discovery of activation state dependent kinase inhibitors, which bind specifically to the inactive conformation of the protein, is considered to be a promising pathway to improved cancer treatments. Identifying such inhibitors is challenging, however, because they can have Kd values similar to molecules known to inhibit kinase function by interacting with the active form. Further, while inhibitor induced changes within the kinase tertiary structure are significant, few technologies are able to correctly assign inhibitor binding modes in a high-throughput fashion based exclusively on protein-inhibitor complex formation and changes in local protein structure. We have developed a new assay, using ion mobility-mass spectrometry, capable of both rapidly detecting inhibitor binding and classifying the resultant kinase binding modes. Here, we demonstrate the ability of our approach to classify a broad set of kinase inhibitors, using micrograms of protein, without the need for protein modification or tagging.
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Affiliation(s)
- Jessica N Rabuck
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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29
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Sivalingam GN, Yan J, Sahota H, Thalassinos K. Amphitrite: A program for processing travelling wave ion mobility mass spectrometry data. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 345-347:54-62. [PMID: 25844045 PMCID: PMC4375678 DOI: 10.1016/j.ijms.2012.09.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/04/2012] [Accepted: 09/13/2012] [Indexed: 05/11/2023]
Abstract
Since the introduction of travelling wave (T-Wave)-based ion mobility in 2007 a large number of research laboratories have embraced the technique, particularly those working in the field of structural biology. The development of software to process the data generated from this technique, however, has been limited. We present a novel software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest. A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.
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Affiliation(s)
- Ganesh N. Sivalingam
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Jun Yan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Corresponding author. Tel.: +44 20 7679 2197; fax: +44 20 7679 7193.
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30
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Chen C, Huang Y, Jiang X, Xiao Y. Binding free-energy calculation of an ion-peptide complex by constrained dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062705. [PMID: 23848713 DOI: 10.1103/physreve.87.062705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 04/06/2013] [Indexed: 06/02/2023]
Abstract
Binding free energy is the most important physical parameter that describes the binding affinity of a receptor-ligand complex. Conventionally, it was obtained based on the thermodynamic cycle or alchemical reaction. These strategies have been widely used, but they would be problematic if the receptors and/or ligands have large conformational changes during the binding processes. In this paper, we present a way to calculate the binding free energy: constrained dynamics along a fragmental and high-dimensional transition path. This method directly considers unbound states in the simulation. The application to the calmodulin loop-calcium complexes shows that it is practical and the calculated relative binding affinities are in good agreement with experimental results.
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Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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Dilger JM, Valentine SJ, Glover MS, Clemmer DE. A database of alkaline-earth-coordinated peptide cross sections: insight into general aspects of structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:768-79. [PMID: 23512423 DOI: 10.1007/s13361-013-0579-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 05/18/2023]
Abstract
A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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32
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Williams DM, Pukala TL. Novel insights into protein misfolding diseases revealed by ion mobility-mass spectrometry. MASS SPECTROMETRY REVIEWS 2013; 32:169-187. [PMID: 23345084 DOI: 10.1002/mas.21358] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 05/23/2012] [Accepted: 05/29/2012] [Indexed: 06/01/2023]
Abstract
Amyloid disorders incorporate a wide range of human diseases arising from the failure of a specific peptide or protein to adopt, or remain in, its native functional conformational state. These pathological conditions, such as Parkinson's disease, Alzheimer's disease and Huntington's disease are highly debilitating, exact enormous costs on both individuals and society, and are predicted to increase in prevalence. Consequently, they form the focus of a topical and rich area of current scientific research. A major goal in attempts to understand and treat protein misfolding diseases is to define the structures and interactions of protein species intermediate between fully folded and aggregated, and extract a description of the aggregation process. This has proven a difficult task due to the inability of traditional structural biology approaches to analyze structurally heterogeneous systems. Continued developments in instrumentation and analytical approaches have seen ion mobility-mass spectrometry (IM-MS) emerge as a complementary approach for protein structure determination, and in some cases, a structural biology tool in its own right. IM-MS is well suited to the study of protein misfolding, and has already yielded significant structural information for selected amyloidogenic systems during the aggregation process. This review describes IM-MS for protein structure investigation, and provides a summary of current research highlighting how this methodology has unequivocally and unprecedentedly provided structural and mechanistic detail pertaining to the oligomerization of a variety of disease related proteins.
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Affiliation(s)
- Danielle M Williams
- School of Chemistry and Physics, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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33
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Sokratous K, Layfield R, Oldham NJ. The effects of cation adduction upon the conformation of three-helix bundle protein domains. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12127-012-0114-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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34
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Chawner R, McCullough B, Giles K, Barran PE, Gaskell SJ, Eyers CE. QconCAT standard for calibration of ion mobility-mass spectrometry systems. J Proteome Res 2012; 11:5564-72. [PMID: 22985290 DOI: 10.1021/pr3005327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) is a useful technique for determining information about analyte ion conformation in addition to mass/charge ratio. The physical principles that govern the mobility of an ion through a gas in the presence of a uniform electric field are well understood, enabling rotationally averaged collision cross sections (Ω) to be directly calculated from measured drift times under well-defined experimental conditions. However, such "first principle" calculations are not straightforward for Traveling Wave (T-Wave) mobility separations due to the range of factors that influence ion motion through the mobility cell. If collision cross section information is required from T-Wave mobility separations, then calibration of the instruments using known standards is essential for each set of experimental conditions. To facilitate such calibration, we have designed and generated an artificial protein based on the QconCAT technology, QCAL-IM, which upon proteolysis can be used as a universal ion mobility calibration standard. This single unique standard enables empirical calculation of peptide ion collision cross sections from the drift time on a T-Wave mobility instrument.
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Affiliation(s)
- Ross Chawner
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN, United Kingdom
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35
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Ovchinnikov V, Karplus M. Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin. J Phys Chem B 2012; 116:8584-603. [PMID: 22409258 PMCID: PMC3406239 DOI: 10.1021/jp212634z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The popular targeted molecular dynamics (TMD) method for generating transition paths in complex biomolecular systems is revisited. In a typical TMD transition path, the large-scale changes occur early and the small-scale changes tend to occur later. As a result, the order of events in the computed paths depends on the direction in which the simulations are performed. To identify the origin of this bias, and to propose a method in which the bias is absent, variants of TMD in the restraint formulation are introduced and applied to the complex open ↔ closed transition in the protein calmodulin. Due to the global best-fit rotation that is typically part of the TMD method, the simulated system is guided implicitly along the lowest-frequency normal modes, until the large spatial scales associated with these modes are near the target conformation. The remaining portion of the transition is described progressively by higher-frequency modes, which correspond to smaller-scale rearrangements. A straightforward modification of TMD that avoids the global best-fit rotation is the locally restrained TMD (LRTMD) method, in which the biasing potential is constructed from a number of TMD potentials, each acting on a small connected portion of the protein sequence. With a uniform distribution of these elements, transition paths that lack the length-scale bias are obtained. Trajectories generated by steered MD in dihedral angle space (DSMD), a method that avoids best-fit rotations altogether, also lack the length-scale bias. To examine the importance of the paths generated by TMD, LRTMD, and DSMD in the actual transition, we use the finite-temperature string method to compute the free energy profile associated with a transition tube around a path generated by each algorithm. The free energy barriers associated with the paths are comparable, suggesting that transitions can occur along each route with similar probabilities. This result indicates that a broad ensemble of paths needs to be calculated to obtain a full description of conformational changes in biomolecules. The breadth of the contributing ensemble suggests that energetic barriers for conformational transitions in proteins are offset by entropic contributions that arise from a large number of possible paths.
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36
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Calabrese AN, Speechley LA, Pukala TL. Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry. Aust J Chem 2012. [DOI: 10.1071/ch12047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.
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Hamdy OM, Julian RR. Reflections on charge state distributions, protein structure, and the mystical mechanism of electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1-6. [PMID: 22076632 DOI: 10.1007/s13361-011-0284-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 10/18/2011] [Accepted: 10/19/2011] [Indexed: 05/31/2023]
Abstract
The connection between charge state distributions, protein structure, and mechanistic details of electrospray are discussed in relation to the emerging field of gas phase structural biology. Comparisons are drawn with the established area of enzymatic catalysis in organic solvents, which shares many similar challenges. Charge solvation emerges as a dominant force in both systems that must be dealt with to enable kinetic trapping of native structures in foreign environments. Potential methods for mediating unfavorable charge solvation effects are discussed and, ironically, do not include partial solvation by water. The importance of timescale in relation to the evolution of protein structure during the process of electrospray ionization is discussed. Finally several prospects for future endeavors are highlighted.
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Pan J, Heath BL, Jockusch RA, Konermann L. Structural Interrogation of Electrosprayed Peptide Ions by Gas-Phase H/D Exchange and Electron Capture Dissociation Mass Spectrometry. Anal Chem 2011; 84:373-8. [DOI: 10.1021/ac202730d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jingxi Pan
- Department of Chemistry, The University of Western Ontario, London,
Ontario, N6A 5B7, Canada
| | - Brittany L. Heath
- Department of Chemistry, University of Toronto, Toronto, Ontario
M5S 3H6, Canada
| | - Rebecca A. Jockusch
- Department of Chemistry, University of Toronto, Toronto, Ontario
M5S 3H6, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London,
Ontario, N6A 5B7, Canada
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39
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Atilgan AR, Aykut AO, Atilgan C. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J Chem Phys 2011; 135:155102. [DOI: 10.1063/1.3651807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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40
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Wyttenbach T, Bowers MT. Structural Stability from Solution to the Gas Phase: Native Solution Structure of Ubiquitin Survives Analysis in a Solvent-Free Ion Mobility–Mass Spectrometry Environment. J Phys Chem B 2011; 115:12266-75. [DOI: 10.1021/jp206867a] [Citation(s) in RCA: 258] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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41
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Jenner M, Ellis J, Huang WC, Lloyd Raven E, Roberts GCK, Oldham NJ. Detection of a Protein Conformational Equilibrium by Electrospray Ionisation-Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics. PLoS Comput Biol 2011; 7:e1002114. [PMID: 21829336 PMCID: PMC3145654 DOI: 10.1371/journal.pcbi.1002114] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/23/2011] [Indexed: 11/20/2022] Open
Abstract
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells. Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.
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43
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Jenner M, Ellis J, Huang WC, Lloyd Raven E, Roberts GCK, Oldham NJ. Detection of a Protein Conformational Equilibrium by Electrospray Ionisation-Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2011; 50:8291-4. [DOI: 10.1002/anie.201101077] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 05/25/2011] [Indexed: 01/23/2023]
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44
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Jurneczko E, Barran PE. How useful is ion mobility mass spectrometry for structural biology? The relationship between protein crystal structures and their collision cross sections in the gas phase. Analyst 2011; 136:20-8. [DOI: 10.1039/c0an00373e] [Citation(s) in RCA: 261] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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45
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Hilton GR, Thalassinos K, Grabenauer M, Sanghera N, Slade SE, Wyttenbach T, Robinson PJ, Pinheiro TJT, Bowers MT, Scrivens JH. Structural analysis of prion proteins by means of drift cell and traveling wave ion mobility mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:845-854. [PMID: 20206551 DOI: 10.1016/j.jasms.2010.01.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 05/28/2023]
Abstract
The prion protein (PrP) is implicitly involved in the pathogenesis of transmissible spongiform encephalopathies (TSEs). The conversion of normal cellular PrP (PrP(C)), a protein that is predominantly alpha-helical, to a beta-sheet-rich isoform (PrP(Sc)), which has a propensity to aggregate, is the key molecular event in prion diseases. During its short life span, PrP can experience two different pH environments; a mildly acidic environment, whilst cycling within the cell, and a neutral pH when it is glycosyl phosphatidylinositol (GPI)-anchored to the cell membrane. Ion mobility (IM) combined with mass spectrometry has been employed to differentiate between two conformational isoforms of recombinant Syrian hamster prion protein (SHaPrP). The recombinant proteins studied were alpha-helical SHaPrP(90-231) and beta-sheet-rich SHaPrP(90-231) at pH 5.5 and pH 7.0. The recombinant proteins have the same nominal mass-to-charge ratio (m/z) but differ in their secondary and tertiary structures. A comparison of traveling-wave (T-Wave) ion mobility and drift cell ion mobility (DCIM) mass spectrometry estimated and absolute cross-sections showed an excellent agreement between the two techniques. The use of T-Wave ion mobility as a shape-selective separation technique enabled differentiation between the estimated cross-sections and arrival time distributions (ATDs) of alpha-helical SHaPrP(90-231) and beta-sheet-rich SHaPrP(90-231) at pH 5.5. No differences in cross-section or ATD profiles were observed between the protein isoforms at pH 7.0. The findings have potential implications for a new ante-mortem screening assay, in bodily fluids, for prion misfolding diseases such as TSEs.
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Affiliation(s)
- Gillian R Hilton
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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46
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Pan J, Konermann L. Calcium-Induced Structural Transitions of the Calmodulin−Melittin System Studied by Electrospray Mass Spectrometry: Conformational Subpopulations and Metal-Unsaturated Intermediates. Biochemistry 2010; 49:3477-86. [DOI: 10.1021/bi100261c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jingxi Pan
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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