1
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Kienlein M, Zacharias M, Reif MM. Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations. J Chem Theory Comput 2024; 20:2643-2654. [PMID: 38465868 DOI: 10.1021/acs.jctc.3c01356] [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: 03/12/2024]
Abstract
It is well-known that proline (Pro) cis-trans isomerization plays a decisive role in the folding and stabilization of proteins. The conformational coupling between isomerization states of different Pro residues in proteins during conformational adaptation processes is not well understood. In the present work, we investigate the coupled cis-trans isomerization of three Pro residues using bradykinin (BK), a partially unstructured nonapeptide hormone, as a model system. We use a recently developed enhanced-sampling molecular dynamics method (ω-bias potential replica exchange molecular dynamics; ωBP-REMD) that allows us to exhaustively sample all combinations of Pro isomer states and obtain converged probability densities of all eight state combinations within 885 ns ωBP-REMD simulations. In agreement with experiment, the all-trans state is seen to be the preferred isomer of zwitterionic aqueous BK. In about a third of its structures, this state presents the characteristic C-terminal β-turn conformation; however, other isomer combinations also contribute significantly to the structural ensemble. Unbiased probabilities can be projected onto the peptide bond dihedral angles of the three Pro residues. This unveils the interdependence of the individual Pro isomerization states, i.e., a possible coupling of the different Pro isomers. The cis/trans equilibrium of a Pro residue can change by up to 2.5 kcal·mol-1, depending on the isomerization state of other Pro residues. For example, for Pro7, the simulations indicate that its cis state becomes favored compared to its trans state when Pro2 is switched from the trans state to the cis state. Our findings demonstrate the efficiency of the ωBP-REMD methodology and suggest that the coupling of Pro isomerization states may play an even more decisive role in larger folded proteins subject to more conformational restraints.
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Affiliation(s)
- Maximilian Kienlein
- Center for Functional Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Maria M Reif
- Center for Functional Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
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2
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Greive SJ, Bacri L, Cressiot B, Pelta J. Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning. ACS NANO 2024; 18:539-550. [PMID: 38134312 DOI: 10.1021/acsnano.3c08433] [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: 12/24/2023]
Abstract
There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.
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Affiliation(s)
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Benjamin Cressiot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
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3
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Pan H, Raab SA, El-Baba TJ, Schrecke SR, Laganowsky A, Russell DH, Clemmer DE. Variation of CI-2 Conformers upon Addition of Methanol to Water: An IMS-MS-Based Thermodynamic Analysis. J Phys Chem A 2023; 127:9399-9408. [PMID: 37934510 PMCID: PMC11212803 DOI: 10.1021/acs.jpca.3c03651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a well-studied, textbook example of a cooperative, two-state, native ↔ denatured folding transition. A recent hybrid ion mobility spectrometry (IMS)/mass spectrometry (MS) thermal denaturation study of CI-2 (the well-studied truncated 64-residue model) in water reported evidence that this two-state transition involves numerous (∼41) unique native and non-native (denatured) solution conformations. The characterization of so many, often low-abundance, states is possible because of the very high dynamic range of IMS-MS measurements of ionic species that are produced upon electrospraying CI-2 solutions from a variable temperature electrospray ionization source. A thermodynamic analysis of these states revealed large changes in enthalpy (ΔH) and entropy (ΔS) at different temperatures, and it was suggested that such variation might arise because of temperature-dependent conformational changes of the protein in response to changes in the conformational entropy and the dielectric permeability of water, which drops from a value of ε ∼ 79 at 24 °C to ∼ 60 at 82 °C. Herein, we examine how adding methanol to water influences the distributions of CI-2 conformers and their ensuing stabilities. The dielectric constant of a 60:40 water:methanol (MeOH) drops from ε ∼ 60 at 24 °C to ∼ 51 at 64 °C. Although the same set of conformers observed in water appears to be present in 60:40 water:MeOH, the abundance of each is substantially altered by the presence of methanol. Relative free energy values (ΔG) and thermodynamic values [ΔH and ΔS and heat capacities (ΔCp)] are derived from a Gibbs-Helmholtz analysis. A comparison of these data from water and water:MeOH systems allows rare insight into how variations in solvation and temperature affect many-state protein equilibria. While these studies confirm that variations in solvent dielectric constant with temperature affect the distributions of conformers that are observed, our findings suggest that other solvent differences may also affect abundances.
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Affiliation(s)
- Hua Pan
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Samantha R Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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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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Jeanne Dit Fouque K, Sipe SN, Garabedian A, Mejia G, Su L, Hossen ML, Chapagain PP, Leng F, Brodbelt JS, Fernandez-Lima F. Exploring the Conformational and Binding Dynamics of HMGA2·DNA Complexes Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1103-1112. [PMID: 35687119 PMCID: PMC9280850 DOI: 10.1021/jasms.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is an intrinsically disordered DNA-binding protein expressed during embryogenesis. In the present work, the conformational and binding dynamics of HMGA2 and HMGA2 in complex with a 22-nt (DNA22) and a 50-nt (DNA50) AT-rich DNA hairpin were investigated using trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) under native starting solvent conditions (e.g., 100 mM aqueous NH4Ac) and collision-induced unfolding/dissociation (CIU/CID) as well as solution fluorescence anisotropy to assess the role of the DNA ligand when binding to the HMGA2 protein. CIU-TIMS-CID-MS/MS experiments showed a significant reduction of the conformational space and charge-state distribution accompanied by an energy stability increase of the native HMGA2 upon DNA binding. Fluorescence anisotropy experiments and CIU-TIMS-CID-MS/MS demonstrated for the first time that HMGA2 binds with high affinity to the minor groove of AT-rich DNA oligomers and with lower affinity to the major groove of AT-rich DNA oligomers (minor groove occupied by a minor groove binder Hoechst 33258). The HMGA2·DNA22 complex (18.2 kDa) 1:1 and 1:2 stoichiometry suggests that two of the AT-hook sites are accessible for DNA binding, while the other AT-hook site is probably coordinated by the C-terminal motif peptide (CTMP). The HMGA2 transition from disordered to ordered upon DNA binding is driven by the interaction of the three basic AT-hook residues with the minor and/or major grooves of AT-rich DNA oligomers.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - German Mejia
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Linjia Su
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Md Lokman Hossen
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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6
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Li J, Li L, Gao W, Shi S, Yu J, Tang K. Two-Dimensional FAIMS-IMS Characterization of Peptide Conformers with Resolution Exceeding 1000. Anal Chem 2022; 94:6363-6370. [PMID: 35412805 DOI: 10.1021/acs.analchem.2c00805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A high-performance field asymmetric waveform ion mobility spectrometry (FAIMS)-IMS-MS platform was developed and applied to explore the conformational diversity of the singly and doubly charged bradykinin (BK + H+)+ and (BK + 2H+)2+ ions. With pure N2 as the FAIMS carrier gas, more than ten conformers of (BK + H+)+ can be resolved using FAIMS-IMS, as compared to only four conformers resolved using either FAIMS or IMS alone. Interestingly, multiple conformers of (BK + H+)+ were found to have completely different values of FAIMS compensation voltage (CV), while their IMS drift times were essentially the same, which were also proven experimentally to not result from the structural annealing by the collisional heating in the ion funnel. The separations in the FAIMS and IMS dimensions are substantially orthogonal, and the overall resolving power of two-dimensional FAIMS-IMS separation is largely proportional to the product of the separation resolving powers of FAIMS and IMS. Using a gas mixture of N2/He to further improve the resolving power of the FAIMS separation, the total resolving powers of the combined FAIMS and IMS separation were estimated to be about 1020 and 1400 for (BK + H+)+ and (BK + 2H+)2+ ions, respectively, which are significantly higher than the resolving power of any ion mobility-based separation techniques demonstrated so far. The combined FAIMS-IMS can thus be a much more powerful technique to explore the structural diversity of biomolecules.
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Affiliation(s)
- Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Lei Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Wenqing Gao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Shoudong Shi
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Jiancheng Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.,School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
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7
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Meier F, Park MA, Mann M. Trapped Ion Mobility Spectrometry and Parallel Accumulation-Serial Fragmentation in Proteomics. Mol Cell Proteomics 2021; 20:100138. [PMID: 34416385 PMCID: PMC8453224 DOI: 10.1016/j.mcpro.2021.100138] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in efficiency and ease of implementation have rekindled interest in ion mobility spectrometry, a technique that separates gas phase ions by their size and shape and that can be hybridized with conventional LC and MS. Here, we review the recent development of trapped ion mobility spectrometry (TIMS) coupled to TOF mass analysis. In particular, the parallel accumulation-serial fragmentation (PASEF) operation mode offers unique advantages in terms of sequencing speed and sensitivity. Its defining feature is that it synchronizes the release of ions from the TIMS device with the downstream selection of precursors for fragmentation in a TIMS quadrupole TOF configuration. As ions are compressed into narrow ion mobility peaks, the number of peptide fragment ion spectra obtained in data-dependent or targeted analyses can be increased by an order of magnitude without compromising sensitivity. Taking advantage of the correlation between ion mobility and mass, the PASEF principle also multiplies the efficiency of data-independent acquisition. This makes the technology well suited for rapid proteome profiling, an increasingly important attribute in clinical proteomics, as well as for ultrasensitive measurements down to single cells. The speed and accuracy of TIMS and PASEF also enable precise measurements of collisional cross section values at the scale of more than a million data points and the development of neural networks capable of predicting them based only on peptide sequences. Peptide collisional cross section values can differ for isobaric sequences or positional isomers of post-translational modifications. This additional information may be leveraged in real time to direct data acquisition or in postprocessing to increase confidence in peptide identifications. These developments make TIMS quadrupole TOF PASEF a powerful and expandable platform for proteomics and beyond.
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Affiliation(s)
- Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Functional Proteomics, Jena University Hospital, Jena, Germany.
| | - Melvin A Park
- Bruker Daltonics Inc, Billerica, Massachusetts, USA.
| | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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8
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Zhang Z, Conant CR, El-Baba TJ, Raab SA, Fuller DR, Hales DA, Clemmer DE. Diketopiperazine Formation from FPG nK ( n = 1-9) Peptides: Rates of Structural Rearrangements and Mechanisms. J Phys Chem B 2021; 125:8107-8116. [PMID: 34270248 PMCID: PMC10661757 DOI: 10.1021/acs.jpcb.1c03515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptides with penultimate proline residues undergo trans → cis isomerization of the Phe1-Pro2 peptide bond followed by spontaneous bond cleavage at the Pro2-Xxx3 bond (where Xxx is another amino acid residue), leading to cleavage of the Pro2-Xxx3 bond and formation of a diketopiperazine (DKP). In this paper, ion mobility spectrometry and mass spectrometry techniques were used to study the dissociation kinetics of nine peptides [Phe1-Pro2-Glyn-Lysn+3 (n = 1-9)] in ethanol. Shorter (n = 1-3) peptides are found to be more stable than longer (n = 4-9) peptides. Alanine substitution studies indicate that, when experiments are initiated, the Phe1-Pro2 bond of the n = 9 peptide exists exclusively in the cis configuration, while the n = 1-8 peptides appear to exist initially with both cis- and trans-Phe1-Pro2 configured bonds. Molecular dynamics simulations indicate that intramolecular hydrogen bonding interactions stabilize conformations of shorter peptides, thus inhibiting DKP formation. Similar stabilizing interactions appear less frequently in longer peptides. In addition, in smaller peptides, the N-terminal amino group is more likely to be charged compared to the same group in longer peptides, which would inhibit the dissociation through the DKP formation mechanism. Analysis of temperature-dependent kinetics measurements provides insight about the mechanism of bond cleavage. The analysis gives the following transition state thermochemistry: ΔG⧧ values range from 94.6 ± 0.9 to 101.5 ± 1.9 kJ·mol-1, values of ΔH⧧ range from 89.1 ± 0.9 to 116.7 ± 1.5 kJ·mol-1, and ΔS⧧ values range from -25.4 ± 2.6 to 50.8 ± 4.2 J·mol-1·K-1. Proposed mechanisms and thermochemistry are discussed.
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Affiliation(s)
- Zhichao Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Christopher R Conant
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Daniel R Fuller
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
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9
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Raab SA, El-Baba TJ, Laganowsky A, Russell DH, Valentine SJ, Clemmer DE. Protons Are Fast and Smart; Proteins Are Slow and Dumb: On the Relationship of Electrospray Ionization Charge States and Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1553-1561. [PMID: 34151568 PMCID: PMC9003666 DOI: 10.1021/jasms.1c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present simple considerations of how differences in time scales of motions of protons, the lightest and fastest chemical moiety, and the much longer time scales associated with the dynamics of proteins, among the heaviest and slowest analytes, may allow many protein conformations from solution to be kinetically trapped during the process of electrospraying protein solutions into the gas phase. In solution, the quantum nature of protons leads them to change locations by tunneling, an instantaneous process; moreover, the Grotthuss mechanism suggests that these small particles can respond nearly instantaneously to the dynamic motions of proteins that occur on much longer time scales. A conformational change is accompanied by favorable or unfavorable variations in the free energy of the system, providing the impetus for solvent ↔ protein proton exchange. Thus, as thermal distributions of protein conformations interconvert, protonation states rapidly respond, as specific acidic and basic sites are exposed or protected. In the vacuum of the mass spectrometer, protons become immobilized in locations that are specific to the protein conformations from which they were incorporated. In this way, conformational states from solution are preserved upon electrospraying them into the gas phase. These ideas are consistent with the exquisite sensitivity of electrospray mass spectra to small changes of the local environment that alter protein structure in solution. We might remember this approximation for the protonation of proteins in solution with the colloquial expression-protons are fast and smart; proteins are slow and dumb.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Stephen J Valentine
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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10
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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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11
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Deep learning the collisional cross sections of the peptide universe from a million experimental values. Nat Commun 2021; 12:1185. [PMID: 33608539 PMCID: PMC7896072 DOI: 10.1038/s41467-021-21352-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/22/2021] [Indexed: 01/09/2023] Open
Abstract
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF). The scale and precision (CV < 1%) of our data is sufficient to train a deep recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools peptides validate the model within a 1.4% median relative error (R > 0.99). Hydrophobicity, proportion of prolines and position of histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information. Proteomics has been advanced by algorithms that can predict different peptide features, but predicting peptide collisional cross sections (CCS) has remained challenging. Here, the authors measure over one million CCS values of tryptic peptides and develop a deep learning model for peptide CCS prediction.
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Austin CA, Inutan ED, Bohrer BC, Li J, Fischer JL, Wijerathne K, Foley CD, Lietz CB, Woodall DW, Imperial LF, Clemmer DE, Trimpin S, Larsen BS. Resolving Isomers of Star-Branched Poly(Ethylene Glycols) by IMS-MS Using Multiply Charged Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:21-32. [PMID: 32510213 DOI: 10.1021/jasms.0c00045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion mobility spectrometry (IMS) mass spectrometry (MS) centers on the ability to separate gaseous structures by size, charge, shape, and followed by mass-to-charge (m/z). For oligomeric structures, improved separation is hypothesized to be related to the ability to extend structures through repulsive forces between cations electrostatically bonded to the oligomers. Here we show the ability to separate differently branched multiply charged ions of star-branched poly(ethylene glycol) oligomers (up to 2000 Da) regardless of whether formed by electrospray ionization (ESI) charged solution droplets or from charged solid particles produced directly from a surface by matrix-assisted ionization. Detailed structural characterization of isomers of the star-branched compositions was first established using a home-built high-resolution ESI IMS-MS instrument. The doubly charged ions have well-resolved drift times, achieving separation of isomers and also allowing differentiation of star-branched versus linear oligomers. An IMS-MS "snapshot" approach allows visualization of architectural dispersity and (im)purity of samples in a straightforward manner. Analyses capabilities are shown for different cations and ionization methods using commercially available traveling wave IMS-MS instruments. Analyses directly from surfaces using the new ionization processes are, because of the multiply charging, not only associated with the benefits of improved gas-phase separations, relative to that of ions produced by matrix-assisted laser desorption/ionization, but also provide the potential for spatially resolved measurements relative to ESI and other ionization methods.
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Affiliation(s)
- Calvin A Austin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Brian C Bohrer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jing Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Joshua L Fischer
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Kanchana Wijerathne
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Casey D Foley
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Christopher B Lietz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Daniel W Woodall
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Lorelie F Imperial
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara S Larsen
- DuPont, Nutrition & Biosciences, Wilmington, Delaware 19808, United States
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13
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Raab SA, El-Baba TJ, Woodall DW, Liu W, Liu Y, Baird Z, Hales DA, Laganowsky A, Russell DH, Clemmer DE. Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. J Am Chem Soc 2020; 142:17372-17383. [PMID: 32866376 DOI: 10.1021/jacs.0c05365] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a classic model for two-state cooperative protein folding and is one of the most extensively studied systems. Alan Fersht, a pioneer in the field of structural biology, has studied the wild-type (wt) and over 100 mutant forms of CI-2 with traditional analytical and biochemical techniques. Here, we examine wt CI-2 and three mutant forms (A16G, K11A, L32A) to demonstrate the utility of variable-temperature (vT) electrospray ionization (ESI) paired with ion mobility spectrometry (IMS) and mass spectrometry (MS) to map the free energy folding landscape. As the solution temperature is increased, the abundance of each of the six ESI charge states for wt CI-2 and each mutant is found to vary independently. These results require that at least six unique types of CI-2 solution conformers are present. Ion mobility analysis reveals that within each charge state there are additional conformers having distinct solution temperature profiles. A model of the data at ∼30 different temperatures for all four systems suggests the presence of 41 unique CI-2 solution conformations. A thermodynamic analysis of this system yields values of ΔCp as well as ΔG, ΔH, and ΔS for each state at every temperature studied. Detailed energy landscapes derived from these data provide a rare glimpse into Anfinsen's thermodynamic hypothesis and the process of thermal denaturation, normally thought of as a cooperative two-state transition involving the native state and unstructured denatured species. Specifically, as the temperature is varied, the entropies and enthalpies of different conformers undergo dramatic changes in magnitude and relative order to maintain the delicate balance associated with equilibrium.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Wen Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zane Baird
- Baxter Healthcare Corporation, 927 South Curry Pike, Bloomington, Indiana 47403, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas 72032, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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15
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Jeanne Dit Fouque K, Fernandez-Lima F. Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. J Phys Chem B 2020; 124:6257-6265. [PMID: 32560586 PMCID: PMC8341290 DOI: 10.1021/acs.jpcb.0c04276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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16
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Brown CJ, Woodall DW, El-Baba TJ, Clemmer DE. Characterizing Thermal Transitions of IgG with Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2438-2445. [PMID: 31363989 PMCID: PMC6866664 DOI: 10.1007/s13361-019-02292-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 06/02/2023]
Abstract
Variable temperature electrospray ionization (ESI) is coupled with mass spectrometry techniques in order to investigate structural transitions of monoclonal antibody immunoglobulin G (IgG) in a 100-mM ammonium acetate (pH 7.0) solution from 26 to 70 °C. At 26 °C, the mass spectrum for intact IgG shows six charge states + 22 to + 26. Upon increasing the solution temperature, the fraction of low-charge states decreases and new, higher-charge state ions are observed. Upon analysis, it appears that heating the solution aids in desolvation of the intact IgG precursor. Above ~ 50 °C, a cleavage event between the light and heavy chains is observed. An analysis of the kinetics for these processes at different temperatures yields transition state thermochemistry of ΔH‡ = 95 ± 10 kJ mol-1, ΔS‡ = 8 ± 1 J mol-1 K-1, and ΔG‡ = 92 ± 11 kJ mol-1. The mechanism for light chain dissociation appears to involve disulfide bond scrambling that ultimately results in a non-native Cys199-Cys217 disulfide bond in the light chain product. Above ~ 70 °C, we are unable to produce a stable ESI signal. The loss of signal is ascribed to aggregation that is primarily associated with the remaining portion of the antibody after having lost the light chain. Graphical Abstract.
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Affiliation(s)
- Christopher J Brown
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA.
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17
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Talbert LE, Julian RR. Methionine and Selenomethionine as Energy Transfer Acceptors for Biomolecular Structure Elucidation in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1601-1608. [PMID: 31222676 PMCID: PMC6697561 DOI: 10.1007/s13361-019-02262-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 06/09/2023]
Abstract
Mass spectrometry affords rapid and sensitive analysis of peptides and proteins. Coupling spectroscopy with mass spectrometry allows for the development of new methods to enhance biomolecular structure determination. Herein, we demonstrate two new energy acceptors that can be utilized for action-excitation energy transfer experiments. In the first system, C-S bonds in methionine act as energy acceptors from native chromophores, including tyrosine, tryptophan, and phenylalanine. Comparison among chromophores reveals that tyrosine transfers energy most efficiently at 266 nm, but phenylalanine and tryptophan also transfer energy with comparable efficiencies. Overall, the C-S bond dissociation yields following energy transfer are low for methionine, which led to an investigation of selenomethionine, a common analog that is found in many naturally occurring proteins. Sulfur and selenium are chemically similar, but C-Se bonds are weaker than C-S bonds and have lower lying σ* anti-bonding orbitals. Excitation of peptides containing tyrosine and tryptophan results in efficient energy transfer to selenomethionine and abundant C-Se bond dissociation. A series of helical peptides were examined where the positions of the donor or acceptor were systematically scanned to explore the influence of distance and helix orientation on energy transfer. The distance was found to be the primary factor affecting energy transfer efficiency, suggesting that selenomethionine may be a useful acceptor for probing protein structure in the gas phase.
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Affiliation(s)
- Lance E Talbert
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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18
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Kirk SR, Liu FC, Cropley TC, Carlock HR, Bleiholder C. On the Preservation of Non-covalent Peptide Assemblies in a Tandem-Trapped Ion Mobility Spectrometer-Mass Spectrometer (TIMS-TIMS-MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1204-1212. [PMID: 31025294 DOI: 10.1007/s13361-019-02200-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 05/21/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) has demonstrated the ability to characterize structures of weakly-bound peptide assemblies. However, these assemblies can potentially dissociate during the IMS-MS measurement if they undergo energetic ion-neutral collisions. Here, we investigate the ability of tandem-trapped ion mobility spectrometry-mass spectrometry (TIMS-TIMS-MS) to retain weakly-bound peptide assemblies. We assess ion heating and dissociaton in the tandem-TIMS instrument using bradykinin and its assemblies as reference systems. Our data indicate that non-covalent bradykinin assemblies are largely preserved in TIMS-TIMS under carefully selected operating conditions. Importantly, we observe quadruply-charged bradykinin tetramers, which attests to the "softness" of our instrument. Graphical Abstract.
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Affiliation(s)
- Samuel R Kirk
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Fanny C Liu
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Tyler C Cropley
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Hunter R Carlock
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Christian Bleiholder
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4390, USA.
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Jeanne Dit Fouque K, Moreno J, Fernandez-Lima F. Exploring the Conformational Space of Growth-Hormone-Releasing Hormone Analogues Using Dopant Assisted Trapped Ion Mobility Spectrometry–Mass Spectrometry. J Phys Chem B 2019; 123:6169-6177. [DOI: 10.1021/acs.jpcb.9b03777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Javier Moreno
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., AHC4-211, Miami, Florida 33199, United States
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Conant CR, Fuller DR, Zhang Z, Woodall DW, Russell DH, Clemmer DE. Substance P in the Gas Phase: Conformational Changes and Dissociations Induced by Collisional Activation in a Drift Tube. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:932-945. [PMID: 30980379 PMCID: PMC6865269 DOI: 10.1007/s13361-019-02160-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 05/02/2023]
Abstract
The work presented below is related to our companion paper in this issue, entitled: Substance P in solution: trans-to-cis configurational changes of penultimate prolines initiate non-enzymatic peptide bond cleavages. Two-dimensional ion mobility spectrometry (IMS-IMS) and mass spectrometry techniques are used to investigate structural transitions for [M+3H]3+ ions of substance P (subP) upon collisional activation (CA) in the gas phase. In this approach, different conformations of ions having a specified mobility are selected after an initial IMS separation, collisionally activated to produce new conformers, and these product structures are separated again using a second IMS region. In this way, it is possible to follow folding and unfolding transitions of different conformations. The analysis shows evidence for five conformations. Unlike other systems, every transition is irreversible. Studies as a function of activation voltage are used to discern pathways of structural changes prior to reaching the energy required for dissociation. Thresholds associated with the onsets of transitions are calibrated to obtain estimates of the energetic barriers between different structures and semi-quantitative potential energy diagrams are presented. Overall, barriers associated with structural transitions of [subP+3H]3+ in the absence of solvent are on the order of ~ 40 kJ mol-1, substantially lower than the ~ 90 kJ mol-1 required for some similar structural transitions in solutions of ethanol. Comparisons of the transition energies in the gas phase with thermochemistry for similar transitions in solution provide clues about why reverse transitions are prohibited. Graphical Abstract.
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Affiliation(s)
- Christopher R Conant
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel R Fuller
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Zhichao Zhang
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA.
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Trimpin S, Inutan ED, Karki S, Elia EA, Zhang WJ, Weidner SM, Marshall DD, Hoang K, Lee C, Davis ETJ, Smith V, Meher AK, Cornejo MA, Auner GW, McEwen CN. Fundamental Studies of New Ionization Technologies and Insights from IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1133-1147. [PMID: 31062287 DOI: 10.1007/s13361-019-02194-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Exceptional ion mobility spectrometry mass spectrometry (IMS-MS) developments by von Helden, Jarrold, and Clemmer provided technology that gives a view of chemical/biological compositions previously not achievable. The ionization method of choice used with IMS-MS has been electrospray ionization (ESI). In this special issue contribution, we focus on fundamentals of heretofore unprecedented means for transferring volatile and nonvolatile compounds into gas-phase ions singly and multiply charged. These newer ionization processes frequently lead to different selectivity relative to ESI and, together with IMS-MS, may provide a more comprehensive view of chemical compositions directly from their original environment such as surfaces, e.g., tissue. Similarities of results using solvent- and matrix-assisted ionization are highlighted, as are differences between ESI and the inlet ionization methods, especially with mixtures such as bacterial extracts. Selectivity using different matrices is discussed, as are results which add to our fundamental knowledge of inlet ionization as well as pose additional avenues for inquiry. IMS-MS provides an opportunity for comparison studies relative to ESI and will prove valuable using the new ionization technologies for direct analyses. Our hypothesis is that some ESI-IMS-MS applications will be replaced by the new ionization processes and by understanding mechanistic aspects to aid enhanced source and method developments this will be hastened.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
- Cardiovascular Research Institute, School of Medicine, Wayne State University, Detroit, MI, USA.
- MSTM, LLC, Newark, DE, USA.
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | | | - Wen-Jing Zhang
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Steffen M Weidner
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Darrell D Marshall
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Khoa Hoang
- University of the Sciences, Philadelphia, PA, USA
| | - Chuping Lee
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Eric T J Davis
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Anil K Meher
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Mario A Cornejo
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Gregory W Auner
- Department of Surgery, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Charles N McEwen
- MSTM, LLC, Newark, DE, USA
- University of the Sciences, Philadelphia, PA, USA
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22
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Choi CM, Kulesza A, Daly S, MacAleese L, Antoine R, Dugourd P, Chirot F. Ion mobility resolved photo-fragmentation to discriminate protomers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 1:28-34. [PMID: 29885203 DOI: 10.1002/rcm.8202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Among the sources of structural diversity in biomolecular ions, the co-existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas-phase data. METHODS We investigated the sensitivity of gas-phase photo-fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo-fragmentation measurements on mobility-selected ions. All results were interpreted based on molecular dynamics simulations. RESULTS We show that protonation can significantly affect the photo-fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo-fragmentation yields in relation with different protonation patterns. CONCLUSIONS We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo-fragmentation and IMS can help to identify the signature of protomer co-existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes.
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Affiliation(s)
- Chang Min Choi
- Mass Spectrometry and Advanced Instrumentation Research Group, Div. of Scientific Instrumentation, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Alexander Kulesza
- CNRS, UMR5306 Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne cedex, France
| | - Steven Daly
- CNRS, UMR5306 Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne cedex, France
| | - Luke MacAleese
- CNRS, UMR5306 Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne cedex, France
| | - Rodolphe Antoine
- CNRS, UMR5306 Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne cedex, France
| | - Philippe Dugourd
- CNRS, UMR5306 Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne cedex, France
| | - Fabien Chirot
- CNRS, Ens de Lyon, UMR5280 Institut Sciences Analytiques, Univ Lyon, Université Claude Bernard Lyon 1, 69100, Villeurbanne, France
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23
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Butcher D, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F. The effects of solution additives and gas-phase modifiers on the molecular environment and conformational space of common heme proteins. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:399-404. [PMID: 30421840 DOI: 10.1002/rcm.8347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE The molecular environment is known to impact the secondary and tertiary structures of biomolecules both in solution and in the gas phase, shifting the equilibrium between different conformational and oligomerization states. However, there is a lack of studies monitoring the impacts of solution additives and gas-phase modifiers on biomolecules characterized using ion mobility techniques. METHODS The effect of solution additives and gas-phase modifiers on the molecular environment of two common heme proteins, bovine cytochrome c and equine myoglobin, is investigated as a function of the time after desolvation (e.g., 100-500 ms) using nanoelectrospray ionization coupled to trapped ion mobility spectrometry with detection by time-of-flight mass spectrometry. Organic compounds used as additives/modifiers (methanol, acetonitrile, acetone) were either added to the aqueous protein solution before ionization or added to the ion mobility bath gas by nebulization. RESULTS Changes in the mobility profiles are observed depending on the starting solution composition (i.e., in aqueous solution at neutral pH or in the presence of organic content: methanol, acetone, or acetonitrile) and the protein. In the presence of gas-phase modifiers (i.e., N2 doped with methanol, acetone, or acetonitrile), a shift in the mobility profiles driven by the gas-modifier mass and size and changes in the relative abundances and number of IMS bands are observed. CONCLUSIONS We attribute the observed changes in the mobility profiles in the presence of gas-phase modifiers to a clustering/declustering mechanism by which organic molecules adsorb to the protein ion surface and lower energetic barriers for interconversion between conformational states, thus redefining the free energy landscape and equilibria between conformers. These structural biology experiments open new avenues for manipulation and interrogation of biomolecules in the gas phase with the potential to emulate a large suite of solution conditions, ultimately including conditions that more accurately reflect a variety of intracellular environments.
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Affiliation(s)
- David Butcher
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Jaroslava Miksovska
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | | | | | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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24
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Jeanne Dit Fouque K, Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS OMEGA 2019; 4:3619-3626. [PMID: 30842985 PMCID: PMC6396120 DOI: 10.1021/acsomega.8b02887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/11/2019] [Indexed: 05/14/2023]
Abstract
Topoisomerases are important complex enzymes that modulate DNA topology to maintain chromosome superstructure and integrity. These enzymes are involved in many cellular processes that resolve specific DNA superstructures and intermediates. The low abundance combined with the biological heterogeneity of relevant intermediates of topoisomerases makes their structural information not readily accessible using traditional structural biology tools (e.g., NMR and X-ray crystallography). In the present work, a second-generation trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was used to study Escherichia coli topoisomerase IA (EcTopIA) and variola virus topoisomerase IB (vTopIB) as well as their complexes with a single-stranded DNA and a stem-loop DNA under native conditions. The higher trapping efficiency and extended mass range of the new, convex TIMS geometry allowed for the separation and identification of multiple conformational states for the two topoisomerases and their DNA complexes. Inspection of the conformational space of EcTopIA and vTopIB in complex with DNA showed that upon DNA binding, the number of conformational states is significantly reduced, suggesting that the DNA binding selects for a narrow range of conformers restricted by the interaction with the DNA substrate. The large microheterogeneity observed for the two DNA binding proteins suggests that they can have multiple biological functions. This work highlights the potential of TIMS-MS for the structural investigations of intrinsically disordered proteins (e.g., DNA binding proteins) as a way to gain a better understanding of the mechanisms involved in DNA substrate recognition, binding, and assembly of the catalytically active enzyme-DNA complex.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
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25
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He M, Luo P, Hong J, Wang X, Wu H, Zhang R, Qu F, Xiang Y, Xu W. Structural Analysis of Biomolecules through a Combination of Mobility Capillary Electrophoresis and Mass Spectrometry. ACS OMEGA 2019; 4:2377-2386. [PMID: 31459477 PMCID: PMC6648644 DOI: 10.1021/acsomega.8b03224] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/24/2019] [Indexed: 05/08/2023]
Abstract
The 3D structures of biomolecules determine their biological function. Established methods in biomolecule structure determination typically require purification, crystallization, or modification of target molecules, which limits their applications for analyzing trace amounts of biomolecules in complex matrices. Here, we developed instruments and methods of mobility capillary electrophoresis (MCE) and its coupling with MS for the 3D structural analysis of biomolecules in the liquid phase. Biomolecules in complex matrices could be separated by MCE and sequentially detected by MS. The effective radius and the aspect ratio of each separated biomolecule were simultaneously determined through the separation by MCE, which were then used as restraints in determining biomolecule conformations through modeling. Feasibility of this method was verified by analyzing a mixture of somatostatin and bradykinin, two peptides with known liquid-phase structures. Proteins could also be structurally analyzed using this method, which was demonstrated for lysozyme. The combination of MCE and MS for complex sample analysis was also demonstrated. MCE and MCE-MS would allow us to analyze trace amounts of biomolecules in complex matrices, which has the potential to be an alternative and powerful biomolecule structure analysis technique.
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Affiliation(s)
- Muyi He
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Pan Luo
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jie Hong
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaofeng Wang
- Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Haimei Wu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ye Xiang
- Beijing
Advanced Innovation Center for Structural Biology, Department of Basic
Medical Sciences, School of Medicine, Tsinghua
University, Beijing 100084, China
- E-mail: (Y.X.)
| | - Wei Xu
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
- E-mail: (W.X.)
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26
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El-Baba TJ, Fuller DR, Hales DA, Russell DH, Clemmer DE. Solvent Mediation of Peptide Conformations: Polyproline Structures in Water, Methanol, Ethanol, and 1-Propanol as Determined by Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:77-84. [PMID: 30069641 PMCID: PMC6503664 DOI: 10.1007/s13361-018-2034-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/03/2018] [Accepted: 07/07/2018] [Indexed: 05/30/2023]
Abstract
Ion mobility spectrometry and circular dichroism spectroscopy are used to examine the populations of the small model peptide, polyproline-13 in water, methanol, ethanol, and 1-propanol over a range of solution temperatures (from 288 to 318 K). At low temperatures, the less-polar solvents (1-propanol and ethanol) favor the all-cis polyproline I helix (PPI); as the temperature is increased, the trans-configured polyproline II helix (PPII) is formed. In polar solvents (methanol and water), PPII is favored at all temperatures. From the experimental data, we determine the relative stabilities of the eight structures in methanol, ethanol, and 1-propanol, as well as four in water, all with respect to PPII. Although these conformers show relatively small differences in free energies, substantial variability is observed in the enthalpies and entropies across the structures and solvents. This requires that enthalpies and entropies be highly correlated: in 1-propanol, cis-configured PPI conformations are energetically favorable but entropically disfavored. In more polar solvents, PPI is enthalpically less favorable and entropy favors trans-configured forms. While either ΔH0 or ΔS0 can favor different structures, no conformation in any solvent is simultaneously energetically and entropically stabilized. These data present a rare opportunity to examine the origin of conformational stability. Graphical Abstract ᅟ.
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Affiliation(s)
- Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel R Fuller
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, AR, 72032, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA.
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27
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Dyachenko A, Tamara S, Heck AJR. Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:7-15. [PMID: 29736602 PMCID: PMC6318259 DOI: 10.1007/s13361-018-1910-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. Graphical Abstract.
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Affiliation(s)
- Andrey Dyachenko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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28
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Karanji AK, Khakinejad M, Kondalaji SG, Majuta SN, Attanayake K, Valentine SJ. Comparison of Peptide Ion Conformers Arising from Non-Helical and Helical Peptides Using Ion Mobility Spectrometry and Gas-Phase Hydrogen/Deuterium Exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2402-2412. [PMID: 30324261 PMCID: PMC6553874 DOI: 10.1007/s13361-018-2053-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/17/2018] [Accepted: 08/03/2018] [Indexed: 05/06/2023]
Abstract
The dominant gas-phase conformer of [M+3H]3+ ions of the model peptide acetyl-PSSSSKSSSSKSSSSKSSSSK has been examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. The [M+3H]3+ peptide ions are observed predominantly as a relatively compact conformer type. Upon subjecting these ions to electron transfer dissociation (ETD), the level of protection for each amino acid residue in the peptide sequence is assessed. The overall per-residue deuterium uptake is observed to be relatively more efficient for the neutral residues than for the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. In comparison, the N-terminal and C-terminal regions of the serine peptide show greater relative protection compared with interior residues. Molecular dynamics (MD) simulations have been used to generate candidate structures for collision cross section and HDX reactivity matching. Hydrogen accessibility scoring (HAS) for select structural candidates from MD simulations has been used to suggest conformer types that could contribute to the observed HDX patterns. The results are discussed with respect to recent studies employing extensive MD simulations of gas-phase structure establishment of a peptide system. Graphical Abstract ᅟ.
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Affiliation(s)
- Ahmad Kiani Karanji
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Mahdiar Khakinejad
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | | | - Sandra N Majuta
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Kushani Attanayake
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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29
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Consta S, In Oh M, Kwan V, Malevanets A. Strengths and Weaknesses of Molecular Simulations of Electrosprayed Droplets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2287-2296. [PMID: 30259408 DOI: 10.1007/s13361-018-2039-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/05/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
The origin and the magnitude of the charge in a macroion are critical questions in mass spectrometry analysis coupled to electrospray and other ionization techniques that transfer analytes from the bulk solution into the gaseous phase via droplets. In many circumstances, it is the later stages of the existence of a macroion in the containing solvent drop before the detection that determines the final charge state. Experimental characterization of small (with linear dimensions of several nanometers) and short-lived droplets is quite challenging. Molecular simulations in principle may provide insight exactly in this challenging for experiments regime. We discuss the strengths and weaknesses of the molecular modeling of electrosprayed droplets using molecular dynamics. We illustrate the limitations of the molecular modeling in the analysis of large macroions and specifically proteins away from their native states. Graphical Abstract ᅟ.
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Affiliation(s)
- Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada.
| | - Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Victor Kwan
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Anatoly Malevanets
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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30
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Musbat L, Assis S, Dilger JM, El-Baba TJ, Fuller DR, Knudsen JL, Kiefer HV, Hirshfeld A, Friedman N, Andersen LH, Sheves M, Clemmer DE, Toker Y. Action and Ion Mobility Spectroscopy of a Shortened Retinal Derivative. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2152-2159. [PMID: 30062478 DOI: 10.1007/s13361-018-2033-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
The development of tandem ion mobility spectroscopy (IMS) known as IMS-IMS has led to extensive research into isomerizations of isolated molecules. Many recent works have focused on the retinal chromophore which is the optical switch used in animal vision. Here, we study a shortened derivative of the chromophore, which exhibits a rich IM spectrum allowing for a detailed analysis of its isomerization pathways, and show that the longer the chromophore is, the lower the barrier energies for isomerization are. Graphical Abstract.
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Affiliation(s)
- Lihi Musbat
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Shirrel Assis
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Jonathan M Dilger
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, IN, 47522, USA
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | - Daniel R Fuller
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | | | - Hjalte V Kiefer
- Department of Physics and Astronomy, Aarhus University, 8000, Aarhus C, Denmark
| | - Amiram Hirshfeld
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noga Friedman
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, 8000, Aarhus C, Denmark
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - David E Clemmer
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | - Yoni Toker
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
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31
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Bell MR, Cruzeiro VWD, Cismesia AP, Tesler LF, Roitberg AE, Polfer NC. Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy. J Phys Chem A 2018; 122:7427-7436. [DOI: 10.1021/acs.jpca.8b05896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Matthew R. Bell
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Vinícius Wilian D. Cruzeiro
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Adam P. Cismesia
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Larry F. Tesler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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32
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Fuller DR, Conant CR, El-Baba TJ, Brown CJ, Woodall DW, Russell DH, Clemmer DE. Conformationally Regulated Peptide Bond Cleavage in Bradykinin. J Am Chem Soc 2018; 140:9357-9360. [PMID: 30028131 PMCID: PMC6503673 DOI: 10.1021/jacs.8b04751] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion mobility and mass spectrometry techniques are used to investigate the stabilities of different conformations of bradykinin (BK, Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9). At elevated solution temperatures, we observe a slow protonation reaction, i.e., [BK+2H]2++H+ → [BK+3H]3+, that is regulated by trans → cis isomerization of Arg1-Pro2, resulting in the Arg1- cis-Pro2- cis-Pro3-Gly4-Phe5-Ser6- cis-Pro7-Phe8-Arg9 (all- cis) configuration. Once formed, the all- cis [BK+3H]3+ spontaneously cleaves the bond between Pro2-Pro3 with perfect specificity, a bond that is biologically resistant to cleavage by any human enzyme. Temperature-dependent kinetics studies reveal details about the intrinsic peptide processing mechanism. We propose that nonenzymatic cleavage at Pro2-Pro3 occurs through multiple intermediates and is regulated by trans → cis isomerization of Arg1-Pro2. From this mechanism, we can extract transition state thermochemistry: Δ G‡ = 94.8 ± 0.2 kJ·mol-1, Δ H‡ = 79.8 ± 0.2 kJ·mol-1, and Δ S‡ = -50.4 ± 1.7 J·mol-1·K-1 for the trans → cis protonation event; and, Δ G‡ = 94.1 ± 9.2 kJ·mol-1, Δ H‡ = 107.3 ± 9.2 kJ·mol-1, and Δ S‡ = 44.4 ± 5.1 J·mol-1·K-1 for bond cleavage. Biological resistance to the most favored intrinsic processing pathway prevents formation of Pro3-Gly4-Phe5-Ser6- cis-Pro7-Phe8-Arg9 that is approximately an order of magnitude more antigenic than BK.
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Affiliation(s)
- Daniel R. Fuller
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher R. Conant
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Tarick J. El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher J. Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel W. Woodall
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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33
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Jeanne Dit Fouque K, Salgueiro LM, Cai R, Sha W, Schally AV, Fernandez-Lima F. Structural Motif Descriptors as a Way To Elucidate the Agonistic or Antagonistic Activity of Growth Hormone-Releasing Hormone Peptide Analogues. ACS OMEGA 2018; 3:7432-7440. [PMID: 31458901 PMCID: PMC6644384 DOI: 10.1021/acsomega.8b00375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/21/2018] [Indexed: 05/05/2023]
Abstract
The synthesis of analogues of hypothalamic neuropeptide growth hormone-releasing hormone (GHRH) is an efficient strategy for designing new therapeutic agents. Several promising synthetic agonist and antagonist analogues of GHRH have been developed based on amino acid mutations of the GHRH (1-29) sequence. Because structural information on the activity of the GHRH agonists or antagonists is limited, there is a need for more effective analytical workflows capable of correlating the peptide sequence with biological activity. In the present work, three GHRH agonists-MR-356, MR-406, and MR-409-and three GHRH antagonists-MIA-602, MIA-606, and MIA-690-were investigated to assess the role of substitutions in the amino acid sequence on structural motifs and receptor binding affinities. The use of high resolution trapped ion mobility spectrometry coupled to mass spectrometry allowed the observation of a large number of peptide-specific mobility bands (or structural motif descriptors) as a function of the amino acid sequence and the starting solution environment. A direct correlation was observed between the amino acid substitutions (i.e., basic residues and d/l-amino acids), the structural motif descriptors, and the biological function (i.e., receptor binding affinities of the GHRH agonists and antagonists). The simplicity, ease, and high throughput of the proposed workflow based on the structural motif descriptors can significantly reduce the cost and time during screening of new synthetic peptide analogues.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry, Florida International
University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| | - Luis M. Salgueiro
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Renzhi Cai
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Wei Sha
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Andrew V. Schally
- Veterans
Affairs Medical Center, 1201 NW 16th Street, Research Service (151), Room
2A103C, Miami, Florida 33125, United States
- Departments
of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology,
Miller School of Medicine, University of
Miami, 1600 NW 10th Avenue
#1140, Miami, Florida 33136, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular
Sciences Institute, Florida International
University, 11200 SW 8th Street, AHC4-211, Miami, Florida 33199, United States
- E-mail:
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34
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Garabedian A, Bolufer A, Leng F, Fernandez-Lima F. Peptide Sequence Influence on the Conformational Dynamics and DNA binding of the Intrinsically Disordered AT-Hook 3 Peptide. Sci Rep 2018; 8:10783. [PMID: 30018295 PMCID: PMC6050235 DOI: 10.1038/s41598-018-28956-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
The intrinsically disordered ATHP3 was studied at native conditions and in complex with DNA using single amino acid substitutions and high-resolution ion mobility spectrometry coupled to mass spectrometry (trapped IMS-MS). Results showed that ATHP3 can exist in multiple conformations at native conditions (at least 10 conformers were separated), with a variety of proline cis/trans orientations, side chain orientations and protonation sites. When in complex with AT rich DNA hairpins, the -RGRP- core is essential for stabilizing the ATHP3: DNA complex. In particular, the arginine in the sixth position plays an important role during binding to AT-rich regions of hairpin DNA, in good agreement with previous NMR and X-ray data. Mobility based correlation matrices are proposed as a way to reveal differences in structural motifs across the peptide mutants based on the conformational space and relative conformer abundance.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Alexander Bolufer
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States. .,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States.
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35
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Garabedian A, Leng F, Ridgeway ME, Park MA, Fernandez-Lima F. Tailoring peptide conformational space with organic gas modifiers in TIMS-MS. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s12127-018-0231-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Jayasekharan T, Gupta SL, Dhiman V. Binding of Cu + and Cu 2+ with peptides: Peptides = oxytocin, Arg 8 -vasopressin, bradykinin, angiotensin-I, substance-P, somatostatin, and neurotensin. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:296-313. [PMID: 29333632 DOI: 10.1002/jms.4062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
The intrinsic binding ability of 7 natural peptides (oxytocin, arg8 -vasopressin, bradykinin, angiotensin-I, substance-P, somatostatin, and neurotensin) with copper in 2 different oxidation states (CuI/II ) derived from different Cu+/2+ precursor sources have been investigated for their charge-dependent binding characteristics. The peptide-CuI/II complexes, [M - (n-1)H + nCuI ] and [M - (2n-1)H + nCuII ], are prepared/generated by the reaction of peptides with CuI solution/Cu-target and CuSO4 solution and are analyzed by using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. The MALDI mass spectra of both [M - (n-1)H + nCuI ] and [M - (2n-1)H + nCuII ] complexes show no mass shift due to the loss of ─H atoms in the main chain ─NH of these peptides by Cu+ and Cu2+ deprotonation. The measured m/z value indicates the reduction of CuI/II oxidation state into Cu0 during MALDI processes. The number and relative abundance of Cu+ bound to the peptides are greater compared with the Cu2+ bound peptides. Oxytocin, arg8 -vasopressin, bradykinin, substance-P, and somatostatin show the binding of 5Cu+ , and angiotensin-I and neurotensin show the binding of 7Cu+ from both CuI and Cu targets, while bradykinin shows the binding of 2Cu2+ , oxytocin, arg8 -vasopressin, angiotensin-I, and substance-P; somatostatin shows the binding of 3Cu2+ ; and neurotensin shows 4Cu2+ binding. The binding of more Cu+ with these small peptides signifies that the bonding characteristics of both Cu+ and Cu2+ are different. The amino acid residues responsible for the binding of both Cu+ and Cu2+ in these peptides have been identified based on the density functional theory computed binding energy values of Cu+ and the fragment transformation method predicted binding preference of Cu2+ for individual amino acids.
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Affiliation(s)
- Thankan Jayasekharan
- Atomic and Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Shyam L Gupta
- Atomic and Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Vikas Dhiman
- Atomic and Molecular Physics Division, Physics Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
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37
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Stocks BB, Melanson JE. In-Source Reduction of Disulfide-Bonded Peptides Monitored by Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:742-751. [PMID: 29450858 DOI: 10.1007/s13361-018-1894-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/15/2018] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Many peptides with antimicrobial activity and/or therapeutic potential contain disulfide bonds as a means to enhance stability, and their quantitation is often performed using electrospray ionization mass spectrometry (ESI-MS). Disulfides can be reduced during ESI under commonly used instrument conditions, which has the potential to hinder accurate peptide quantitation. We demonstrate that this in-source reduction (ISR) is predominantly observed for peptides infused from acidic solutions and subjected to elevated ESI voltages (3-4 kV). ISR is readily apparent in the mass spectrum of oxytocin-a small, single disulfide-containing peptide. However, subtle m/z shifts due to partial ISR of highly charged (z ≥ 3) peptides with multiple disulfide linkages may proceed unnoticed. Ion mobility (IM)-MS separates ions on the basis of charge and shape in the gas phase, and using insulin as a model system, we show that IM-MS arrival time distributions (ATDs) are particularly sensitive to partial ISR of large peptides. Isotope modeling allows for the relative quantitation of disulfide-intact and partially reduced states of the mobility-separated peptide conformers. Interestingly, hepcidin peptides ionized from acidic solutions at elevated ESI voltages undergo gas-phase compaction, ostensibly due to partial disulfide ISR. Our IM-MS results lead us to propose that residual acid is the likely cause of disparate ATDs recently measured for hepcidin from different suppliers [Anal. Bioanal. Chem. 409, 2559-2567 (2017)]. Overall, our results demonstrate the utility of IM-MS to detect partial ISR of disulfide-bonded peptides and reinforce the notion that peptide/protein measurements should be carried out using minimally activating instrument conditions. Graphical Abstract ᅟ.
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Affiliation(s)
- Bradley B Stocks
- National Research Council of Canada, Measurement Science and Standards, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada.
| | - Jeremy E Melanson
- National Research Council of Canada, Measurement Science and Standards, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
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38
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Du Z, Sun T, Zhao J, Wang D, Zhang Z, Yu W. Development of a plug-type IMS-MS instrument and its applications in resolving problems existing in in-situ detection of illicit drugs and explosives by IMS. Talanta 2018; 184:65-72. [PMID: 29674084 DOI: 10.1016/j.talanta.2018.02.086] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/12/2017] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
Abstract
Ion mobility spectrometry (IMS) which acts as a rapid analysis technique is widely used in the field detection of illicit drugs and explosives. Due to limited separation abilities of the pint-sized IMS challenges and problems still exist regarding high false positive and false negative responses due to the interference of the matrix. In addition, the gas-phase ion chemistry and special phenomena in the IMS spectra, such one substance showing two peaks, were not identified unambiguously. In order to explain or resolve these questions, in this paper, an ion mobility spectrometry was coupled to a mass spectrometry (IMS-MS). A commercial IMS is embedded in a custom-built ion chamber shell was attached to the mass spectrometer. The faraday plate of IMS was fabricated with a hole for the ions to passing through to the mass spectrometer. The ion transmission efficiency of IMS-MS was optimized by optimizing the various parameters, especially the distance between the faraday plate and the cone of mass spectrum. This design keeps the integrity of the two original instruments and the mass spectrometry still works with multimode ionization source (i.e., IMS-MS, ESI-MS, APCI-MS modes). The illicit drugs and explosive samples were analyzed by the IMS-MS with 63Ni source. The results showed that the IMS-MS is of high sensitivity. The ionization mechanism of the illicit drug and explosive samples with 63Ni source were systematically studied. In addition, the interferent which interfered the detection of cocaine was identified as dibutyl phthalate (DBP) by this platform. The reason why the acetone solution of amphetamine showed two peaks was explained.
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Affiliation(s)
- Zhenxia Du
- College of Science, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, China.
| | - Tangqiang Sun
- College of Science, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, China
| | - Jianan Zhao
- College of Science, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, China
| | - Di Wang
- College of Science, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing, China
| | | | - Wenlian Yu
- Chinese Academy of Inspection and Quarantine, Beijing, China
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39
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Garabedian A, Baird M, Porter J, Jeanne Dit Fouque K, Shliaha PV, Jensen ON, Williams TD, Fernandez-Lima F, Shvartsburg A. Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms. Anal Chem 2018; 90:2918-2925. [PMID: 29359922 PMCID: PMC6366606 DOI: 10.1021/acs.analchem.7b05224] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Comprehensive characterization of proteomes comprising the same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS), relying on the mobility increment at high electric fields, but not previously by linear IMS on the basis of absolute mobility. We now use complete histone tails with diverse PTMs on alternative sites to demonstrate that high-resolution linear IMS, here trapped IMS (TIMS), broadly resolves the variants of ∼50 residues in full or into binary mixtures quantifiable by tandem MS, largely thanks to orthogonal separations across charge states. Separations using traveling-wave (TWIMS) and/or involving various time scales and electrospray ionization source conditions are similar (with lower resolution for TWIMS), showing the transferability of results across linear IMS instruments. The linear IMS and FAIMS dimensions are substantially orthogonal, suggesting FAIMS/IMS/MS as a powerful platform for proteoform analyses.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
| | - Matthew Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260
| | - Jacob Porter
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
| | | | - Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Todd D. Williams
- Mass Spectrometry Laboratory, University of Kansas, Lawrence, KS 66045
| | | | - Alexandre Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260
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40
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Jacobs A, Hoover H, Smith E, Clemmer DE, Kim CH, Kao CC. The intrinsically disordered N-terminal arm of the brome mosaic virus coat protein specifically recognizes the RNA motif that directs the initiation of viral RNA replication. Nucleic Acids Res 2018; 46:324-335. [PMID: 29140480 PMCID: PMC5758871 DOI: 10.1093/nar/gkx1087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 12/18/2022] Open
Abstract
In the brome mosaic virus (BMV) virion, the coat protein (CP) selectively contacts the RNA motifs that regulate translation and RNA replication (Hoover et al., 2016. J. Virol. 90, 7748). We hypothesize that the unstructured N-terminal arm (NTA) of the BMV CP can specifically recognize RNA motifs. Using ion mobility spectrometry-mass spectrometry, we demonstrate that peptides containing the NTA of the CP were found to preferentially bind to an RNA hairpin motif that directs the initiation of BMV RNA synthesis. RNA binding causes the peptide to change from heterogeneous structures to a single family of structures. Fluorescence anisotropy, fluorescence quenching and size exclusion chromatography experiments all confirm that the NTA can specific recognize the RNA motif. The peptide introduced into plants along with BMV virion increased accumulation of the BMV CP and accelerated the rate of minus-strand RNA synthesis. The intrinsically disordered BMV NTA could thus specifically recognize BMV RNAs to affect viral infection.
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Affiliation(s)
- Alexander Jacobs
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Haley Hoover
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Edward Smith
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Chul-Hyun Kim
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - C Cheng Kao
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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41
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Initiation of prolyl cis-trans isomerisation in the CDR-H3 loop of an antibody in response to antigen binding. Sci Rep 2017; 7:16964. [PMID: 29208911 PMCID: PMC5717248 DOI: 10.1038/s41598-017-16766-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/16/2017] [Indexed: 01/12/2023] Open
Abstract
Proline cis-trans isomerisation is a regulatory mechanism used in a range of biological processes, and is related to various diseases such as Alzheimers disease and cancer. However, the details of the exact molecular mechanism by which it occurs are not known. Using X-ray crystallography, proline isomerisation has been shown to occur following formation of an antigen-antibody complex between the target epiregulin (EPR) and the antibody 9E5, at proline (Pro103), located in the third complementarity-determining region (CDR) of the heavy chain of 9E5. To obtain an accurate description of the pathway involved in cis-trans isomerisation in this system, we performed ten independent long molecular dynamics (MD) simulations starting at a stable transient bound structure obtained from many short binding MD simulations. As a result, we were able to describe the process by which cis-trans isomerisation is initiated, and suggest a catalysis mechanism for cis-trans isomerization in this antigen-antibody system. We found that Asp102, which is immediately adjacent to Pro103, rotates while changing its interacting partner residues in the light chain of 9E5, and at the same time EPR polar residues help to stabilise the intermediate states in the isomerisation process by interacting strongly with Asp102.
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42
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Dodds JN, May JC, McLean JA. Correlating Resolving Power, Resolution, and Collision Cross Section: Unifying Cross-Platform Assessment of Separation Efficiency in Ion Mobility Spectrometry. Anal Chem 2017; 89:12176-12184. [PMID: 29039942 PMCID: PMC5744666 DOI: 10.1021/acs.analchem.7b02827] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we examine the relationship among resolving power (Rp), resolution (Rpp), and collision cross section (CCS) for compounds analyzed in previous ion mobility (IM) experiments representing a wide variety of instrument platforms and IM techniques. Our previous work indicated these three variables effectively describe and predict separation efficiency for drift tube ion mobility spectrometry experiments. In this work, we seek to determine if our previous findings are a general reflection of IM behavior that can be applied to various instrument platforms and mobility techniques. Results suggest IM distributions are well characterized by a Gaussian model and separation efficiency can be predicted on the basis of the empirical difference in the gas-phase CCS and a CCS-based resolving power definition (CCS/ΔCCS). Notably traveling wave (TWIMS) was found to operate at resolutions substantially higher than a single-peak resolving power suggested. When a CCS-based Rp definition was utilized, TWIMS was found to operate at a resolving power between 40 and 50, confirming the previous observations by Giles and co-workers. After the separation axis (and corresponding resolving power) is converted to cross section space, it is possible to effectively predict separation behavior for all mobility techniques evaluated (i.e., uniform field, trapped ion mobility, traveling wave, cyclic, and overtone instruments) using the equations described in this work. Finally, we are able to establish for the first time that the current state-of-the-art ion mobility separations benchmark at a CCS-based resolving power of >300 that is sufficient to differentiate analyte ions with CCS differences as small as 0.5%.
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Affiliation(s)
| | | | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville Tennessee 37235, United States
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43
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Pracht P, Bauer CA, Grimme S. Automated and efficient quantum chemical determination and energetic ranking of molecular protonation sites. J Comput Chem 2017; 38:2618-2631. [DOI: 10.1002/jcc.24922] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4; 53115 Bonn Germany
| | - Christoph Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4; 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4; 53115 Bonn Germany
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44
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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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45
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Ghassabi Kondalaji S, Khakinejad M, Tafreshian A, J Valentine S. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:947-959. [PMID: 28211014 PMCID: PMC5942881 DOI: 10.1007/s13361-017-1599-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/07/2017] [Accepted: 01/09/2017] [Indexed: 05/02/2023]
Abstract
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Amirmahdi Tafreshian
- Department of Statistics, West Virginia University, P.O. Box 6330, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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46
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El-Baba TJ, Woodall DW, Raab SA, Fuller DR, Laganowsky A, Russell DH, Clemmer DE. Melting Proteins: Evidence for Multiple Stable Structures upon Thermal Denaturation of Native Ubiquitin from Ion Mobility Spectrometry-Mass Spectrometry Measurements. J Am Chem Soc 2017; 139:6306-6309. [DOI: 10.1021/jacs.7b02774] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tarick J. El-Baba
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W. Woodall
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Shannon A. Raab
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel R. Fuller
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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47
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DeBlase AF, Harrilal CP, Lawler JT, Burke NL, McLuckey SA, Zwier TS. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical “Twist” on the β-Hairpin Turn. J Am Chem Soc 2017; 139:5481-5493. [PMID: 28353347 DOI: 10.1021/jacs.7b01315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P. Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John T. Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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48
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Rauschenbach S, Rinke G, Gutzler R, Abb S, Albarghash A, Le D, Rahman TS, Dürr M, Harnau L, Kern K. Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces. ACS NANO 2017; 11:2420-2427. [PMID: 28122181 DOI: 10.1021/acsnano.6b06145] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar-nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.
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Affiliation(s)
- Stephan Rauschenbach
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Gordon Rinke
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Rico Gutzler
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Sabine Abb
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Alyazan Albarghash
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Duy Le
- University of Central Florida , Orlando, Florida 32816, United States
| | - Talat S Rahman
- University of Central Florida , Orlando, Florida 32816, United States
| | - Michael Dürr
- Justus Liebig University Giessen, Institute of Applied Physics , Heinrich-Buff-Ring 16, Giessen DE-35392, Germany
| | - Ludger Harnau
- University of Stuttgart , Bernhäuserstr. 75, Leinfelden-Echterdingen DE-70771, Germany
| | - Klaus Kern
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
- Ecole Polytechnique Fédérale de Lausanne, Institut de Physique , Lausanne CH-1015, Switzerland
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49
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Eschweiler JD, Martini RM, Ruotolo BT. Chemical Probes and Engineered Constructs Reveal a Detailed Unfolding Mechanism for a Solvent-Free Multidomain Protein. J Am Chem Soc 2017; 139:534-540. [PMID: 27959526 PMCID: PMC5724362 DOI: 10.1021/jacs.6b11678] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite the growing application of gas-phase measurements in structural biology and drug discovery, the factors that govern protein stabilities and structures in a solvent-free environment are still poorly understood. Here, we examine the solvent-free unfolding pathway for a group of homologous serum albumins. Utilizing a combination of chemical probes and noncovalent reconstructions, we draw new specific conclusions regarding the unfolding of albumins in the gas phase, as well as more general inferences regarding the sensitivity of collision induced unfolding to changes in protein primary and tertiary structure. Our findings suggest that the general unfolding pathway of low charge state albumin ions is largely unaffected by changes in primary structure; however, the stabilities of intermediates along these pathways vary widely as sequences diverge. Additionally, we find that human albumin follows a domain associated unfolding pathway, and we are able to assign each unfolded form observed in our gas-phase data set to the disruption of specific domains within the protein. The totality of our data informs the first detailed mechanism for multidomain protein unfolding in the gas phase, and highlights key similarities and differences from the known solution-phase pathway.
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Affiliation(s)
| | - Rachel M. Martini
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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50
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Musbat L, Nihamkin M, Toker Y, Dilger JM, Fuller DR, El-Baba TJ, Clemmer DE, Sarkar S, Kronik L, Hirshfeld A, Friedman N, Sheves M. Measurements of the stabilities of isolated retinal chromophores. Phys Rev E 2017; 95:012406. [PMID: 28208402 DOI: 10.1103/physreve.95.012406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 06/06/2023]
Abstract
The barrier energies for isomerization and fragmentation were measured for a series of retinal chromophore derivatives using a tandem ion mobility spectrometry approach. These measurements allow us to quantify the effect of charge delocalization on the rigidity of chromophores. We find that the role of the methyl group on the C13 position is pivotal regarding the ground state dynamics of the chromophore. Additionally, a correlation between quasi-equilibrium isomer distribution and fragmentation pathways is observed.
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Affiliation(s)
- L Musbat
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - M Nihamkin
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Y Toker
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - J M Dilger
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, Indiana 47522, USA
| | - D R Fuller
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
| | - T J El-Baba
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
| | - D E Clemmer
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
| | - S Sarkar
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - L Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - A Hirshfeld
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - N Friedman
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - M Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
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