101
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Bioactivity and structural properties of chimeric analogs of the starfish SALMFamide neuropeptides S1 and S2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1842-50. [PMID: 25110179 DOI: 10.1016/j.bbapap.2014.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 11/23/2022]
Abstract
The starfish SALMFamide neuropeptides S1 (GFNSALMFamide) and S2 (SGPYSFNSGLTFamide) are the prototypical members of a family of neuropeptides that act as muscle relaxants in echinoderms. Comparison of the bioactivity of S1 and S2 as muscle relaxants has revealed that S2 is ten times more potent than S1. Here we investigated a structural basis for this difference in potency by comparing the bioactivity and solution conformations (using NMR and CD spectroscopy) of S1 and S2 with three chimeric analogs of these peptides. A peptide comprising S1 with the addition of S2's N-terminal tetrapeptide (Long S1 or LS1; SGPYGFNSALMFamide) was not significantly different to S1 in its bioactivity and did not exhibit concentration-dependent structuring seen with S2. An analog of S1 with its penultimate residue substituted from S2 (S1(T); GFNSALTFamide) exhibited S1-like bioactivity and structure. However, an analog of S2 with its penultimate residue substituted from S1 (S2(M); SGPYSFNSGLMFamide) exhibited loss of S2-type bioactivity and structural properties. Collectively, our data indicate that the C-terminal regions of S1 and S2 are the key determinants of their differing bioactivity. However, the N-terminal region of S2 may influence its bioactivity by conferring structural stability in solution. Thus, analysis of chimeric SALMFamides has revealed how neuropeptide bioactivity is determined by a complex interplay of sequence and conformation.
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102
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Hyung SJ, Feng X, Che Y, Stroh JG, Shapiro M. Detection of conformation types of cyclosporin retaining intramolecular hydrogen bonds by mass spectrometry. Anal Bioanal Chem 2014; 406:5785-94. [DOI: 10.1007/s00216-014-8023-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/02/2014] [Accepted: 07/07/2014] [Indexed: 11/24/2022]
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103
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Chen SH, Chen L, Russell DH. Metal-induced conformational changes of human metallothionein-2A: a combined theoretical and experimental study of metal-free and partially metalated intermediates. J Am Chem Soc 2014; 136:9499-508. [PMID: 24918957 DOI: 10.1021/ja5047878] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Electrospray ionization ion mobility mass spectrometry (ESI IM-MS) and molecular dynamics (MD) simulations reveal new insights into metal-induced conformational changes and the mechanism for metalation of human metallothionein-2A (MT), an intrinsically disordered protein. ESI of solutions containing apoMT yields multiple charge states of apoMT; following addition of Cd(2+) to the solution, ESI yields a range of CdiMT (i = 1-7) product ions (see Chen et al. Anal. Chem. 2013, 85, 7826-33). Ion mobility arrival-time distributions (ATDs) for the CdiMT (i = 0-7) ions reveal a diverse population of ion conformations. The ion mobility data clearly show that the conformational diversity for apoMT and partially metalated ions converges toward ordered, compact conformations as the number of bound Cd(2+) ions increase. MD simulations provide additional information on conformation candidates of CdiMT (i = 0-7) that supports the convergence of distinct conformational populations upon metal binding. Integrating the IM-MS and MD data provides a global view that shows stepwise conformational transition of an ensemble as a function of metal ion bound. ApoMT is comprised of a wide range of conformational states that populate between globular-like compact and coil-rich extended conformations. During the initial stepwise metal addition (number of metal ions bound i = 1-3), the metal ions bind to different sites to yield distinct conformations, whereas for i > 4, the conformational changes appear to be domain-specific, attributed to different degrees of disorder of the β domain; the β domain becomes more ordered as additional metal ions are added, promoting convergences to the dumbbell-shaped conformation.
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Affiliation(s)
- Shu-Hua Chen
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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104
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Silveira JA, Ridgeway ME, Park MA. High Resolution Trapped Ion Mobility Spectrometery of Peptides. Anal Chem 2014; 86:5624-7. [DOI: 10.1021/ac501261h] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua A. Silveira
- Bruker Daltonics, 40 Manning
Road, Billerica, Massachusetts 01821, United States
| | - Mark E. Ridgeway
- Bruker Daltonics, 40 Manning
Road, Billerica, Massachusetts 01821, United States
| | - Melvin A. Park
- Bruker Daltonics, 40 Manning
Road, Billerica, Massachusetts 01821, United States
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105
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Abstract
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The Crk adaptor proteins play a central
role as a molecular timer
for the formation of protein complexes including various growth and
differentiation factors. The loss of regulation of Crk results in
many kinds of cancers. A self-regulatory mechanism for Crk was recently
proposed, which involves domain–domain rearrangement. It is
initiated by a cis–trans isomerization of a specific proline
residue (Pro238 in chicken Crk II) and can be accelerated by Cyclophilin
A. To understand how the proline switch controls the autoinhibition
at the molecular level, we performed large-scale molecular dynamics
and metadynamics simulations in the context of short peptides and
multidomain constructs of chicken Crk II. We found that the equilibrium
and kinetic properties of the macrostates are regulated not only by
the local environments of specified prolines but also by the global
organization of multiple domains. We observe the two macrostates (cis
closed/autoinhibited and trans open/uninhibited) consistent with NMR
experiments and predict barriers. We also propose an intermediate
state, the trans closed state, which interestingly was reported to
be a prevalent state in human Crk II. The existence of this macrostate
suggests that the rate of switching off the autoinhibition by Cyp
A may be limited by the relaxation rate of this intermediate state.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854, United States
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106
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Wyttenbach T, Pierson NA, Clemmer DE, Bowers MT. Ion Mobility Analysis of Molecular Dynamics. Annu Rev Phys Chem 2014; 65:175-96. [DOI: 10.1146/annurev-physchem-040513-103644] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106;
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405;
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106;
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107
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Abstract
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Ion mobility spectrometry coupled
with mass spectrometry (IMS–MS)
is used to investigate the populations of different states for ubiquitin
in water:methanol solutions. In these experiments, ubiquitin is electrosprayed
from 20 water:methanol (100:0 to 5:95, pH = 2) solutions, ranging
from native to denaturing conditions. With an increased percentage
of methanol in solution, ubiquitin ions ([M + 7H]7+ to
[M + 12H]12+) show substantial variations in both charge
state distributions and ion mobility distributions. Analysis of these
data provides evidence for the existence of five ubiquitin states
in solution: the native N state, favored in solutions of 100:0 to
70:30 water:methanol for the +7 and +8 charge states; the more helical
A state and a new closely related A′ state, favored in solutions
of 70:30 to 5:95 water:methanol for the +9 to +12 charge states; the
unfolded U state, populated in 40:60 to 5:95 water:methanol solutions
for the +8 to +10 and +12 charge states; and a new low-abundance state
termed the B state, observed for 100:0 to 70:30 water:methanol solutions
in the +8 to +10 and +12 charge states. The relative abundances for
different states in different solutions are determined. The analysis
presented here provides insight into how solution structures evolve
into anhydrous conformations and demonstrates the utility of IMS–MS
methods as a means of characterizing populations of conformers for
proteins in solution.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University , 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
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108
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Schenk E, Mendez V, Landrum JT, Ridgeway ME, Park MA, Fernandez-Lima F. Direct observation of differences of carotenoid polyene chain cis/trans isomers resulting from structural topology. Anal Chem 2014; 86:2019-24. [PMID: 24428664 PMCID: PMC3983025 DOI: 10.1021/ac403153m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/15/2014] [Indexed: 02/07/2023]
Abstract
In the present paper, trapped ion mobility spectrometry (TIMS) and theoretical calculations have been used to study carotenoid geometrical motifs generated by photoisomerization from the all-trans geometry. Multiple geometric isomers of the carotenoids lutein and zeaxanthin were separated using TIMS (R > 110) for [M](+), [M + H](+), and [M - 18](+) molecular species. Comparison of observed cross sections with those obtained from molecular dynamics calculations showed that the number of cis double bonds and s-cis single bonds in the polyene chain determine the topology space of the carotenoid. The intensities of IMS signals are correlated with the relative stability of these geometric isomers.1,2 The most stable isomer is the all-trans geometry regardless of the ionization state ([M - 18](+), [M](+), and [M + H](+)), and structural stability decreases with the increasing number of cis and/or s-cis bonds in the polyene chain.
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Affiliation(s)
- Emily
R. Schenk
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
| | - Vanesa Mendez
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
| | - John T. Landrum
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
| | | | - Melvin A. Park
- Bruker
Daltonics,
Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
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109
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Schenk ER, Ridgeway ME, Park MA, Leng F, Fernandez-Lima F. Isomerization kinetics of AT hook decapeptide solution structures. Anal Chem 2014; 86:1210-4. [PMID: 24364733 PMCID: PMC3935383 DOI: 10.1021/ac403386q] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mammalian high mobility group protein HMGA2 contains three DNA binding motifs associated with many physiological functions including oncogenesis, obesity, stem cell youth, human height, and human intelligence. In the present paper, trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) has been utilized to study the conformational dynamics of the third DNA binding motif using the "AT hook" decapeptide unit (Lys(1)-Arg(2)-Prol(3)-Arg(4)-Gly(5)-Arg(6)-Prol(7)-Arg(8)-Lys(9)-Trp(10), ATHP) as a function of the solvent state. Solvent state distributions were preserved during electrospray ion formation, and multiple IMS bands were identified for the [M + 2H](2+) and for the [M + 3H](3+) charge states. Conformational isomer interconversion rates were measured as a function of the trapping time for the [M + 2H](2+) and [M + 3H](3+) charge states. Candidate structures were proposed for all IMS bands observed. Protonation site, proline residue conformation, and side chain orientations were identified as the main motifs governing the conformational interconversion processes. Conformational dynamics from the solvent state distribution to the gas-phase "de-solvated" state distribution demonstrated that ATHP is "structured", and relative abundances are associated with the relative stability between the proposed conformers. The most stable ATHP [M + 2H](2+) conformation at the "de-solvated" state corresponds to the AT hook motif observed in AT-rich DNA regions.
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Affiliation(s)
- Emily R. Schenk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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110
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Lee SJC, Lee JW, Choi TS, Jin KS, Lee S, Ban C, Kim HI. Probing Conformational Change of Intrinsically Disordered α-Synuclein to Helical Structures by Distinctive Regional Interactions with Lipid Membranes. Anal Chem 2014; 86:1909-16. [DOI: 10.1021/ac404132g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shin Jung C. Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Jong Wha Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Tae Su Choi
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Kyeong Sik Jin
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Seonghwan Lee
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Changill Ban
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
| | - Hugh I. Kim
- Department of Chemistry, ‡Pohang Accelerator
Laboratory, §Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang, North Gyeongsang 790-784, South Korea
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111
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112
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Jia C, Wu Z, Lietz CB, Liang Z, Cui Q, Li L. Gas-phase ion isomer analysis reveals the mechanism of peptide sequence scrambling. Anal Chem 2013; 86:2917-24. [PMID: 24313304 DOI: 10.1021/ac401578p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values, which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M → (c)b) pathway is less energetically (or kinetically) favored.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy and ‡Department of Chemistry, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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113
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Silveira JA, Fort KL, Kim D, Servage KA, Pierson NA, Clemmer DE, Russell DH. From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals the Origin of Peptide Conformations. J Am Chem Soc 2013; 135:19147-53. [DOI: 10.1021/ja4114193] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Joshua A. Silveira
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kyle L. Fort
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - DoYong Kim
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kelly A. Servage
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nicholas A. Pierson
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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114
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Zhong Y, Feng J, Ruotolo BT. Robotically assisted titration coupled to ion mobility-mass spectrometry reveals the interface structures and analysis parameters critical for multiprotein topology mapping. Anal Chem 2013; 85:11360-8. [PMID: 24164205 DOI: 10.1021/ac402276k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multiprotein complexes have three-dimensional shapes and dynamic functions that impact almost every aspect of biochemistry. Despite this, our ability to rapidly assess the structures of such macromolecules lags significantly behind high-throughput efforts to identify their function, especially in the context of human disease. Here, we describe results obtained by coupling ion mobility-mass spectrometry with automated robotic sampling of different solvent compositions. This combination of technologies has allowed us to explore an extensive set of solution conditions for a group of eight protein homotetramers, representing a broad sample of protein structure and stability space. We find that altering solution ionic strength in concert with dimethylsulfoxide content is sufficient to disrupt the protein-protein interfaces of all of the complexes studied here. Ion mobility measurements captured for both intact assemblies and subcomplexes match expected values from available X-ray structures in all cases save two. For these exceptions, we find that distorted subcomplexes result from extreme disruption conditions, and are accompanied by small shifts in intact tetramers size, thus enabling the removal of distorted subcomplex data in downstream models. Furthermore, we find strong correlations between the relative intensities of disrupted protein tetramers and the relative number and type of interactions present at interfaces as a function of disrupting agent added. In most cases, this correlation appears strong enough to quantify various types of protein interfacial interactions within unknown proteins following appropriate calibration.
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Affiliation(s)
- Yueyang Zhong
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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115
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Fort KL, Silveira JA, Russell DH. The periodic focusing ion funnel: theory, design, and experimental characterization by high-resolution ion mobility-mass spectrometry. Anal Chem 2013; 85:9543-8. [PMID: 24044574 DOI: 10.1021/ac401629b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Simulation-based development and experimental characterization of a DC-only ion funnel is described herein. Radial ion confinement is achieved via periodic focusing whereby a collisionally dampened effective potential is generated in the inertial frame of an ion traversing the device with appreciable velocity. The new device, termed a periodic focusing ion funnel (PF IF), provides an efficient alternative to the rf ion funnel providing high ion transmission with fewer electrodes, simplified electrical circuitry, and reduced power supply requirements. The utility of the PF IF for structural ion mobility-mass spectrometry (IM-MS) studies is demonstrated using model peptide ions (bradykinin, gramicidin S, and trpzip 1).
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Affiliation(s)
- Kyle L Fort
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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116
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Nonose S, Yamashita K, Sudo A, Kawashima M. Proton transfer and complex formation of angiotensin I ions with gaseous molecules at various temperature. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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117
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Han L, Ruotolo BT. Hofmeister Salts Recover a Misfolded Multiprotein Complex for Subsequent Structural Measurements in the Gas Phase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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118
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Han L, Ruotolo BT. Hofmeister salts recover a misfolded multiprotein complex for subsequent structural measurements in the gas phase. Angew Chem Int Ed Engl 2013; 52:8329-32. [PMID: 23818426 DOI: 10.1002/anie.201301893] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/26/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Linjie Han
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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119
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Mui W, Thomas DA, Downard AJ, Beauchamp JL, Seinfeld JH, Flagan RC. Ion Mobility-Mass Spectrometry with a Radial Opposed Migration Ion and Aerosol Classifier (ROMIAC). Anal Chem 2013; 85:6319-26. [DOI: 10.1021/ac400580u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wilton Mui
- Division of Engineering
and
Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Daniel A. Thomas
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Andrew J. Downard
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jesse L. Beauchamp
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - John H. Seinfeld
- Division of Engineering
and
Applied Science, California Institute of Technology, Pasadena, California 91125, United States
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Richard C. Flagan
- Division of Engineering
and
Applied Science, California Institute of Technology, Pasadena, California 91125, United States
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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120
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Pierson NA, Chen L, Russell DH, Clemmer DE. Cis-trans isomerizations of proline residues are key to bradykinin conformations. J Am Chem Soc 2013; 135:3186-92. [PMID: 23373819 PMCID: PMC3624761 DOI: 10.1021/ja3114505] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A recent ion mobility-mass spectrometry (IM-MS) study of the nonapeptide bradykinin (BK, amino acid sequence Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) found evidence for 10 populations of conformations that depend upon the solution composition [J. Am. Chem. Soc. 2011, 133, 13810]. Here, the role of the three proline residues (Pro(2), Pro(3), and Pro(7)) in establishing these conformations is investigated using a series of seven analogue peptides in which combinations of alanine residues are substituted for prolines. IM-MS distributions of the analogue peptides, when compared to the distribution for BK, indicate the multiple structures are associated with different combinations of cis and trans forms of the three proline residues. These data are used to assign the structures to different peptide populations that are observed under various solution conditions. The assignments also show the connectivity between structures when collisional activation is used to convert one state into another.
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Affiliation(s)
| | - Liuxi Chen
- 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
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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121
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Silveira JA, Servage KA, Gamage CM, Russell DH. Cryogenic Ion Mobility-Mass Spectrometry Captures Hydrated Ions Produced During Electrospray Ionization. J Phys Chem A 2013; 117:953-61. [DOI: 10.1021/jp311278a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joshua A. Silveira
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
| | - Kelly A. Servage
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
| | - Chaminda M. Gamage
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
| | - David H. Russell
- Texas A&M University, Department of Chemistry, College Station, Texas 77843, United States
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122
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Shi H, Gu L, Clemmer DE, Robinson RAS. Effects of Fe(II)/H2O2 oxidation on ubiquitin conformers measured by ion mobility-mass spectrometry. J Phys Chem B 2013; 117:164-73. [PMID: 23211023 PMCID: PMC3552375 DOI: 10.1021/jp3099544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxidative modifications can have significant effects on protein structure in solution. Here, the structures and stabilities of oxidized ubiquitin ions electrosprayed from an aqueous solution (pH 2) are studied by ion mobility spectrometry-mass spectrometry (IMS-MS). IMS-MS has proven to be a valuable technique to assess gas phase and in many cases, solution structures. Herein, in vitro oxidation is performed by Fenton chemistry with Fe(II)/hydrogen peroxide. Most molecules in solution remain unmodified, whereas ∼20% of the population belongs to an M+16 Da oxidized species. Ions of low charge states (+7 and +8) show substantial variance in collision cross section distributions between unmodified and oxidized species. Novel and previously reported gaussian conformers are used to model cross section distributions for +7 and +8 oxidized ubiquitin ions, respectively, in order to correlate variances in observed gas-phase distributions to changes in populations of solution states. Based on gaussian modeling, oxidized ions of charge state +7 have an A-state conformation which is more populated for oxidized relative to unmodified ions. Oxidized ubiquitin ions of charge state +8 have a distribution of conformers arising from native-state ubiquitin and higher intensities of A- and U-state conformers relative to unmodified ions. This work provides evidence that incorporation of a single oxygen atom to ubiquitin leads to destabilization of the native state in an acidic solution (pH ∼2) and to unfolding of gas-phase compact structures.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Liqing Gu
- Department of Chemistry, University of Pittsburgh, 200 University Drive, Pittsburgh, PA 15260
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Renã A. S. Robinson
- Department of Chemistry, University of Pittsburgh, 200 University Drive, Pittsburgh, PA 15260
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123
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Lee JW, Heo SW, Lee SJC, Ko JY, Kim H, Kim HI. Probing conformational changes of ubiquitin by host-guest chemistry using electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:21-29. [PMID: 23247966 DOI: 10.1007/s13361-012-0496-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/04/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
We report mechanistic studies of structural changes of ubiquitin (Ub) by host-guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916-7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys(6) or Lys(11) in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host-guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys(48) and Lys(63) in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys(11). The complexation prohibits salt bridge formation between Lys(11) and Glu(34) and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host-guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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124
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Meyer T, Gabelica V, Grubmüller H, Orozco M. Proteins in the gas phase. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1130] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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125
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Chang TM, Prell JS, Warrick ER, Williams ER. Where’s the Charge? Protonation Sites in Gaseous Ions Change with Hydration. J Am Chem Soc 2012; 134:15805-13. [DOI: 10.1021/ja304929h] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Terrence M. Chang
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - James S. Prell
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - Erika R. Warrick
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
| | - Evan R. Williams
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United
States
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126
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Calvo F, Chirot F, Albrieux F, Lemoine J, Tsybin YO, Pernot P, Dugourd P. Statistical analysis of ion mobility spectrometry. II. Adaptively biased methods and shape correlations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1279-1288. [PMID: 22573497 DOI: 10.1007/s13361-012-0391-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 05/31/2023]
Abstract
Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptively biased molecular dynamics (ABMD) simulations are used to sample the configuration space and to achieve flat-histogram sampling along the reaction coordinates of the first two moments of the gyration tensor. The method is tested and compared with replica-exchange simulations on triply-protonated bradykinin and on a larger 25-residue peptide. It is found to have a much higher efficiency for producing large sets of conformations in a broad range of diffusion cross-sections, whereas it does not compete with conventional replica-exchange molecular dynamics in locating the lowest-energy structure. Nevertheless, the broad sampling obtained from the ABMD method allows to quantitatively correlate the diffusion cross-section Ω with other geometric order parameters that have simpler interpretation. The strong correlations found between the diffusion cross-section and the radius of gyration, the surface area and the volume of the convex hull suggest an optimal template for accurately mimicking the variations of Ω in a broad range of conformations, using only geometrical information and doing so at a very moderate computational cost. The existence of such a correlation is confirmed on the much larger protein α-lactalbumin.
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Affiliation(s)
- Florent Calvo
- Université de Lyon, Université Lyon 1, Villeurbanne, 69622, France
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127
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Conformational distribution of bradykinin [bk + 2 H]2+ revealed by cold ion spectroscopy coupled with FAIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1173-81. [PMID: 22528205 DOI: 10.1007/s13361-012-0384-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 05/25/2023]
Abstract
We employ cold ion spectroscopy (CIS) in conjunction with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk + 2 H](2+)). Using FAIMS, we partially separate the electrosprayed [bk + 2 H](2+) ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer, we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.
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Affiliation(s)
- Georgios Papadopoulos
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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128
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Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Ion mobility separation of variant histone tails extending to the "middle-down" range. Anal Chem 2012; 84:4271-6. [PMID: 22559289 PMCID: PMC3353003 DOI: 10.1021/ac300612y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Differential ion mobility spectrometry (FAIMS) can baseline-resolve multiple variants of post-translationally modified peptides extending to the 3-4 kDa range, which differ in the localization of a PTM as small as acetylation. Essentially orthogonal separations for different charge states expand the total peak capacity with the number of observed states that increases for longer polypeptides. This potentially enables resolving localization variants for yet larger peptides and even intact proteins.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.
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129
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Leavitt CM, Wolk AB, Fournier JA, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap. J Phys Chem Lett 2012; 3:1099-105. [PMID: 26288043 DOI: 10.1021/jz3003074] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Isomer-specific vibrational predissociation spectra are reported for the gas-phase GlySarH(+) and SarSarH(+) [Gly = glycine; Sar = sarcosine] ions prepared by electrospray ionization and tagged with weakly bound D2 adducts using a cryogenic ion trap. The contributions of individual isomers to the overlapping vibrational band patterns are completely isolated using a pump-probe photochemical hole-burning scheme involving two tunable infrared lasers and two stages of mass selection (hence IR(2)MS(2)). These patterns are then assigned by comparison with harmonic (MP2/6-311+G(d,p)) spectra for various possible conformers. Both systems occur in two conformations based on cis and trans configurations with respect to the amide bond. In addition to the usual single intramolecular hydrogen bond motif between the protonated amine and the nearby amide oxygen atom, cis-SarSarH(+) adopts a previous unreported conformation in which both amino NH's act as H-bond donors. The correlated red shifts in the NH donor and C═O acceptor components of the NH···O═C linkage to the acid group are unambiguously assigned in the double H-bonded conformer.
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Affiliation(s)
- Christopher M Leavitt
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Arron B Wolk
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Joseph A Fournier
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Michael Z Kamrath
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Etienne Garand
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Michael J Van Stipdonk
- ‡Department of Chemistry, Lawrence University, 711 East Boldt Way, Appleton, Wisconsin 54911, United States
| | - Mark A Johnson
- †Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
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130
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Shi H, Pierson NA, Valentine SJ, Clemmer DE. Conformation types of ubiquitin [M+8H]8+ Ions from water:methanol solutions: evidence for the N and A States in aqueous solution. J Phys Chem B 2012; 116:3344-52. [PMID: 22315998 PMCID: PMC3351143 DOI: 10.1021/jp210797x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ion mobility and mass spectrometry measurements are used to examine the gas-phase populations of [M+8H](8+) ubiquitin ions formed upon electrospraying 20 different solutions from 100:0 to 5:95 water:methanol that are maintained at pH = 2.0. Over this range of solution conditions, mobility distributions for the +8 charge state show substantial variations. Here we develop a model that treats the combined measurements as one data set. By varying the relative abundances of a discrete set of conformation types, it is possible to represent distributions obtained from any solution. For solutions that favor the well-known A-state ubiquitin, it is possible to represent the gas-phase distributions with seven conformation types. Aqueous conditions that favor the native structure require four more structural types to represent the distribution. This analysis provides the first direct evidence for trace amounts of the A state under native conditions. The method of analysis presented here should help illuminate how solution populations evolve into new gas-phase structures as solvent is removed. Evidence for trace quantities of previously unknown states under native solution conditions may provide insight about the relationship of dynamics to protein function as well as misfolding and aggregation phenomena.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Nicholas A. Pierson
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Stephen J. Valentine
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
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131
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Silveira JA, Jeon J, Gamage CM, Pai PJ, Fort KL, Russell DH. Damping factor links periodic focusing and uniform field ion mobility for accurate determination of collision cross sections. Anal Chem 2012; 84:2818-24. [PMID: 22404635 DOI: 10.1021/ac203294q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The methodology for obtaining accurate ion-neutral collision cross section (Ω) values for peptides and proteins using periodic focusing ion mobility spectrometry (PF IMS) is presented. A mobility dampening factor (represented by the term α) is introduced to account for the relative increase in ion-neutral collisions in PF IMS compared to uniform field ion mobility spectrometry (UF IMS) for equivalent operating conditions. The results show that α may be easily quantified both theoretically and empirically for a specific PF IMS design operating at a given pressure based upon the charge state of the analyte. By simply incorporating an α term into traditional UF IMS expressions, accurate Ω values were obtained with excellent agreement (≤4% difference) compared to UF IMS measurements found in the current literature.
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Affiliation(s)
- Joshua A Silveira
- Texas A&M University, Department of Chemistry, Laboratory for Biological Mass Spectrometry, College Station, Texas 77843, United States
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132
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Fasciotti M, Gomes AF, Gozzo FC, Iglesias BA, de Sá GF, Daroda RJ, Toganoh M, Furuta H, Araki K, Eberlin MN. Corrole isomers: intrinsic gas-phase shapes via traveling wave ion mobility mass spectrometry and dissociation chemistries via tandem mass spectrometry. Org Biomol Chem 2012; 10:8396-402. [DOI: 10.1039/c2ob26209f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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133
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Chen L, Gao YQ, Russell DH. How Alkali Metal Ion Binding Alters the Conformation Preferences of Gramicidin A: A Molecular Dynamics and Ion Mobility Study. J Phys Chem A 2011; 116:689-96. [DOI: 10.1021/jp209430q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liuxi Chen
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi Qin Gao
- Beijing National Lab for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China 100871
| | - David H. Russell
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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134
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Shvartsburg AA, Smith RD. Accelerated high-resolution differential ion mobility separations using hydrogen. Anal Chem 2011; 83:9159-66. [PMID: 22074292 PMCID: PMC3234991 DOI: 10.1021/ac202386w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The resolving power of differential ion mobility spectrometry (FAIMS) was dramatically increased recently by carrier gases comprising up to 75% He or various vapors, enabling many new applications. However, the need for resolution of complex mixtures is virtually open-ended and many topical analyses demand yet finer separations. Also, the resolving power gains are often at the expense of speed, in particular making high-resolution FAIMS poorly compatible with online liquid-phase separations. Here, we report FAIMS employing hydrogen, specifically in mixtures with N(2) containing up to 90% H(2). Such compositions raise the mobilities of all ions and thus the resolving power beyond that previously feasible, while avoiding the electrical breakdown inevitable in He-rich mixtures. The increases in resolving power and ensuing peak resolution are especially significant at H(2) fractions above ~50%. Higher resolution can be exchanged for acceleration of the analyses by up to ~4 times. For more mobile species such as multiply charged peptides, this exchange is presently forced by the constraints of existing FAIMS devices, but future designs optimized for H(2) should consistently improve resolution for all analytes.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
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