1
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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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2
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Valadbeigi Y, Ilbeigi V, Michalczuk B, Sabo M, Matejcik S. Study of Atmospheric Pressure Chemical Ionization Mechanism in Corona Discharge Ion Source with and without NH3 Dopant by Ion Mobility Spectrometry combined with Mass Spectrometry: A Theoretical and Experimental Study. J Phys Chem A 2018; 123:313-322. [DOI: 10.1021/acs.jpca.8b11417] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Younes Valadbeigi
- Department of Chemistry, Faculty of Science, Imam Khomeini International University, Qazvin, Iran
| | - Vahideh Ilbeigi
- TOF Tech. Pars Company, Isfahan Science & Technology Town, Isfahan, Iran
| | - Bartosz Michalczuk
- Department of Experimental Physics, Comenius University, Mlynska dolina F2, 84248 Bratislava, Slovak Republic
| | - Martin Sabo
- Department of Experimental Physics, Comenius University, Mlynska dolina F2, 84248 Bratislava, Slovak Republic
| | - Stefan Matejcik
- Department of Experimental Physics, Comenius University, Mlynska dolina F2, 84248 Bratislava, Slovak Republic
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3
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Do TD, Checco JW, Tro M, Shea JE, Bowers MT, Sweedler JV. Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit. Phys Chem Chem Phys 2018; 20:22047-22057. [PMID: 30112548 DOI: 10.1039/c8cp03661f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins and peptides in nature are almost exclusively made from l-amino acids, and this is even more absolute in the metazoan. With the advent of modern bioanalytical techniques, however, previously unappreciated roles for d-amino acids in biological processes have been revealed. Over 30 d-amino acid containing peptides (DAACPs) have been discovered in animals where at least one l-residue has been isomerized to the d-form via an enzyme-catalyzed process. In Aplysia californica, GdFFD and GdYFD (the lower-case letter "d" indicates a d-amino acid residue) modulate the feeding behavior by activating the Aplysia achatin-like neuropeptide receptor (apALNR). However, little is known about how the three-dimensional conformation of DAACPs influences activity at the receptor, and the role that d-residues play in these peptide conformations. Here, we use a combination of computational modeling, drift-tube ion-mobility mass spectrometry, and receptor activation assays to create a simple model that predicts bioactivities for a series of GdFFD analogs. Our results suggest that the active conformations of GdFFD and GdYFD are similar to their lowest energy conformations in solution. Our model helps connect the predicted structures of GdFFD analogs to their activities, and highlights a steric effect on peptide activity at position 1 on the GdFFD receptor apALNR. Overall, these methods allow us to understand ligand-receptor interactions in the absence of high-resolution structural data.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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4
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Peng X, Zhang Y, Li Y, Liu Q, Chu H, Zhang D, Li G. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations. J Chem Theory Comput 2018; 14:1216-1227. [DOI: 10.1021/acs.jctc.7b01211] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiangda Peng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Chinese
Academy of Science, University of Chinese Academy Sciences, Beijing 100049, P. R. China
| | - Yuebin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - QingLong Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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5
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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6
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Kölbel K, Warnke S, Seo J, von Helden G, Moretti R, Meiler J, Pagel K, Sinz A. Conformational Shift of a β-Hairpin Peptide upon Complex Formation with an Oligo-proline Peptide Studied by Mass Spectrometry. ChemistrySelect 2016; 1:3651-3656. [PMID: 30547079 DOI: 10.1002/slct.201600934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
So-called super-secondary structures such as the β-hairpin, studied here, form an intermediate hierarchy between secondary and tertiary structures of proteins. Their sequence-derived 'pure' peptide backbone conformation is combined with 'remote' interstrand or interresidue contacts reminiscent of the 3D-structure of full-length proteins. This renders them ideally suited for studying potential nucleation sites of protein folding reactions as well as intermolecular interactions. But β-hairpins do not merely serve as model systems; their unique structure characteristics warrant a central role in structural studies on their own. In this study we applied photo cross-linking in combination with high-resolution mass spectrometry and computational modeling as well as with ion mobility-mass spectrometry to elucidate these structural properties. Using variants of a known β-hairpin representative, the so-called trpzip peptide and its ligands, we found evidence for a conformational transition of the β-hairpin and its impact on ligand binding.
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Affiliation(s)
- Knut Kölbel
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute for Pharmacy, Martin-Luther-Universit t Halle-Wittenberg W.-Langenbeck-Straße 4, 06120 Halle (Germany).,Chemistry Department Universiteit Antwerpen Campus Groenenborger, Groenenborgerlaan 171 G.V. 416, 2020 Antwer-pen (Belgi)
| | - Stephan Warnke
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany)
| | - Jongcheol Seo
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany)
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany)
| | - Rocco Moretti
- Department of Chemistry and the Center for Structural Biology Vanderbilt University 465 21Ave South BIOSCi/MRBIII Nashville TN (USA)
| | - Jens Meiler
- Department of Chemistry and the Center for Structural Biology Vanderbilt University 465 21Ave South BIOSCi/MRBIII Nashville TN (USA)
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany).,Freie Universit t Berlin Institute of Chemistry and Biochemistry Takustraße 3 14195 Berlin (Germany)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute for Pharmacy, Martin-Luther-Universit t Halle-Wittenberg W.-Langenbeck-Straße 4, 06120 Halle (Germany)
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7
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Yang L, Liu CW, Shao Q, Zhang J, Gao YQ. From thermodynamics to kinetics: enhanced sampling of rare events. Acc Chem Res 2015; 48:947-55. [PMID: 25781363 DOI: 10.1021/ar500267n] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Despite great advances in molecular dynamics simulations, there remain large gaps between the simulations and experimental observations in terms of the time and length scales that can be approached. Developing fast and accurate algorithms and methods is of ultimate importance to bridge these gaps. In this Account, we briefly summarize recent efforts in such directions. In particular, we focus on integrated tempering sampling. The efficiency of this sampling method has been demonstrated by applications to a range of chemical and biological problems: protein folding, molecular cluster structure searches, and chemical reactions. The combination of integrated tempering sampling and a trajectory sampling method allows the calculation of rate constants and reaction pathways without predefined collective coordinates.
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Affiliation(s)
| | | | - Qiang Shao
- Drug
Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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8
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Fort KL, Silveira JA, Pierson NA, Servage KA, Clemmer DE, Russell DH. From Solution to the Gas Phase: Factors That Influence Kinetic Trapping of Substance P in the Gas Phase. J Phys Chem B 2014; 118:14336-44. [DOI: 10.1021/jp5103687] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kyle L. Fort
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua A. Silveira
- 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
| | - Kelly A. Servage
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, 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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9
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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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10
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Nabuchi Y, Hirose K, Takayama M. The pH Dependence of Product Ion Spectra Obtained from Precursor Ions with the Same Charge Number in ESI of Carbonic Anhydrase 2. Mass Spectrom (Tokyo) 2013; 2:A0016. [PMID: 24349917 DOI: 10.5702/massspectrometry.a0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/23/2013] [Indexed: 11/23/2022] Open
Abstract
The effect of solvent conditions, including pH, on product ion spectra obtained from precursor ions produced by electrospray ionization (ESI) was examined. Bovine carbonic anhydrase 2 was used as a model protein and the product ions generated by collision induced dissociation of the whole protein were measured under several different solvent conditions (pH 5.0, 3.7, and 0.1% HCOOH (pH 2.6)/MeCN (1/1)). The product ion spectra from precursor ions with the same charge number, the observed m/z values and the relative intensities of the product ions were similar. It therefore appears that the solvent conditions used have no effect on the product ion that is generated. On the other hand, different profiles of the product ion were obtained from precursor ions having different charge numbers. This indicates that the charge number of the precursor ion appears to be a major determinant of the product ion species and its relative intensity in product ion spectra of proteins.
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11
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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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12
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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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13
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Fadda E, Woods RJ. Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations. CAN J CHEM 2013; 91:859-865. [PMID: 25418993 PMCID: PMC4239032 DOI: 10.1139/cjc-2012-0542] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work we analyze the effect of the inclusion of an empirical dispersion term to standard DFT (DFT-D) in the prediction of the conformational energy of the alanine dipeptide (Ala2) and in assessing the relative stabilities of short polyala-nine peptides in helical conformations, i.e., α and 310 helices, from Ala4 to Ala16. The Ala2 conformational energies obtained with the dispersion-corrected GGA functional B97-D are compared to previously published high level MP2 data. Meanwhile, the B97-D performance on larger polyalanine peptides is compared to MP2, B3LYP and RHF calculations obtained at a lower level of theory. Our results show that electron correlation affects the conformational energies of short peptides with a weight that increases with the peptide length. Indeed, while the contribution of vdW forces is significant for larger peptides, in the case of Ala2 it is negligible when compared to solvent effects. Even for short peptides, the inclusion of an empirical dispersion term greatly improves accuracy of DFT methods, providing results that correlate very well with the MP2 reference at no additional computational cost.
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Affiliation(s)
- Elisa Fadda
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Robert J Woods
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland; Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
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14
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de Carvalho RV, Lopez-Ferrer D, Guimarães KS, Lins RD. IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol. J Comput Chem 2013; 34:1707-18. [PMID: 23609240 DOI: 10.1002/jcc.23299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/17/2013] [Accepted: 03/25/2013] [Indexed: 11/06/2022]
Abstract
Introduction of ion mobility mass spectrometry (IMS/MS) into the proteomic workflow provides an orthogonal separation to the widely used LC-MS platforms. IMS also provides structural information that could facilitate peptide identification. However, the lack of tools capable of predictive power in a high-throughput fashion makes peptide global profiling quite challenging. To target this issue, a computational workflow was developed based on biophysical principles to predict the collision cross-section area (CCS) of peptides as measured from IMS/MS experiments. Hosted on a web server, it allows the user to input a primary sequence (query) and retrieve information on peptide structure, sequence, and corresponding CCS. The current version is designed to identify peptide sequences up to 23 residues in length, in its higher charge state, based on a match of the molecule m/z and CCS. The protocol was validated against a 128-sequences-dataset and CCS predicted within 2.8% average error.
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Affiliation(s)
- Ranieri V de Carvalho
- Center of Informatics, Federal University of Pernambuco, Recife, PE, 50740-560, Brazil
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15
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Shao Q, Zhu W, Gao YQ. Robustness in Protein Folding Revealed by Thermodynamics Calculations. J Phys Chem B 2012; 116:13848-56. [DOI: 10.1021/jp307684h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiang Shao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
- Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203,
China
| | - Weiliang Zhu
- Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203,
China
| | - Yi Qin Gao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
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16
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Shao Q, Shi J, Zhu W. Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein. J Chem Phys 2012; 137:125103. [DOI: 10.1063/1.4754656] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Hall Z, Robinson CV. Do charge state signatures guarantee protein conformations? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1161-8. [PMID: 22562394 DOI: 10.1007/s13361-012-0393-z] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 05/11/2023]
Abstract
The extent to which proteins in the gas phase retain their condensed-phase structure is a hotly debated issue. Closely related to this is the degree to which the observed charge state reflects protein conformation. Evidence from electron capture dissociation, hydrogen/deuterium exchange, ion mobility, and molecular dynamics shows clearly that there is often a strong correlation between the degree of folding and charge state, with the most compact conformations observed for the lowest charge states. In this article, we address recent controversies surrounding the relationship between charge states and folding, focussing also on the manipulation of charge in solution and its effect on conformation. 'Supercharging' reagents that have been used to effect change in charge state can promote unfolding in the electrospray droplet. However for several protein complexes, supercharging does not appear to perturb the structure in that unfolding is not detected. Consequently, a higher charge state does not necessarily imply unfolding. Whilst the effect of charge manipulation on conformation remains controversial, there is strong evidence that a folded, compact state of a protein can survive in the gas phase, at least on a millisecond timescale. The exact nature of the side-chain packing and secondary structural elements in these compact states, however, remains elusive and prompts further research.
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Affiliation(s)
- Zoe Hall
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
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18
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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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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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20
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Hall Z, Politis A, Bush MF, Smith LJ, Robinson CV. Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics. J Am Chem Soc 2012; 134:3429-38. [DOI: 10.1021/ja2096859] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Zoe Hall
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Argyris Politis
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Matthew F. Bush
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Lorna J. Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory,
South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
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21
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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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22
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Pierson NA, Chen L, Valentine SJ, Russell DH, Clemmer DE. Number of solution states of bradykinin from ion mobility and mass spectrometry measurements. J Am Chem Soc 2011; 133:13810-3. [PMID: 21830821 DOI: 10.1021/ja203895j] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion mobility and mass spectrometry measurements have been used to examine the populations of different solution structures of the nonapeptide bradykinin. Over the range of solution compositions studied, from 0:100 to 100:0 methanol:water and 0:100 to 90:10 dioxane:water, evidence for 10 independent populations of bradykinin structures in solution is found. In some solutions as many as eight structures may coexist. The solution populations are substantially different than the gas-phase equilibrium distribution of ions, which exhibits only three distinct states. Such a large number of coexisting structures explains the inability of traditional methods of characterization such as nuclear magnetic resonance spectroscopy and crystallography to determine detailed structural features for some regions of this peptide.
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Affiliation(s)
- Nicholas A Pierson
- Department of Chemistry, Indiana University, Bloomington, 47405, United States
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