1
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Peris-Díaz M, Guran R, Domene C, de los Rios V, Zitka O, Adam V, Krężel A. An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species. J Am Chem Soc 2021; 143:16486-16501. [PMID: 34477370 PMCID: PMC8517974 DOI: 10.1021/jacs.1c05495] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 12/16/2022]
Abstract
Mammalian metallothioneins (MTs) are a group of cysteine-rich proteins that bind metal ions in two α- and β-domains and represent a major cellular Zn(II)/Cu(I) buffering system in the cell. At cellular free Zn(II) concentrations (10-11-10-9 M), MTs do not exist in fully loaded forms with seven Zn(II)-bound ions (Zn7MTs). Instead, MTs exist as partially metal-depleted species (Zn4-6MT) because their Zn(II) binding affinities are on the nano- to picomolar range comparable to the concentrations of cellular Zn(II). The mode of action of MTs remains poorly understood, and thus, the aim of this study is to characterize the mechanism of Zn(II) (un)binding to MTs, the thermodynamic properties of the Zn1-6MT2 species, and their mechanostability properties. To this end, native mass spectrometry (MS) and label-free quantitative bottom-up and top-down MS in combination with steered molecular dynamics simulations, well-tempered metadynamics (WT-MetaD), and parallel-bias WT-MetaD (amounting to 3.5 μs) were integrated to unravel the chemical coordination of Zn(II) in all Zn1-6MT2 species and to explain the differences in binding affinities of Zn(II) ions to MTs. Differences are found to be the result of the degree of water participation in MT (un)folding and the hyper-reactive character of Cys21 and Cys29 residues. The thermodynamics properties of Zn(II) (un)binding to MT2 are found to differ from those of Cd(II), justifying their distinctive roles. The potential of this integrated strategy in the investigation of numerous unexplored metalloproteins is attested by the results highlighted in the present study.
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Affiliation(s)
- Manuel
David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Roman Guran
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Carmen Domene
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Vivian de los Rios
- Functional
Proteomics, Department of Cellular and Molecular Medicine and Proteomic
Facility, Centro de Investigaciones Biológicas
(CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ondrej Zitka
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department
of Chemistry and Biochemistry, Mendel University
in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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2
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Malik A, Lin YF, Pratihar S, Angel LA, Hase WL. Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation. J Phys Chem A 2019; 123:6868-6885. [DOI: 10.1021/acs.jpca.9b05218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Yu-Fu Lin
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Laurence A. Angel
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
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3
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Kluska K, Adamczyk J, Krężel A. Metal binding properties of zinc fingers with a naturally altered metal binding site. Metallomics 2019; 10:248-263. [PMID: 29230465 DOI: 10.1039/c7mt00256d] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc fingers (ZFs) are among the most abundant motifs found in proteins, and are commonly known for their structural role. Classical ZFs (CCHH) are part of the transcription factors that participate in DNA binding. Although biochemical studies of classical ZFs have a long history, there is limited knowledge about the sequential and structural diversity of ZFs. We have found that classical ZFs, with metal binding sites consisting of amino acids other than conserved Cys or His residues, are frequently encoded in the human genome, and we refer to these peptides as ZFs with a naturally altered metal binding site. The biological role of the altered ZFs remains undiscovered. In this study, we characterized nine natural XCHH, CXHH, CCXH and CCHX ZFs in terms of their Zn(ii) and Co(ii) binding properties, such as complex stoichiometry, spectroscopic properties and metal-to-peptide affinity. We revealed that XCHH and CXHH ZFs form ML complexes that are 4-5 orders of magnitude weaker in comparison to CCHH ZFs. Nevertheless, spectroscopic studies demonstrate that, depending on the altered position, they may adopt an open coordination geometry with one or two water molecules bound to a central metal ion, which has not been demonstrated in natural ZFs before. Stability data show that both CCXH and CCHX peptides have high Zn(ii) affinity (with a Kd of 10-9 to 10-11 M), suggesting their potential biological function. This study is a comprehensive overview of the relationship between the sequence, structure, and stability of ZFs.
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Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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4
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Jeanne Dit Fouque K, Moreno J, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers. Analyst 2018; 143:2323-2333. [DOI: 10.1039/c8an00138c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.
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Affiliation(s)
| | - Javier Moreno
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | | | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
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5
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Belczyk-Ciesielska A, Csipak B, Hajdu B, Sparavier A, Asaka MN, Nagata K, Gyurcsik B, Bal W. Nickel(ii)-promoted specific hydrolysis of zinc finger proteins. Metallomics 2018; 10:1089-1098. [DOI: 10.1039/c8mt00098k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The (S/T)XH sequence in Cys2His2zinc fingers can be hydrolytically cleaved by Ni(ii) ions. This reaction can be applied for purification, inhibition or activation of designed zinc finger fusion proteins.
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Affiliation(s)
| | - Brigitta Csipak
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | | | - Masamitsu N. Asaka
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Kyosuke Nagata
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- Warsaw
- Poland
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6
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Tóth EN, May NV, Rockenbauer A, Peintler G, Gyurcsik B. Exploring the boundaries of direct detection and characterization of labile isomers - a case study of copper(ii)-dipeptide systems. Dalton Trans 2017; 46:8157-8166. [PMID: 28607997 DOI: 10.1039/c7dt00884h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The investigation of the linkage isomers of biologically essential and kinetically labile metal complexes in aqueous solutions poses a challenge, as these microspecies cannot be separately studied. Therefore, derivatives are commonly used to initially determine the stability or spectral characteristics of at least one of the isomers. Here we directly detect the isomers, describe the metal ion coordination sphere, speciation and thermodynamic parameters by a synergistic application of temperature dependent EPR and CD spectroscopic measurements in copper(ii)-dipeptide systems including His-Gly and His-Ala ligands. The ΔH = (-23 ± 4) kJ mol-1 value of the standard enthalpy change corresponding to the peptide-type to histamine-type isomerisation equilibrium of the [CuL]+ complex was corroborated by several techniques. The preferential coordination of the side-chains was observed at lower temperatures, whereas, metal-binding of the backbone atoms became favourable upon increasing temperature. This study exemplifies the necessity of using temperature dependent multiple methodologies for a reliable description of similar systems for upstream applications.
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Affiliation(s)
- Eszter N Tóth
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary. and PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Japan
| | - Nóra V May
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Magyar tudósok körútja 2, Hungary
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Magyar tudósok körútja 2, Hungary and Department of Physics, Budapest University of Technology and Economics and MTA-BME Lendület Spintronics Research Group (PROSPIN), P.O. Box 91, H-1521 Budapest, Hungary
| | - Gábor Peintler
- Department of Physical Chemistry and Material Sciences, University of Szeged, Aradi Vértanuk tere 1, H-6720 Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary.
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7
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Wagoner SM, Deeconda M, Cumpian KL, Ortiz R, Chinthala S, Angel LA. The multiple conformational charge states of zinc(II) coordination by 2His-2Cys oligopeptide investigated by ion mobility-mass spectrometry, density functional theory and theoretical collision cross sections. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1120-1129. [PMID: 27594546 DOI: 10.1002/jms.3846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Whether traveling wave ion mobility-mass spectrometry (IM-MS), B3LYP/LanL2DZ density functional theory, and ion size scaled Lennard-Jones (LJ) collision cross sections (CCS) from the B3LYP optimized structures could be used to determine the type of Zn(II) coordination by the oligopeptide acetyl-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5 ) was investigated. The IM-MS analyses of a pH titration of molar equivalents of Zn(II):amb5 showed that both negatively and positively charged complexes formed and coordination of Zn(II) increased as the His and Cys deprotonated near their pKa values. The B3LYP method was used to generate a series of alternative coordination structures to compare with the experimental results. The method predicted that the single negatively charged complex coordinated Zn(II) in a distorted tetrahedral geometry via the 2His-2Cys substituent groups, whereas, the double negatively charged and positively charged complexes coordinated Zn(II) via His, carbonyl oxygens and the C-terminus. The CCS of the B3LYP complexes were calculated using the LJ method and compared with those measured by IM-MS for the various charge state complexes. The LJ method provided CCS that agreed with five of the alternative distorted tetrahedral and trigonal bipyramidal coordinations for the doubly charged complexes, but provided CCS that were 15 to 31 Å2 larger than those measured by IM-MS for the singly charged complexes. Collision-induced dissociation of the Zn(II) complexes and a further pH titration study of amb5B , which included amidation of the C-terminus, suggested that the 2His-2Cys coordination was more significant than coordinations that included the C-terminus. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Stephanie M Wagoner
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Manogna Deeconda
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Kayleah L Cumpian
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Rafael Ortiz
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Swetha Chinthala
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
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8
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Berezovskaya Y, Porrini M, Nortcliffe C, Barran PE. The use of ion mobility mass spectrometry to assist protein design: a case study on zinc finger fold versus coiled coil interactions. Analyst 2016; 140:2847-56. [PMID: 25734188 DOI: 10.1039/c4an00427b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dramatic conformational change in zinc fingers on binding metal ions for DNA recognition makes their structure-function behaviour an attractive target to mimic in de novo designed peptides. Mass spectrometry, with its high throughput and low sample consumption provides insight into how primary amino acid sequence can encode stable tertiary fold. We present here the use of ion mobility mass spectrometry (IM-MS) coupled with molecular dynamics (MD) simulations as a rapid analytical platform to inform de novo design efforts for peptide-metal and peptide-peptide interactions. A dual peptide-based synthetic system, ZiCop based on a zinc finger peptide motif, and a coiled coil partner peptide Pp, have been investigated. Titration mass spectrometry determines the relative binding affinities of different divalent metal ions as Zn(2+) > Co(2+) ≫ Ca(2+). With collision induced dissociation (CID), we probe complex stability, and establish that peptide-metal interactions are stronger and more 'specific' than those of peptide-peptide complexes, and the anticipated hetero-dimeric complex is more stable than the two homo-dimers. Collision cross-sections (CCS) measurements by IM-MS reveal increased stability with respect to unfolding of the metal-bound peptide over its apo-form, and further, larger collision cross sections for the hetero-dimeric forms suggest that dimeric species formed in the absence of metal are coiled coil like. MD supports these structural assignments, backed up by data from visible light absorbance measurements.
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9
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Verma N, Kaur G. Trends on Biosensing Systems for Heavy Metal Detection. BIOSENSORS FOR SUSTAINABLE FOOD - NEW OPPORTUNITIES AND TECHNICAL CHALLENGES 2016. [DOI: 10.1016/bs.coac.2016.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Hill AR, Edgar M, Chatzigeorgiou M, Reynolds JC, Kelly PF, Creaser CS. Analysis of triacetone triperoxide complexes with alkali metal ions by electrospray and extractive electrospray ionisation combined with ion mobility spectrometry and mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:265-274. [PMID: 26307706 DOI: 10.1255/ejms.1348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The complexation of triacetone triperoxide (TATP) with a range of alkali metals has been studied by electrospray ionisation-mass spectrometry yield [M+Cat](+) ions for all of the alkali metals. The formation of [2TATP+Li+LiX](+) (X = Br, Cl) sandwich complexes was also observed. Collision cross- sections for the lithium-containing complexes of TATP were measured by travelling wave ion mobility spectrometry mass spectrometry, and compared well with computationally determined structures. Extractive electrospray ionisation (EESI) using a lithium doped electrospray is demonstrated for the detection of TATP vapours desorbed from a metal surface. The limit of detection for EESI was shown to be 20 ng using the [TATP+Li](+) ion.
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Affiliation(s)
- Alex R Hill
- Centr e for Analytical Science, Department of Chemistry, Loughborough University, Leicestershire, LE11 3TU, UK.
| | - Mark Edgar
- Centre for Analytical Science, Department of Chemistry, Loughborough University, Leicestershire, LE11 3TU, UK.
| | - Maria Chatzigeorgiou
- Centre for Analytical Science, Department of Chemistry, Loughborough University, Leicestershire, LE11 3TU, UK. m.chatzigeorgiou- 13@
| | - James C Reynolds
- Centre for Analytical Science, Department of Chemistry, Loughborough University, Leicestershire, LE11 3TU, UK.
| | - Paul F Kelly
- Cent re for Analytical Science, Department of Chemistry, Loughborough University, Leicestershire, LE11 3TU, UK.
| | - Colin S Creaser
- C entre for Analytical Science, Department of Chemistry, Loughborough University, Leicestershire, LE11 3TU, UK.
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11
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Chan KL, Bakman I, Marts AR, Batir Y, Dowd TL, Tierney D, Gibney BR. Characterization of the Zn(II) binding properties of the human Wilms' tumor suppressor protein C-terminal zinc finger peptide. Inorg Chem 2014; 53:6309-20. [PMID: 24893204 PMCID: PMC4066921 DOI: 10.1021/ic500862b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/19/2022]
Abstract
Zinc finger proteins that bind Zn(II) using a Cys2His2 coordination motif within a ββα protein fold are the most abundant DNA binding transcription factor domains in eukaryotic systems. These classic zinc fingers are typically unfolded in the apo state and spontaneously fold into their functional ββα folds upon incorporation of Zn(II). These metal-induced protein folding events obscure the free energy cost of protein folding by coupling the protein folding and metal-ion binding thermodynamics. Herein, we determine the formation constant of a Cys2His2/ββα zinc finger domain, the C-terminal finger of the Wilms' tumor suppressor protein (WT1-4), for the purposes of determining its free energy cost of protein folding. Measurements of individual conditional dissociation constants, Kd values, at pH values from 5 to 9 were determined using fluorescence spectroscopy by direct or competition titration. Potentiometric titrations of apo-WT1-4 followed by NMR spectroscopy provided the intrinsic pKa values of the Cys2His2 residues, and corresponding potentiometric titrations of Zn(II)-WT1-4 followed by fluorescence spectroscopy yielded the effective pKa(eff) values of the Cys2His2 ligands bound to Zn(II). The Kd, pKa, and pKa(eff) values were combined in a minimal, complete equilibrium model to yield the pH-independent formation constant value for Zn(II)-WT1-4, Kf(ML) value of 7.5 × 10(12) M(-1), with a limiting Kd value of 133 fM. This shows that Zn(II) binding to the Cys2His2 site in WT1-4 provides at least -17.6 kcal/mol in driving force to fold the protein scaffold. A comparison of the conditional dissociation constants of Zn(II)-WT1-4 to those from the model peptide Zn(II)-GGG-Cys2His2 over the pH range 5.0 to 9.0 and a comparison of their pH-independent Kf(ML) values demonstrates that the free energy cost of protein folding in WT1-4 is less than +2.1 kcal/mol. These results validate our GGG model system for determining the cost of protein folding in natural zinc finger proteins and support the conclusion that the cost of protein folding in most zinc finger proteins is ≤+4.2 kcal/mol, a value that pales in comparison to the free energy contribution of Zn(II) binding, -17.6 kcal/mol.
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Affiliation(s)
- Ka Lam Chan
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Inna Bakman
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - Amy R. Marts
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yuksel Batir
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Terry L. Dowd
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - David
L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Brian R. Gibney
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
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12
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Dilger JM, Valentine SJ, Glover MS, Clemmer DE. A database of alkaline-earth-coordinated peptide cross sections: insight into general aspects of structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:768-79. [PMID: 23512423 DOI: 10.1007/s13361-013-0579-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 05/18/2023]
Abstract
A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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13
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Wright VE, Castro-Gómez F, Jurneczko E, Reynolds JC, Poulton A, Christie SDR, Barran P, Bo C, Creaser CS. Structural studies of metal ligand complexes by ion mobility-mass spectrometry. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0122-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Harvey SR, Porrini M, Stachl C, MacMillan D, Zinzalla G, Barran PE. Small-molecule inhibition of c-MYC:MAX leucine zipper formation is revealed by ion mobility mass spectrometry. J Am Chem Soc 2012; 134:19384-92. [PMID: 23106332 DOI: 10.1021/ja306519h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The leucine zipper interaction between MAX and c-MYC has been studied using mass spectrometry and drift time ion mobility mass spectrometry (DT IM-MS) in addition to circular dichroism spectroscopy. Peptides comprising the leucine zipper sequence with (c-MYC-Zip residues 402-434) and without a postulated small-molecule binding region (c-MYC-ZipΔDT residues 406-434) have been synthesized, along with the corresponding MAX leucine zipper (MAX-Zip residues 74-102). c-MYC-Zip:MAX-Zip complexes are observed both in the absence and in the presence of the reported small-molecule inhibitor 10058-F4 for both forms of c-MYC-Zip. DT IM-MS, in combination with molecular dynamics (MD), shows that the c-MYC-Zip:MAX-Zip complex [M+5H](5+) exists in two conformations, one extended with a collision cross section (CCS) of 1164 ± 9.3 Å(2) and one compact with a CCS of 982 ± 6.6 Å(2); similar values are observed for the two forms of c-MYC-ZipΔDT:MAX-Zip. Candidate geometries for the complexes have been evaluated with MD simulations. The helical leucine zipper structure previously determined from NMR measurements (Lavigne, P.; et al. J. Mol. Biol. 1998, 281, 165), altered to include the DT region and subjected to a gas-phase minimization, yields a CCS of 1247 Å(2), which agrees with the extended conformation we observe experimentally. More extensive MD simulations provide compact complexes which are found to be highly disordered, with CCSs that correspond to the compact form from experiment. In the presence of the ligand, the leucine zipper conformation is completely inhibited and only the more disordered species is observed, providing a novel method to study the effect of interactions of disordered systems and subsequent inhibition of the formation of an ordered helical complex.
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Affiliation(s)
- Sophie R Harvey
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
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15
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Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Hofstetter TE, Howder C, Berden G, Oomens J, Armentrout PB. Structural Elucidation of Biological and Toxicological Complexes: Investigation of Monomeric and Dimeric Complexes of Histidine with Multiply Charged Transition Metal (Zn and Cd) Cations using IR Action Spectroscopy. J Phys Chem B 2011; 115:12648-61. [DOI: 10.1021/jp207294b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Theresa E. Hofstetter
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, United States
| | - Collin Howder
- Department of Biology and Chemistry, Spring Arbor University, 106 E. Main St., Spring Arbor, Michigan 49283, United States
| | - Giel Berden
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, United States
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Harvey SR, Macphee CE, Barran PE. Ion mobility mass spectrometry for peptide analysis. Methods 2011; 54:454-61. [PMID: 21669288 DOI: 10.1016/j.ymeth.2011.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/04/2011] [Accepted: 05/22/2011] [Indexed: 02/03/2023] Open
Abstract
The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.
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Affiliation(s)
- Sophie R Harvey
- The School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
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