1
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Shang X, Chu W, Chu X, Liu C, Xu L, Wang J. Effects of flexibility and electrostatic interactions on the coupled binding–folding mechanisms of Chz.core and H2A.z–H2B. MOLECULAR BIOSYSTEMS 2017; 13:2152-2159. [DOI: 10.1039/c7mb00103g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The intrinsically disordered protein (IDP) Chz.core, which is the interaction core of Chz1, shows binding preference to histone variant H2A.z. The coupled folding–binding mechanism of the complex can be quantified by the free energy landscapes.
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Affiliation(s)
- Xu Shang
- College of Physics
- Jilin University
- Changchun 130012
- China
- State Key Laboratory of Electroanalytical Chemistry
| | - Wenting Chu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | | | - Chuanbo Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Liufang Xu
- College of Physics
- Jilin University
- Changchun 130012
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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2
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Chen HJC, Fan CH, Yang YF. Stability and Application of Reactive Nitrogen and Oxygen Species-Induced Hemoglobin Modifications in Dry Blood Spots As Analyzed by Liquid Chromatography Tandem Mass Spectrometry. Chem Res Toxicol 2016; 29:2157-2163. [DOI: 10.1021/acs.chemrestox.6b00334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Chih-Huang Fan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Ya-Fen Yang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
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3
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Umezawa K, Ohnuki J, Higo J, Takano M. Intrinsic disorder accelerates dissociation rather than association. Proteins 2016; 84:1124-33. [DOI: 10.1002/prot.25057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/16/2016] [Accepted: 04/24/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Umezawa
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Jun Ohnuki
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University; Suita Osaka 565-0871 Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
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4
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The chaperone role of the pyridoxal 5′-phosphate and its implications for rare diseases involving B6-dependent enzymes. Clin Biochem 2014; 47:158-65. [DOI: 10.1016/j.clinbiochem.2013.11.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/28/2013] [Accepted: 11/30/2013] [Indexed: 02/06/2023]
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5
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Liu J, Dong Y, Zheng J, He Y, Sheng Q. Investigation on the conformation change of hemoglobin immobilized on MPA-modified electrode by electrochemical method. ANAL SCI 2013; 29:1075-81. [PMID: 24212734 DOI: 10.2116/analsci.29.1075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The conformation change of bovine hemoglobin (Hb) during the unfolding process induced by urea and acid was investigated by an electrochemical method. Hb unfolding induced by urea of different concentrations was realized by bonding Hb onto a 3-mercaptopropionic acid (MPA) modified gold electrode. The difference in unfolding percentage showed that the Hb unfolding induced by urea was a two-step, three-state transition process, while the unfolding induced by acid was a two-state transition process. The results obtained by the electrochemical method coincided closely with those obtained by UV-vis spectroscopy and fluorescence spectroscopy. Some thermodynamic parameters during the conformational change were also calculated to study the intermediate state during the Hb unfolding process. The present work may lead to an easy and effective way to study metalloproteins unfolding, and holds great promise for the design of novel sensitive biosensors.
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Affiliation(s)
- Jianbo Liu
- Institute of Analytical Science/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University
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6
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Liu J, Konermann L. Assembly of Hemoglobin from Denatured Monomeric Subunits: Heme Ligation Effects and Off-Pathway Intermediates Studied by Electrospray Mass Spectrometry. Biochemistry 2013; 52:1717-24. [DOI: 10.1021/bi301693g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jiangjiang Liu
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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7
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Chen HJC, Chen YC. Reactive nitrogen oxide species-induced post-translational modifications in human hemoglobin and the association with cigarette smoking. Anal Chem 2012; 84:7881-90. [PMID: 22958097 DOI: 10.1021/ac301597r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nitric oxide (NO) is essential for normal physiology, but excessive production of NO during inflammatory processes can damage the neighboring tissues. Reactive nitrogen oxide species (RNOx), including peroxynitrite (ONOO(-)), are powerful nitrating agents. Biological protein nitration is involved in several disease states, including inflammatory diseases, and it is evident by detection of 3-nitrotyrosine (3NT) in inflamed tissues. In this study, we identified peroxynitrite-induced post-translational modifications (PTMs) in human hemoglobin by accurate mass measurement as well as by the MS(2) and MS(3) spectra. Nitration on Tyr-24, Tyr-42 (α-globin), and Tyr-130 (β-globin) as well as nitrosation on Tyr-24 (α-globin) were identified. Also characterized were oxidation of all three methionine residues, α-Met-32, α-Met-76, and β-Met-55 to the sulfoxide, as well as cysteine oxidation determined as sulfinic acid on α-Cys-104 and sulfonic acid on α-Cys-104, β-Cys-93, and β-Cys-112. These modifications are detected in hemoglobin freshly isolated from human blood and the extents of modifications were semiquantified relative to the reference peptides by nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry (nanoLC-NSI/MS/MS) under the selected reaction monitoring (SRM) mode. The results showed a statistically significant positive correlation between cigarette smoking and the extents of tyrosine nitration at α-Tyr-24 and at α-Tyr-42. To our knowledge, this is the first report on identification and quantification of multiple PTMs in hemoglobin from human blood and association of a specific 3NT-containing peptide with cigarette smoking. This highly sensitive and specific assay only requires hemoglobin isolated from one drop (∼10 μL) of blood. Thus, measurement of these PTMs in hemoglobin might be feasible for assessing nitrative stress in vivo.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Ming-Hsiung, Chia-Yi, Taiwan.
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8
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Higo J, Nishimura Y, Nakamura H. A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. J Am Chem Soc 2011; 133:10448-58. [PMID: 21627111 DOI: 10.1021/ja110338e] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The N-terminal repressor domain of neural restrictive silencer factor (NRSF) is an intrinsically disordered protein (IDP) that binds to the paired amphipathic helix (PAH) domain of mSin3. An NMR experiment revealed that the minimal binding unit of NRSF is a 15-residue segment that adopts a helical structure upon binding to a cleft of mSin3. We computed a free-energy landscape of this system by an enhanced conformational sampling method, all-atom multicanonical molecular dynamics. The simulation started from a configuration where the NRSF segment was fully disordered and distant from mSin3 in explicit solvent. In the absence of mSin3, the disordered NRSF segment thermally fluctuated between hairpins, helices, and bent structures. In the presence of mSin3, the segment bound to mSin3 by adopting the structures involved in the isolated state, and non-native and native complexes were formed. The free-energy landscape comprised three superclusters, and free-energy barriers separated the superclusters. The native complex was located at the center of the lowest free-energy cluster. When NRSF landed in the largest supercluster, the generated non-native complex moved on the landscape to fold into the native complex, by increasing the interfacial hydrophobic contacts and the helix content. When NRSF landed in other superclusters, the non-native complex overcame the free-energy barriers between the various segment orientations in the binding cleft of mSin3. Both population-shift and induced-fit (or induced-folding) mechanisms work cooperatively in the coupled folding and binding. The diverse structural adaptability of NRSF may be related to the hub properties of the IDP.
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Affiliation(s)
- Junichi Higo
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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9
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Direct probing of the folding/unfolding event of bovine hemoglobin at montmorillonite clay modified electrode by adsorptive-transfer voltammetry. Talanta 2011; 84:148-54. [DOI: 10.1016/j.talanta.2010.12.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 12/16/2010] [Accepted: 12/21/2010] [Indexed: 11/22/2022]
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10
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Konermann L, Stocks BB, Pan Y, Tong X. Mass spectrometry combined with oxidative labeling for exploring protein structure and folding. MASS SPECTROMETRY REVIEWS 2010; 29:651-667. [PMID: 19672951 DOI: 10.1002/mas.20256] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review discusses various mass spectrometry (MS)-based approaches for exploring structural aspects of proteins in solution. Electrospray ionization (ESI)-MS, in particular, has found fascinating applications in this area. For example, when used in conjunction with solution-phase hydrogen/deuterium exchange (HDX), ESI-MS is a highly sensitive tool for probing conformational dynamics. The main focus of this article is a technique that is complementary to HDX, that is, the covalent labeling of proteins by hydroxyl radicals. The reactivity of individual amino acid side chains with *OH is strongly affected by their degree of solvent exposure. Thus, analysis of the oxidative labeling pattern by peptide mapping and tandem mass spectrometry provides detailed structural information. A convenient method for *OH production is the photolysis of H(2)O(2) by a pulsed UV laser, resulting in oxidative labeling on the microsecond time scale. Selected examples demonstrate the use of this technique for structural studies on membrane proteins, and the combination with rapid mixing devices for characterizing the properties of short-lived protein (un)folding intermediates.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7.
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11
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Mai Z, Zhao X, Dai Z, Zou X. Contributions of Components in Guanidine Hydrochloride to Hemoglobin Unfolding Investigated by Protein Film Electrochemistry. J Phys Chem B 2010; 114:7090-7. [DOI: 10.1021/jp101082d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Zhibin Mai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Xiaojuan Zhao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Zong Dai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Xiaoyong Zou
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
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12
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Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J Mol Biol 2009; 393:1143-59. [PMID: 19747922 DOI: 10.1016/j.jmb.2009.09.010] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 06/29/2009] [Accepted: 09/04/2009] [Indexed: 11/20/2022]
Abstract
Intrinsically disordered proteins (IDPs) are recognized to play important roles in many biological functions such as transcription and translation regulation, cellular signal transduction, protein phosphorylation, and molecular assemblies. The coupling of folding with binding through a "fly-casting" mechanism has been proposed to account for the fast binding kinetics of IDPs. In this article, experimental data from the literature were collated to verify the kinetic advantages of IDPs, while molecular simulations were performed to clarify the origin of the kinetic advantages. The phosphorylated KID-kinase-inducible domain interacting domain (KIX) complex was used as an example in the simulations. By modifying a coarse-grained model with a native-centric Gō-like potential, we were able to continuously tune the degree of disorder of the phosphorylated KID domain and thus investigate the intrinsic role of chain flexibility in binding kinetics. The simulations show that the "fly-casting" effect is not only due to the greater capture radii of IDPs. The coupling of folding with binding of IDPs leads to a significant reduction in binding free-energy barrier. Such a reduction accelerates the binding process. Although the greater capture radius has been regarded as the main factor in promoting the binding rate of IDPs, we found that this parameter will also lead to the slower translational diffusion of IDPs when compared with ordered proteins. As a result, the capture rate of IDPs was found to be slower than that of ordered proteins. The main origin of the faster binding for IDPs are the fewer encounter times required before the formation of the final binding complex. The roles of the interchain native contacts fraction (Q(b)) and the mass-center distance (DeltaR) as reaction coordinates are also discussed.
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13
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Rea AM, Thurston V, Searle MS. Mechanism of Ligand-Induced Folding of a Natively Unfolded Helixless Variant of Rabbit I-BABP. Biochemistry 2009; 48:7556-64. [DOI: 10.1021/bi900805s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anita M. Rea
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Victoria Thurston
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Mark S. Searle
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
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14
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Fruk L, Kuo CH, Torres E, Niemeyer CM. Apoenzyme reconstitution as a chemical tool for structural enzymology and biotechnology. Angew Chem Int Ed Engl 2009; 48:1550-74. [PMID: 19165853 DOI: 10.1002/anie.200803098] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Many enzymes contain a nondiffusible organic cofactor, often termed a prosthetic group, which is located in the active site and essential for the catalytic activity of the enzyme. These cofactors can often be extracted from the protein to yield the respective apoenzyme, which can subsequently be reconstituted with an artificial analogue of the native cofactor. Nowadays a large variety of synthetic cofactors can be used for the reconstitution of apoenzymes and, thus, generate novel semisynthetic enzymes. This approach has been refined over the past decades to become a versatile tool of structural enzymology to elucidate structure-function relationships of enzymes. Moreover, the reconstitution of apoenzymes can also be used to generate enzymes possessing enhanced or even entirely new functionality. This Review gives an overview on historical developments and the current state-of-the-art on apoenzyme reconstitution.
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Affiliation(s)
- Ljiljana Fruk
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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15
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Fruk L, Kuo CH, Torres E, Niemeyer C. Rekonstitution von Apoenzymen als chemisches Werkzeug für die strukturelle Enzymologie und Biotechnologie. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803098] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Narayanan R, Ganesh OK, Edison AS, Hagen SJ. Kinetics of Folding and Binding of an Intrinsically Disordered Protein: The Inhibitor of Yeast Aspartic Proteinase YPrA. J Am Chem Soc 2008; 130:11477-85. [DOI: 10.1021/ja803221c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ranjani Narayanan
- Physics Department and Department of Biochemistry and Molecular Biology, University of Florida, P.O. Box 118440, Gainesville FL 32611-8440
| | - Omjoy K. Ganesh
- Physics Department and Department of Biochemistry and Molecular Biology, University of Florida, P.O. Box 118440, Gainesville FL 32611-8440
| | - Arthur S. Edison
- Physics Department and Department of Biochemistry and Molecular Biology, University of Florida, P.O. Box 118440, Gainesville FL 32611-8440
| | - Stephen J. Hagen
- Physics Department and Department of Biochemistry and Molecular Biology, University of Florida, P.O. Box 118440, Gainesville FL 32611-8440
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17
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Abzalimov RR, Dubin PL, Kaltashov IA. Glycosaminoglycans as Naturally Occurring Combinatorial Libraries: Developing a Mass Spectrometry-Based Strategy for Characterization of Anti-Thrombin Interaction with Low Molecular Weight Heparin and Heparin Oligomers. Anal Chem 2007; 79:6055-63. [PMID: 17658885 DOI: 10.1021/ac0710432] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heparin is a densely charged polysaccharide, which is best known for its anticoagulant activity, although it also modulates a plethora of other biological processes. Unlike biopolymers whose synthesis is strictly controlled by a unique genetic template, heparin molecules exhibit a remarkable degree of structural heterogeneity, which poses a serious challenge for studies of heparin-protein interactions. This analytical challenge is often dealt with by reducing the enormous structural repertoire of heparin to a model small molecule. In this paper, we describe a different approach inspired by the experimental methodologies from the arsenal of combinatorial chemistry. Interaction of anti-thrombin III (AT) with heparinoids is studied using a mixture of oligoheparin molecules of fixed degree of polymerization, but varying chemical composition (heparin hexasaccharides obtained by size exclusion chromatography of an enzymatic digest of porcine intestinal heparin with bacterial heparinase), as well as a heparin-derived pharmaceutical preparation Tinzaparin (heparin oligosaccharides up to a 22-mer). AT binders are identified based on the results of ESI MS measurements of complexes formed by protein-oligoheparin association. Additionally, differential depletion of free heparin oligomers in solution in the presence of AT is used to verify the binding preferences. ESI MS characterization of oligoheparin-AT interaction under partially denaturing conditions allowed the conformer specificity of the protein-polyanion binding to be monitored. A model emerging from these studies invokes the notion of a well-defined binding site on AT, to which a flexible partner (heparin) adapts to maximize favorable intermolecular electrostatic interactions. This study demonstrates the enormous potential of ESI MS as an analytical tool to study the interactions of highly heterogeneous glycosaminoglycans with their cognate proteins outside of the commonly accepted reductionist paradigm, which reduces the intrinsic complexity of heparin by using structurally defined homogeneous low molecular weight mimetics.
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Affiliation(s)
- Rinat R Abzalimov
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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18
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Frimpong AK, Abzalimov RR, Eyles SJ, Kaltashov IA. Gas-Phase Interference-Free Analysis of Protein Ion Charge-State Distributions: Detection of Small-Scale Conformational Transitions Accompanying Pepsin Inactivation. Anal Chem 2007; 79:4154-61. [PMID: 17477507 DOI: 10.1021/ac0704098] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Analysis of protein ion charge-state distributions in electrospray ionization (ESI) mass spectra has become an indispensable tool in the studies of protein dynamics. However, applications of this technique have been thus far limited to detection of large-scale conformational transitions, which typically change the extent of multiple charging in a very significant way. However, more subtle conformational changes often elude detection, since the resulting changes of the extent of multiple charging are often smaller than the charge-state shifts caused by other external factors. Proton-transfer reactions involving protein ions and residual solvent molecules are the major extrinsic factors causing changes of charge-state distributions unrelated to conformational transitions. Since the extent of such reactions depends on the amount of various solvent components transferred to the ESI interface, profound changes of solvent composition may affect protein ion charge-state distributions not only by affecting protein higher order structure in solution but also through modulation of the efficiency of proton-transfer reactions in the gas phase. Here we demonstrate that it is possible to choose experimental conditions in such a way that the influence of gas-phase ion chemistry on protein ion charge-state distributions is not altered over a wide pH range. This methodology (gas-phase interference-free analysis of protein ion charge-state distributions, or GIFPICS) is sensitive enough to allow detection of pepsin inactivation under mildly acidic conditions. Pepsin is active and tightly folded in its native strongly acidic environment. Inactivation of pepsin at mildly acidic pH is not accompanied by global unfolding, as spectroscopic measurements suggest the protein remains compact. GIFPICS provides a means to observe this small-scale conformational transition that does not result in protein unfolding and may in fact elude detection by traditional spectroscopic techniques.
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Affiliation(s)
- Agya K Frimpong
- Department of Chemistry, University of Massachusetts at Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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19
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Landfried DA, Vuletich DA, Pond MP, Lecomte JTJ. Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins. Gene 2007; 398:12-28. [PMID: 17550789 PMCID: PMC2394511 DOI: 10.1016/j.gene.2007.02.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 02/05/2007] [Indexed: 01/09/2023]
Abstract
The binding of a cofactor to a protein matrix often involves a reorganization of the polypeptide structure. b Hemoproteins provide multiple examples of this behavior. In this minireview, selected monomeric and single b heme proteins endowed with distinct topological properties are inspected for the extent of induced refolding upon heme binding. To complement the data reported in the literature, original results are presented on a two-on-two globin of cyanobacterial origin (Synechococcus sp. PCC 7002 GlbN) and on the heme-containing module of FixL, an oxygen-sensing protein with the mixed alpha/beta topology of PAS domains. GlbN had a stable apoprotein that was further stabilized and locally refolded by heme binding; in contrast, apoFixLH presented features of a molten globule. Sequence analyses (helicity, disorder, and polarity) and solvent accessibility calculations were performed to identify trends in the architecture of b hemoproteins. In several cases, the primary structure appeared biased toward a partially disordered binding pocket in the absence of the cofactor.
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Affiliation(s)
- Daniel A Landfried
- The Pennsylvania State University, Department of Chemistry, University Park, PA 16802, USA
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20
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Boys BL, Konermann L. Folding and assembly of hemoglobin monitored by electrospray mass spectrometry using an on-line dialysis system. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:8-16. [PMID: 16979901 DOI: 10.1016/j.jasms.2006.08.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 08/07/2006] [Accepted: 08/11/2006] [Indexed: 05/11/2023]
Abstract
The native structure of hemoglobin (Hb) comprises two alpha- and two beta-subunits, each of which carries a heme group. There appear to be no previous studies that report the in vitro folding and assembly of Hb from highly unfolded alpha- and beta-globin in a "one-pot" reaction. One difficulty that has to be overcome for studies of this kind is the tendency of Hb to aggregate during refolding. This work demonstrates that denaturation of Hb in 40% acetonitrile at pH 10.0 is reversible. A dialysis-mediated solvent change to a purely aqueous environment of pH 8.0 results in Hb refolding without any apparent aggregation. Fluorescence, Soret absorption, circular dichroism, and ESI mass spectra of the protein recorded before unfolding and after refolding are almost identical. By employing an externally pressurized dialysis cell that is coupled on-line to an ESI mass spectrometer, changes in heme binding behavior, protein conformation, and quaternary structure can be monitored as a function of time. The process occurs in a stepwise sequential manner, leading from monomeric alpha- and beta-globin to heterodimeric species, which then assemble into tetramers. Overall, this mechanism is consistent with previous studies employing the mixing of folded alpha- and beta-globin. However, some unexpected features are observed, e.g., a heme-deficient beta-globin dimer that represents an off-pathway intermediate. Monomeric beta-globin is capable of binding heme before forming a complex with an alpha-subunit. This observation suggests that holo-alpha-apo-beta globin does not represent an obligatory intermediate during Hb assembly, as had been proposed previously. The on-line dialysis/ESI-MS approach developed for this work represents a widely applicable tool for studying the folding and self-assembly of noncovalent biological complexes.
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Affiliation(s)
- Brian L Boys
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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21
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Pan J, Rintala-Dempsey AC, Li Y, Shaw GS, Konermann L. Folding kinetics of the S100A11 protein dimer studied by time-resolved electrospray mass spectrometry and pulsed hydrogen-deuterium exchange. Biochemistry 2006; 45:3005-13. [PMID: 16503655 DOI: 10.1021/bi052349a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports the application of electrospray ionization (ESI) mass spectrometry (MS) with on-line rapid mixing for millisecond time-resolved studies of the refolding and assembly of a dimeric protein complex. Acid denaturation of S100A11 disrupts the native homodimeric protein structure. Circular dichroism and HSQC nuclear magnetic resonance measurements reveal that the monomeric subunits unfold to a moderate degree but retain a significant helicity and some tertiary structural elements. Following a rapid change in solution conditions to a slightly basic pH, the native protein reassembles with an effective rate constant of 6 s(-)(1). The ESI charge state distributions measured during the reaction suggest the presence of three kinetic species, namely, a relatively unfolded monomer (M(U)), a more tightly folded monomeric reaction intermediate (M(F)), and dimeric S100A11. These three forms exhibit distinct calcium binding properties, with very low metal loading levels for M(U), up to two calcium ions for M(F), and up to four for the dimer. Surprisingly, on-line pulsed hydrogen-deuterium exchange (HDX) reveals that each of the monomeric forms of the protein comprises two subspecies that can be distinguished on the basis of their isotope exchange levels. As the reaction proceeds, the more extensively labeled species are depleted. The exponential nature of the measured intensity-time profiles implies that the rate-determining step of the overall process is a unimolecular event. The kinetics are consistent with a sequential folding and assembly mechanism involving two increasingly nativelike monomeric intermediates en route to the native S100A11 dimer.
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Affiliation(s)
- Jingxi Pan
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Muralidhara BK, Rathinakumar R, Wittung-Stafshede P. Folding of Desulfovibrio desulfuricans flavodoxin is accelerated by cofactor fly-casting. Arch Biochem Biophys 2006; 451:51-8. [PMID: 16730634 DOI: 10.1016/j.abb.2006.03.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 03/07/2006] [Accepted: 03/31/2006] [Indexed: 11/27/2022]
Abstract
Folding of cofactor-binding proteins involves ligand binding in addition to polypeptide folding. We here assess the kinetic folding/binding landscape for Desulfovibrio desulfuricans flavodoxin that coordinates an FMN cofactor. The apo-form folds in a two-step process involving a burst-phase intermediate. Studies on Tyr98Ala and Trp60Ala variants reveal that these aromatics-that stack with the FMN in the holo-form-are not participating in the apo-protein folding pathway. However, these residues are essential for FMN interactions with the unfolded protein during refolding of holo-flavodoxin. Unfolding of wild-type holo-flavodoxin is coupled to FMN dissociation whereas for Tyr98Ala and Trp60Ala holo-variants, FMN dissociates before polypeptide unfolding. Both variants refold as apo-proteins before FMN rebinds. In sharp contrast, refolding of unfolded wild-type holo-flavodoxin is over an order of magnitude faster than that of the apo-form, the pathway does not include a burst-phase intermediate, and the speed is independent of FMN excess ratio. These observations demonstrate that FMN binds rapidly to the unfolded polypeptide and guides folding straight to the native state. As this path to functional D. desulfuricans holo-flavodoxin is faster than if the cofactor binds to pre-folded apo-protein, this is one of few examples where molecular recognition via a "fly-casting" mechanism is kinetically favored.
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Affiliation(s)
- B K Muralidhara
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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