1
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Bolonova EI, Melnik TN, Potekhin SA. Inside of the burst-phase intermediate of a protein folding. Hydration of hydrophobic groups. Biophys Chem 2024; 312:107268. [PMID: 38843749 DOI: 10.1016/j.bpc.2024.107268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/07/2024] [Accepted: 05/20/2024] [Indexed: 07/22/2024]
Abstract
The thermal effect of the formation of the "burst-phase" folding intermediate has been studied using a titration calorimeter. It is shown that, unlike the total thermal effect of native structure formation, it can be both positive and negative depending on the temperature. The reasons for this paradoxical behavior are analyzed. A conclusion is drawn about the leading role of dehydration of non-polar groups in the first stage of folding.
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Affiliation(s)
- Elena I Bolonova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Sergey A Potekhin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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2
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Jain A, Judy E, Kishore N. Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach. J Phys Chem B 2024; 128:5344-5362. [PMID: 38773936 DOI: 10.1021/acs.jpcb.4c01751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Many studies have demonstrated the manner in which ANS interacts with bovine serum albumin (BSA), although they are limited by the extremely low solubility of dye. The present study demonstrates the binding of ANSA dye with BSA, and since this dye can easily replace ANS, it not only simplifies research but also improves sensor accuracy for serum albumin. A combination of calorimetry and spectroscopy has been employed to establish the thermodynamic signatures associated with the interaction of ANSA with the protein and the consequent conformational changes in the latter. The results of differential scanning calorimetry reveal that when the concentration of ANSA in solution is increased, the thermal stability of the protein increases substantially. The fluorescence data demonstrated a decrease in the binding affinity of ANSA with the protein when pH increased but was unable to identify a change in the mode of interaction of the ligand. ITC has demonstrated that the mode of interaction between ANSA and the protein varies from a single set of binding sites at pH 5 and 7.4 to a sequential binding site at pH 10, emphasizing the potential relevance of protein conformational changes. TCSPC experiments suggested a dynamic type in the presence of ANSA. Molecular docking studies suggest that ANSA molecules are able to find ionic centers in the hydrophobic pockets of BSA. The findings further imply that given its ease of use in experiments, ANSA may be a useful probe for tracking the presence of serum albumin and partially folded protein states.
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Affiliation(s)
- Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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3
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Skvarnavičius G, Toleikis Z, Matulis D, Petrauskas V. Denaturant- or ligand-induced change in protein volume by pressure shift assay. Phys Chem Chem Phys 2022; 24:17279-17288. [DOI: 10.1039/d2cp01046a] [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
A complete thermodynamic description of protein-ligand binding includes parameters related to pressure and temperature. The changes in protein volume and compressibility upon binding a ligand are pressure-related parameters that are...
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4
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Kumar V, Chaudhuri TK. Spontaneous refolding of the large multidomain protein malate synthase G proceeds through misfolding traps. J Biol Chem 2018; 293:13270-13283. [PMID: 29959230 DOI: 10.1074/jbc.ra118.003903] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/28/2018] [Indexed: 11/06/2022] Open
Abstract
Most protein folding studies until now focus on single domain or truncated proteins. Although great insights in the folding of such systems has been accumulated, very little is known regarding the proteins containing multiple domains. It has been shown that the high stability of domains, in conjunction with inter-domain interactions, manifests as a frustrated energy landscape, causing complexity in the global folding pathway. However, multidomain proteins despite containing independently foldable, loosely cooperative sections can fold into native states with amazing speed and accuracy. To understand the complexity in mechanism, studies were conducted previously on the multidomain protein malate synthase G (MSG), an enzyme of the glyoxylate pathway with four distinct and adjacent domains. It was shown that the protein refolds to a functionally active intermediate state at a fast rate, which slowly produces the native state. Although experiments decoded the nature of the intermediate, a full description of the folding pathway was not elucidated. In this study, we use a battery of biophysical techniques to examine the protein's folding pathway. By using multiprobe kinetics studies and comparison with the equilibrium behavior of protein against urea, we demonstrate that the unfolded polypeptide undergoes conformational compaction to a misfolded intermediate within milliseconds of refolding. The misfolded product appears to be stabilized under moderate denaturant concentrations. Further folding of the protein produces a stable intermediate, which undergoes partial unfolding-assisted large segmental rearrangements to achieve the native state. This study reveals an evolved folding pathway of the multidomain protein MSG, which involves surpassing the multiple misfolding traps during refolding.
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Affiliation(s)
- Vipul Kumar
- From the Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi 110016, India
| | - Tapan K Chaudhuri
- From the Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi 110016, India
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5
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Pang YH, Chen JW. Anisodamine Causes the Changes of Structure and Function in the Transmembrane Domain of the Ca2+-ATPase from Sarcoplasmic Reticulum. Biosci Biotechnol Biochem 2014; 68:126-31. [PMID: 14745174 DOI: 10.1271/bbb.68.126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effects of anisodamine on the Ca(2+)-ATPsae of sarcoplasmic reticulum (SR) were investigated by using differential scanning calorimetry to measure the ability of anisodamine to denature the transmembrane domain and the cytoplasmic domain. Anisodamine significantly altered the thermotropic phase behaviors of the transmembrane domain of purified Ca(2+)-ATPase. Specifically, the melting temperature of the transmembrane domain moved toward lower temperatures with the concentrations of anisodamine increasing and the thermotropic phase peak was abolished at 10 mM, indicating that the stabilized structure of the transmembrane domain in the presence of Ca2+ could be destabilized by anisodamine. Decreases of the intrinsic fluorescence and increases of the extrinsic fluorescence of ANS, a fluorescent probe, showed the exposure of tryptophan and hydrophobic region, respectively, suggesting again that anisodamine caused a less compact conformation in the transmembrane domain. A marked inhibition of the Ca2+ uptake activity of SR Ca(2+)-ATPase was observed when the addition of anisodamine. The drug did not affect the cytoplasmic domain of the enzyme and only slightly decreased the ATPase activity of the enzyme at concentrations up to 10 mM. This was likely due to the destabilized protein transmembrane domain. To sum up, our results revealed that anisodamine interacted specifically with the transmembrane domain of SR Ca(2+)-ATPase and inhibited the Ca2+ uptake activity of the enzyme.
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Affiliation(s)
- Yu-Hong Pang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, China
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6
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Chowdhury A, Choudhury A, Banerjee V, Banerjee R, Das KP. Spectroscopic studies of the unfolding of a multimeric protein α-crystallin. Biopolymers 2014; 101:549-60. [DOI: 10.1002/bip.22417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/19/2013] [Accepted: 09/23/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Aritra Chowdhury
- School of Chemistry; University of Manchester; Oxford Road, M13 9PL Manchester UK
- Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology and Department of Biotechnology; Calcutta University; Ballygunge Circular Road Kolkata 700019 India
| | - Aparajita Choudhury
- Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology and Department of Biotechnology; Calcutta University; Ballygunge Circular Road Kolkata 700019 India
| | - Victor Banerjee
- Department of Chemistry; Bose Institute; 93/1 A. P. C. Road Kolkata 700 009 India
| | - Rajat Banerjee
- Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology and Department of Biotechnology; Calcutta University; Ballygunge Circular Road Kolkata 700019 India
| | - K. P. Das
- Department of Chemistry; Bose Institute; 93/1 A. P. C. Road Kolkata 700 009 India
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7
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Feng S, Gong Y, Adilijiang G, Deng H. Effects of the Fc-III tag on activity and stability of green fluorescent protein and human muscle creatine kinase. Protein Sci 2014; 22:1008-15. [PMID: 23661339 DOI: 10.1002/pro.2282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/24/2013] [Accepted: 05/01/2013] [Indexed: 11/11/2022]
Abstract
The Fc-III tag is a newly developed fusion tag that can be applied to protein purification and detection. In the present work, we use the Fc-III-tagged green fluorescent protein (GFP) and human muscle creatine kinase (CK) as model systems to investigate effects of the Fc-III tag on activities and stabilities of the expressed multicysteine-containing proteins. Our results show the Fc-III tag has no adverse effects on the fluorescence of GFP and reduces the occurrence of GFP misfolding due to incorrect Cys oxidation compared with the His-tagged protein. The activity and stability of the Fc-III-tagged CK is slightly lower than that of the tag-free CK, but is higher than that of the His-tagged CK as determined by the ratio of the oxidized versus reduced CK. A major portion of His-tagged CK is in its oxidized form, while that of the Fc-III-tagged CK is in its reduced form. A folding model of CK with different tags was proposed, which may provide insights into the effect of the Fc-III tag on the conformations of disulfide-bridged proteins.
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Affiliation(s)
- Shan Feng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
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8
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Glu434 is an important amino acid residue for the activity, structure and stability of tyrosine hydroxylase of the silkworm, Bombyx mori. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Yu Z, Reid JC, Yang YP. Utilizing dynamic light scattering as a process analytical technology for protein folding and aggregation monitoring in vaccine manufacturing. J Pharm Sci 2013; 102:4284-90. [PMID: 24122727 DOI: 10.1002/jps.23746] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/09/2013] [Accepted: 09/19/2013] [Indexed: 12/25/2022]
Abstract
Protein aggregation is a common challenge in the manufacturing of biological products. It is possible to minimize the extent of aggregation through timely measurement and in-depth characterization of aggregation. In this study, we demonstrated the use of dynamic light scattering (DLS) to monitor inclusion body (IB) solubilization, protein refolding, and aggregation near the production line of a recombinant protein-based vaccine candidate. Our results were in good agreement with those measured by size-exclusion chromatography. DLS was also used to characterize the mechanism of aggregation. As DLS is a quick, nonperturbing technology, it can potentially be used as an at-line process analytical technology to ensure complete IB solubilization and aggregate-free refolding.
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Affiliation(s)
- Zhou Yu
- Bioprocess Research and Development, Sanofi Pasteur, Toronto, Ontario, M2R 3T4, Canada
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10
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Biochemical and biophysical characterization of four EphB kinase domains reveals contrasting thermodynamic, kinetic and inhibition profiles. Biosci Rep 2013; 33:BSR20130028. [PMID: 23627399 PMCID: PMC3673036 DOI: 10.1042/bsr20130028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Eph (erythropoietin-producing hepatocellular carcinoma) B receptors are important in a variety of cellular processes through their roles in cell-to-cell contact and signalling; their up-regulation and down-regulation has been shown to have implications in a variety of cancers. A greater understanding of the similarities and differences within this small, highly conserved family of tyrosine kinases will be essential to the identification of effective therapeutic opportunities for disease intervention. In this study, we have developed a route to production of multi-milligram quantities of highly purified, homogeneous, recombinant protein for the kinase domain of these human receptors in Escherichia coli. Analyses of these isolated catalytic fragments have revealed stark contrasts in their amenability to recombinant expression and their physical properties: e.g., a >16°C variance in thermal stability, a 3-fold difference in catalytic activity and disparities in their inhibitor binding profiles. We find EphB3 to be an outlier in terms of both its intrinsic stability, and more importantly its ligand-binding properties. Our findings have led us to speculate about both their biological significance and potential routes for generating EphB isozyme-selective small-molecule inhibitors. Our comprehensive methodologies provide a template for similar in-depth studies of other kinase superfamily members.
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11
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Chen Z, Chen XJ, Xia M, He HW, Wang S, Liu H, Gong H, Yan YB. Chaperone-like effect of the linker on the isolated C-terminal domain of rabbit muscle creatine kinase. Biophys J 2013; 103:558-566. [PMID: 22947872 DOI: 10.1016/j.bpj.2012.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 11/25/2022] Open
Abstract
Intramolecular chaperones (IMCs), which are specific domains/segments encoded in the primary structure of proteins, exhibit chaperone-like activity against the aggregation of the other domains in the same molecule. In this research, we found that the truncation of the linker greatly promoted the thermal aggregation of the isolated C-terminal domain (CTD) of rabbit muscle creatine kinase (RMCK). Either the existence of the linker covalently linked to CTD or the supply of the synthetic linker peptide additionally could successfully protect the CTD of RMCK against aggregation in a concentration-dependent manner. Truncated fragments of the linker also behaved as a chaperone-like effect with lower efficiency, revealing the importance of its C-terminal half in the IMC function of the linker. The aggregation sites in the CTD of RMCK were identified by molecular dynamics simulations. Mutational analysis of the three key hydrophobic residues resulted in opposing effects on the thermal aggregation between the CTD with intact or partial linker, confirming the role of linker as a lid to protect the hydrophobic residues against exposure to solvent. These observations suggested that the linkers in multidomain proteins could act as IMCs to facilitate the correct folding of the aggregation-prone domains. Furthermore, the intactness of the IMC linker after proteolysis modulates the production of off-pathway aggregates, which may be important to the onset of some diseases caused by the toxic effects of aggregated proteolytic fragments.
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Affiliation(s)
- Zhe Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | - Xiang-Jun Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China; Key Laboratory of Bio-Resources and Eco-Environment of MOE, College of Life Science, Sichuan University, Chengdu, China
| | - Mengdie Xia
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hua-Wei He
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | - Sha Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | - Huihui Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yong-Bin Yan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China.
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12
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Kuznetsova IM, Sulatskaya AI, Povarova OI, Turoverov KK. Reevaluation of ANS binding to human and bovine serum albumins: key role of equilibrium microdialysis in ligand - receptor binding characterization. PLoS One 2012; 7:e40845. [PMID: 22829890 PMCID: PMC3400656 DOI: 10.1371/journal.pone.0040845] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/14/2012] [Indexed: 11/18/2022] Open
Abstract
In this work we return to the problem of the determination of ligand–receptor binding stoichiometry and binding constants. In many cases the ligand is a fluorescent dye which has low fluorescence quantum yield in free state but forms highly fluorescent complex with target receptor. That is why many researchers use dye fluorescence for determination of its binding parameters with receptor, but they leave out of account that fluorescence intensity is proportional to the part of the light absorbed by the solution rather than to the concentration of bound dye. We showed how ligand–receptor binding parameters can be determined by spectrophotometry of the solutions prepared by equilibrium microdialysis. We determined the binding parameters of ANS – human serum albumin (HSA) and ANS – bovine serum albumin (BSA) interaction, absorption spectra, concentration and molar extinction coefficient, as well as fluorescence quantum yield of the bound dye. It was found that HSA and BSA have two binding modes with significantly different affinity to ANS. Correct determination of the binding parameters of ligand–receptor interaction is important for fundamental investigations and practical aspects of molecule medicine and pharmaceutics. The data obtained for albumins are important in connection with their role as drugs transporters.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins of the Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
- Department of Biophysics, of St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation
| | - Anna I. Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins of the Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Olga I. Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins of the Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins of the Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
- * E-mail:
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13
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Molecularly imprinted polymers for the recognition of sodium dodecyl sulfate denatured creatine kinase. J Taiwan Inst Chem Eng 2012. [DOI: 10.1016/j.jtice.2011.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Wang SF, Si YX, Wang ZJ, Yin SJ, Yang JM, Qian GY. Folding studies on muscle type of creatine kinase from Pelodiscus sinensis. Int J Biol Macromol 2012; 50:981-90. [PMID: 22405779 DOI: 10.1016/j.ijbiomac.2012.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/22/2012] [Accepted: 02/22/2012] [Indexed: 10/28/2022]
Abstract
A folding study of creatine kinase from Pelodiscus sinensis has not yet been reported. To gain more insight into structural and folding mechanisms of P. sinensis CK (PSCK), denaturants such as SDS, guanidine HCl, and urea were applied in this study. We purified PSCK from the muscle of P. sinensis and conducted inhibition kinetics with structural unfolding studies under various conditions. The results revealed that PSCK was completely inactivated at 1.8 mM SDS, 1.05 M guanidine HCl, and 7.5 M urea. The kinetics via time-interval measurements showed that the inactivation by SDS, guanidine HCl, and urea were all first-order reactions with kinetic processes shifting from monophase to biphase at increasing concentrations. With respect to tertiary structural changes, PSCK was unfolded in different ways; SDS increased the hydrophobicity but retained the most tertiary structural conformation, while guanidine HCl and urea induced conspicuous changes in tertiary structures and initiated kinetic unfolding mechanisms. Our study provides information regarding PSCK and enhances our knowledge of the reptile-derived enzyme folding.
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Affiliation(s)
- Su-Fang Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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15
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Dissimilarity in the folding of human cytosolic creatine kinase isoenzymes. PLoS One 2011; 6:e24681. [PMID: 21931810 PMCID: PMC3170377 DOI: 10.1371/journal.pone.0024681] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/15/2011] [Indexed: 12/02/2022] Open
Abstract
Creatine kinase (CK, EC 2.7.3.2) plays a key role in the energy homeostasis of excitable cells. The cytosolic human CK isoenzymes exist as homodimers (HMCK and HBCK) or a heterodimer (MBCK) formed by the muscle CK subunit (M) and/or brain CK subunit (B) with highly conserved three-dimensional structures composed of a small N-terminal domain (NTD) and a large C-terminal domain (CTD). The isoforms of CK provide a novel system to investigate the sequence/structural determinants of multimeric/multidomain protein folding. In this research, the role of NTD and CTD as well as the domain interactions in CK folding was investigated by comparing the equilibrium and kinetic folding parameters of HMCK, HBCK, MBCK and two domain-swapped chimeric forms (BnMc and MnBc). Spectroscopic results indicated that the five proteins had distinct structural features depending on the domain organizations. MBCK BnMc had the smallest CD signals and the lowest stability against guanidine chloride-induced denaturation. During the biphasic kinetic refolding, three proteins (HMCK, BnMc and MnBc), which contained either the NTD or CTD of the M subunit and similar microenvironments of the Trp fluorophores, refolded about 10-fold faster than HBCK for both the fast and slow phase. The fast folding of these three proteins led to an accumulation of the aggregation-prone intermediate and slowed down the reactivation rate thereby during the kinetic refolding. Our results suggested that the intra- and inter-subunit domain interactions modified the behavior of kinetic refolding. The alternation of domain interactions based on isoenzymes also provides a valuable strategy to improve the properties of multidomain enzymes in biotechnology.
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Bleul R, Ritzi-Lehnert M, Höth J, Scharpfenecker N, Frese I, Düchs D, Brunklaus S, Hansen-Hagge TE, Meyer-Almes FJ, Drese KS. Compact, cost-efficient microfluidics-based stopped-flow device. Anal Bioanal Chem 2010; 399:1117-25. [PMID: 21116614 DOI: 10.1007/s00216-010-4446-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 11/26/2022]
Abstract
Stopped-flow technology is frequently used to monitor rapid (bio)chemical reactions with high temporal resolution, e.g., in dynamic investigations of enzyme reactions, protein interactions, or molecular transport mechanisms. However, conventional stopped-flow devices are often overly complex, voluminous, or costly. Moreover, excessive amounts of sample are often wasted owing to inefficient designs. To address these shortcomings, we propose a stopped-flow system based on microfluidic design principles. Our simple and cost-efficient approach offers distinct advantages over existing technology. In particular, the use of injection-molded disposable microfluidic chips minimizes required sample volumes and associated costs, simplifies handling, and prevents adverse cross-contamination effects. The cost of the system developed is reduced by an order of magnitude compared with the cost of commercial systems. The system contains a high-precision valve system for fluid control and features automated data acquisition capability with high temporal resolution. Analyses with two well-established reaction kinetics yielded a dead time of approximately 8-9 ms.
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Affiliation(s)
- Regina Bleul
- Institut für Mikrotechnik Mainz GmbH (IMM), Carl-Zeiss-Str. 18-20, 55129 Mainz, Germany
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17
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Ghaouar N, Belbahri L, Trabelsi S, Aschi A, Gharbi A. Study of Cellulase Enzymes Conformational Changes: Numerical Prediction. J MACROMOL SCI B 2010. [DOI: 10.1080/00222341003609237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- N. Ghaouar
- a Laboratoire de Physique de la Matière Molle , Faculté des Sciences de Tunis, Campus Universitaire , Tunisia
- b Institut National des Sciences Appliquées et de Technologie , INSAT, Centre Urbain Nord , Tunis, Tunisia
| | - L. Belbahri
- c Agronomy department , School of Engineering of Lullier, University of Applied Sciences of Western Switzerland , Jussy, Switzerland
| | - S. Trabelsi
- a Laboratoire de Physique de la Matière Molle , Faculté des Sciences de Tunis, Campus Universitaire , Tunisia
| | - A. Aschi
- a Laboratoire de Physique de la Matière Molle , Faculté des Sciences de Tunis, Campus Universitaire , Tunisia
| | - A. Gharbi
- a Laboratoire de Physique de la Matière Molle , Faculté des Sciences de Tunis, Campus Universitaire , Tunisia
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18
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Gao YS, Wang Y, Li C, Chen Z, Yan YB, Zhou HM. Dissecting the key residues crucial for the species-specific thermostability of muscle-type creatine kinase. Int J Biol Macromol 2010; 47:366-70. [PMID: 20558199 DOI: 10.1016/j.ijbiomac.2010.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 06/06/2010] [Indexed: 10/19/2022]
Abstract
Species-specific protein thermal stability is closely correlated to the living conditions of the organism, especially to its body temperature. In this research, human and zebrafish muscle-type creatine kinases (MMCKs) were taken as model proteins to investigate the molecular adaptation of proteins in poikilothermal and homoiothermal animals. Both the optimal temperature for catalysis and the thermal stability of human MMCK was much higher than those of zebrafish MMCK. Sequence alignment identified 9 amino acid variations conserved in either the teleost MMCKs or the mammal and electric ray MMCKs. Bidirectional mutations were performed to find the residues with beneficial mutations. The results showed that two residues close to the dimer interface of MMCK, the 46th and 146th residue, were crucial for species-specific thermal stability.
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Affiliation(s)
- Yan-Song Gao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, China
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19
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Sequential events in the irreversible thermal denaturation of human brain-type creatine kinase by spectroscopic methods. Int J Mol Sci 2010; 11:2584-96. [PMID: 20717523 PMCID: PMC2920553 DOI: 10.3390/ijms11072584] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 06/09/2010] [Accepted: 06/18/2010] [Indexed: 11/16/2022] Open
Abstract
The non-cooperative or sequential events which occur during protein thermal denaturation are closely correlated with protein folding, stability, and physiological functions. In this research, the sequential events of human brain-type creatine kinase (hBBCK) thermal denaturation were studied by differential scanning calorimetry (DSC), CD, and intrinsic fluorescence spectroscopy. DSC experiments revealed that the thermal denaturation of hBBCK was calorimetrically irreversible. The existence of several endothermic peaks suggested that the denaturation involved stepwise conformational changes, which were further verified by the discrepancy in the transition curves obtained from various spectroscopic probes. During heating, the disruption of the active site structure occurred prior to the secondary and tertiary structural changes. The thermal unfolding and aggregation of hBBCK was found to occur through sequential events. This is quite different from that of muscle-type CK (MMCK). The results herein suggest that BBCK and MMCK undergo quite dissimilar thermal unfolding pathways, although they are highly conserved in the primary and tertiary structures. A minor difference in structure might endow the isoenzymes dissimilar local stabilities in structure, which further contribute to isoenzyme-specific thermal stabilities.
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Liu YM, Feng S, Ding XL, Kang CF, Yan YB. Mutation of the conserved Asp122 in the linker impedes creatine kinase reactivation and refolding. Int J Biol Macromol 2009; 44:271-7. [PMID: 19263506 DOI: 10.1016/j.ijbiomac.2008.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Creatine kinase (CK), a key enzyme in maintaining the intracellular energetic homeostasis, contains two domains connected by a long linker. In this research,we found that the mutations of the conserved Asp122 in the linker slightly affected CK activity, structure and stability. The hydrogen bonding and the ion pair contributed 2-5 kJ/mol to the conformational stability of CK. Interestingly, the ability of CK reactivation from the denatured state was completely removed by the mutations. These results suggested that the electrostatic interactions were crucial to the action of the linker in CK reactivation.
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Affiliation(s)
- Yan-Ming Liu
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
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21
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Spatara M, Roberts C, Robinson A. Kinetic folding studies of the P22 tailspike beta-helix domain reveal multiple unfolded states. Biophys Chem 2009; 141:214-21. [DOI: 10.1016/j.bpc.2009.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 02/03/2009] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
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22
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The conserved Cys254 plays a crucial role in creatine kinase refolding under non-reduced conditions but not in its activity or stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:2071-8. [DOI: 10.1016/j.bbapap.2008.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/19/2008] [Accepted: 08/20/2008] [Indexed: 11/22/2022]
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23
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Liang Y. Applications of isothermal titration calorimetry in protein science. Acta Biochim Biophys Sin (Shanghai) 2008; 40:565-76. [PMID: 18604448 DOI: 10.1111/j.1745-7270.2008.00437.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During the past decade, isothermal titration calorimetry (ITC) has developed from a specialist method for understanding molecular interactions and other biological processes within cells to a more robust, widely used method. Nowadays, ITC is used to investigate all types of protein interactions, including protein-protein interactions, protein-DNA/RNA interactions, protein-small molecule interactions and enzyme kinetics; it provides a direct route to the complete thermodynamic characterization of protein interactions. This review concentrates on the new applications of ITC in protein folding and misfolding, its traditional application in protein interactions, and an overview of what can be achieved in the field of protein science using this method and what developments are likely to occur in the near future. Also, this review discusses some new developments of ITC method in protein science, such as the reverse titration of ITC and the displacement method of ITC.
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Affiliation(s)
- Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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24
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Qin G, Jianwei Z, Taotao L, Xicheng W. Intermediates in the refolding of urea-denatured dimeric arginine kinase from Stichopus japonicus. Int J Biol Macromol 2007; 41:521-8. [PMID: 17709134 DOI: 10.1016/j.ijbiomac.2007.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2007] [Revised: 07/11/2007] [Accepted: 07/11/2007] [Indexed: 11/27/2022]
Abstract
The refolding of urea-denatured dimeric AK was investigated by both equilibrium and kinetic measurements. Both studies indicated that the refolding of dimeric AK is a multiphasic process. The equilibrium studies, monitored by enzyme activity, intrinsic protein fluorescence, circular dichroism (CD), 1-anilinonaphtalene-8-sulfonate (ANS) binding, size-exclusion chromatography and glutaraldehyde cross-linking showed that there were at least two intermediates involved in this process: I(1) (existing in 1.8-1.4M urea) and I(2) (existing in 0.8-0.4M urea). I(1) was a monomeric intermediate and possessed characteristic similar to the globular folding intermediates described in the literature. I(2) was an active native-like intermediate. The kinetic studies suggested that the refolding of AK possessed a burst phase, fast phase and slow phase, which involved at least the burst phase intermediates (I(B)). Comparison of the properties of these intermediates suggested that I(B) in the kinetic process corresponded to I(1) in the equilibrium process. Based on these results, a scheme for refolding of urea-denatured AK was proposed.
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Affiliation(s)
- Guo Qin
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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25
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Hansia P, Dev S, Surolia A, Vishveshwara S. Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations. Proteins 2007; 69:32-42. [PMID: 17596827 DOI: 10.1002/prot.21512] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed to follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its secondary structure but considerable loss of the tertiary structure at high temperature. This observation implies the generation of a molten globule-like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal-binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal-ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein.
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Affiliation(s)
- Priti Hansia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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26
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Mu H, Zhou SM, Yang JM, Meng FG, Park YD. Towards creatine kinase aggregation due to the cysteine modification at the flexible active site and refolding pathway. Int J Biol Macromol 2007; 41:439-46. [PMID: 17673285 DOI: 10.1016/j.ijbiomac.2007.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 05/21/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
The dimeric native state of creatine kinase (CK) was aggregated at conspicuous levels during cysteine modification at the active site with using 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) under a high enzyme concentration. Measuring the ANS-binding fluorescence revealed that the hydrophobic surface of CK was increased by cysteine modification due to the flexible active site, and this resulted in insoluble aggregation, probably via non-specific hydrophobic interactions. To determine whether the aggregates can be refolded, 3M guanidine hydrochloride (GdnHCl) was used to dissolve the aggregates into the denatured form. Refolding of the solubilized enzyme sample was then conducted, accompanied by deprivation of DTNB from the CK in the presence of DTT. As a result, CK was reactivated by up to 40% with partial recovery of the tertiary (78%) and secondary structures (77%). To further elucidate its kinetic refolding pathway, both time interval measurements and a continuous substrate reaction were performed. The results showed that the refolding behavior was similar to the manner of normal CK folding with respect to the following two-phase kinetic courses. Additionally, the rate constants for the dimerization of the unfolded CK were dependent on the enzyme concentration and this was irrespective to the DTT concentrations, suggesting the rate-limiting steps of CK reassociation. The present study will expand our insight into the flexibility of the enzyme active site, which might act as a risk factor for inducing the unfavorable aggregation and partial refolding pathway of CK, as well as inducing an intermediate-like state recovery from aggregation.
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Affiliation(s)
- Hang Mu
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, PR China
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27
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Tsutsui Y, Wintrode PL. Cooperative Unfolding of a Metastable Serpin to a Molten Globule Suggests a Link Between Functional and Folding Energy Landscapes. J Mol Biol 2007; 371:245-55. [PMID: 17568610 DOI: 10.1016/j.jmb.2007.05.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 05/02/2007] [Accepted: 05/11/2007] [Indexed: 10/23/2022]
Abstract
Alpha-1 antitrypsin (alpha(1)-AT) is a member of the serpin class of protease inhibitors, and folds to a metastable state rather than its thermodynamically most stable native state. Upon cleavage by a target protease, alpha(1)-AT undergoes a dramatic conformational change to a stable form, translocating the bound protease more than 70 A to form an inhibitory protease-serpin complex. Numerous mutagenesis studies on serpins have demonstrated the trade-off between the stability of the metastable state on the one hand and the inhibitory efficiency on the other. Studies of the equilibrium unfolding of serpins provide insight into this connection between structural plasticity and metastability. We studied equilibrium unfolding of wild-type alpha(1)-AT using hydrogen-deuterium/exchange mass spectrometry to characterize the structure and the stability of an equilibrium intermediate that was observed in low concentrations of denaturant in earlier studies. Our results show that the intermediate observed at low concentrations of denaturant has no protection from hydrogen-deuterium exchange, indicating a lack of stable structure. Further, differential scanning calorimetry of alpha(1)-AT at low concentrations of denaturant shows no heat capacity peak during thermal denaturation, indicating that the transition from the intermediate to the unfolded state is not a cooperative first-order-like phase transition.. Our results show that the unfolding of alpha(1)-AT involves a cooperative transition to a molten globule form, followed by a non-cooperative transition to a random-coil form as more guanidine is added. Thus, the entire alpha(1)-AT molecule consists of one cooperative structural unit rather than multiple structural domains with different stabilities. Furthermore, our results together with previous mutagenesis studies suggest a possible link between an equilibrium molten globule and a functional intermediate that may be populated during the protease inhibition.
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Affiliation(s)
- Yuko Tsutsui
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
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28
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Zhou L, Poh RPC, Marks TS, Chowdhry BZ, Smith ARW. Structure and denaturation of 4-chlorobenzoyl coenzyme A dehalogenase from Arthrobacter sp. strain TM-1. Biodegradation 2007; 19:65-75. [PMID: 17431803 DOI: 10.1007/s10532-007-9115-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 03/09/2007] [Indexed: 11/27/2022]
Abstract
The secondary structure of the trimeric protein 4-chlorobenzoyl coenzyme A dehalogenase from Arthrobacter sp. strain TM-1, the second of three enzymes involved in the dechlorination of 4-chlorobenzoate to form 4-hydroxybenzoate, has been examined. E(mM) for the enzyme was 12.59. Analysis by circular dichroism spectrometry in the far uv indicated that 4-chlorobenzoyl coenzyme A dehalogenase was composed mostly of alpha-helix (56%) with lesser amounts of random coil (21%), beta-turn (13%) and beta-sheet (9%). These data are in close agreement with a computational prediction of secondary structure from the primary amino acid sequence, which indicated 55.8% alpha-helix, 33.7% random coil and 10.5% beta-sheet; the enzyme is, therefore, similar to the 4-chlorobenzoyl coenzyme A dehalogenase from Pseudomonas sp. CBS-3. The three-dimensional structure, including that of the presumed active site, predicted by computational analysis, is also closely similar to that of the Pseudomonas dehalogenase. Study of the stability and physicochemical properties revealed that at room temperature, the enzyme was stable for 24 h but was completely inactivated by heating to 60 degrees C for 5 min; thereafter by cooling at 1 degrees C min(-1) to 45 degrees C, 20.6% of the activity could be recovered. Mildly acidic (pH 5.2) or alkaline (pH 10.1) conditions caused complete inactivation, but activity was fully recovered on returning the enzyme to pH 7.4. Circular dichroism studies also indicated that secondary structure was little altered by heating to 60 degrees C, or by changing the pH from 7.4 to 6.0 or 9.2. Complete, irreversible destruction of, and maximal decrease in the fluorescence yield of the protein at 330-350 nm were brought about by 4.5 M urea or 1.1 M guanidinium chloride. Evidence was obtained to support the hypothetical three-dimensional model, that residues W140 and W167 are buried in a non-polar environment, whereas W182 appears at or close to the surface of the protein. At least one of the enzymes of the dehalogenase system (the combined 4-chlorobenzoate:CoA ligase, the dehalogenase and 4-hydroxybenzoyl coenzyme A thioesterase) appears to be capable of association with the cell membrane.
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Affiliation(s)
- Lihong Zhou
- Department of Life Science, School of Science, University of Greenwich, Medway Campus, Pembroke, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
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29
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Awama AM, Mazon H, Vial C, Marcillat O. Despite its high similarity with monomeric arginine kinase, muscle creatine kinase is only enzymatically active as a dimer. Arch Biochem Biophys 2007; 458:158-66. [PMID: 17239811 DOI: 10.1016/j.abb.2006.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 09/01/2006] [Accepted: 09/02/2006] [Indexed: 10/24/2022]
Abstract
Although having highly similar primary to tertiary structures, the different guanidino kinases exhibit distinct quaternary structures: monomer, dimer or octamer. However, no evidence for communication between subunits has yet been provided, and reasons for these different levels of quaternary complexity that can be observed from invertebrate to mammalian guanidino kinases remain elusive. Muscle creatine kinase is a dimer and disruption of the interface between subunits has been shown to give rise to destabilized monomers with slight residual activity; this low activity could, however, be due to a fraction of protein molecules present as dimer. CK monomer/monomer interface involves electrostatic interactions and increasing salt concentrations unfold and inactivate this enzyme. NaCl and guanidine hydrochloride show a synergistic unfolding effect and, whatever the respective concentrations of these compounds, inactivation is associated with a dissociation of the dimer. Using an interface mutant (W210Y), protein concentration dependence of the NaCl-induced unfolding profile indicates that the active dimer is in equilibrium with an inactive monomeric state. Although highly similar to muscle CK, horse shoe crab (Limulus polyphemus) arginine kinase (AK) is enzymatically active as a monomer. Indeed, high ionic strengths that can monomerize and inactivate CK, have no effect on AK enzymatic activity or on its structure as judged from intrinsic fluorescence data. Our results indicate that expression of muscle creatine kinase catalytic activity is dependent on its dimeric state which is required for a proper stabilization of the monomers.
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Affiliation(s)
- Ayman M Awama
- Université Claude Bernard Lyon 1, UMR CNRS 5013 Bâtiment Chevreul, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
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30
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Feng S, Zhao TJ, Zhou HM, Yan YB. Effects of the single point genetic mutation D54G on muscle creatine kinase activity, structure and stability. Int J Biochem Cell Biol 2007; 39:392-401. [PMID: 17030001 DOI: 10.1016/j.biocel.2006.09.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 08/23/2006] [Accepted: 09/10/2006] [Indexed: 11/30/2022]
Abstract
Aberrant folding of important proteins caused by genetic mutations is closely correlated to many diseases. Due to the important physiological role in excitable cells, the activity and level of creatine kinase (CK) play a crucial role in maintaining body functions. Muscle CK deficiency disease was identified by an unusual CK activity decrease in an acute myocardial infarction patient caused by the single point mutation D54G. In this research, it was found that the D54G mutant had substantially decreased activity, substrate binding affinity and stability. Spectroscopic experiments indicated that the mutation impaired the structure of CK, which resulted in a partially unfolded state with more hydrophobic exposure and exposed Trp residues. The inability to fold to the functional compact state made the mutant be prone to aggregate upon microenvironmental stresses, and might gradually decrease the CK level of the patient.
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Affiliation(s)
- Shan Feng
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
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31
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Du F, Zhou Z, Mo ZY, Shi JZ, Chen J, Liang Y. Mixed Macromolecular Crowding Accelerates the Refolding of Rabbit Muscle Creatine Kinase: Implications for Protein Folding in Physiological Environments. J Mol Biol 2006; 364:469-82. [PMID: 17027032 DOI: 10.1016/j.jmb.2006.09.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 08/28/2006] [Accepted: 09/03/2006] [Indexed: 11/21/2022]
Abstract
The effects of four single macromolecular crowding agents, Ficoll 70, dextran 70, polyethylene glycol (PEG) 2000, and calf thymus DNA (CT DNA), and three mixed crowding agents containing both CT DNA and polysaccharide (or PEG 2000) on the refolding of guanidine hydrochloride-denatured rabbit muscle creatine kinase (MM-CK) have been examined by activity assay. When the total concentration of the mixed crowding agent is 100 g/l, in which the weight ratio of CT DNA to Ficoll 70 is 1:9, the refolding yield of MM-CK after refolding for 3 h under these conditions increases 23% compared with that in the presence of 10 g/l CT DNA, 18% compared with 100 g/l Ficoll 70, and 19% compared with that in the absence of crowding agents. A remarkable increase in the refolding yield of MM-CK by a mixed crowding agent containing CT DNA and dextran 70 (or PEG 2000) is also observed. Further folding kinetics analyses show that these three mixed crowding agents remarkably accelerate the refolding of MM-CK, compared with single crowding agents. Aggregation of MM-CK in the presence of any of the three mixed crowding agents is less serious than that in the presence of a single crowding agent at the same concentration but more serious than that in the absence of crowding agents. Both the refolding yield and the refolding rate of MM-CK in mixtures of these agents are increased relative to the individual agents by themselves, indicating that mixed macromolecular crowding agents are more favorable to MM-CK folding and can be used to reflect the physiological environment more accurately than single crowding agents.
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Affiliation(s)
- Fen Du
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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32
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Zhao TJ, Feng S, Wang YL, Liu Y, Luo XC, Zhou HM, Yan YB. Impact of intra-subunit domain-domain interactions on creatine kinase activity and stability. FEBS Lett 2006; 580:3835-40. [PMID: 16797013 DOI: 10.1016/j.febslet.2006.05.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 05/29/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
Creatine kinase (CK) is a key enzyme in vertebrate excitable tissues. In this research, five conserved residues located on the intra-subunit domain-domain interface were mutated to explore their role in the activity and structural stability of CK. The mutations of Val72 and Gly73 decreased both the activity and stability of CK. The mutations of Cys74 and Val75, which had no significant effect on CK activity and structure, gradually decreased the stability and reactivation of CK. Our results suggested that the mutations might modify the correct positioning of the loop contributing to domain-domain interactions, and result in decreased stability against denaturation.
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Affiliation(s)
- Tong-Jin Zhao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
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33
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Li S, Bai JH, Park YD, Zhou HM. Capture of monomeric refolding intermediate of human muscle creatine kinase. Protein Sci 2006; 15:171-81. [PMID: 16373479 PMCID: PMC2242377 DOI: 10.1110/ps.051738406] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Human muscle creatine kinase (CK) is an enzyme that plays an important physiological role in the energy metabolism of humans. It also serves as a typical model for studying refolding of proteins. A study of the refolding and reactivation process of guanidine chloride-denatured human muscle CK is described in the present article. The results show that the refolding process can be divided into fast and slow folding phases and that an aggregation process competes with the proper refolding process at high enzyme concentration and high temperature. An intermediate in the early stage of refolding was captured by specific protein molecules: the molecular chaperonin GroEL and alpha(s)-casein. This intermediate was found to be a monomer, which resembles the "molten globule" state in the CK folding pathway. To our knowledge, this is the first monomeric intermediate captured during refolding of CK. We propose that aggregation is caused by interaction between such monomeric intermediates. Binding of GroEL with this intermediate prevents formation of aggregates by decreasing the concentration of free monomeric intermediates, whereas binding of alpha(s)-casein with this intermediate induces more aggregation.
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Affiliation(s)
- Sen Li
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, PR China.
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34
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Pan JC, Yu Z, Su XY, Sun YQ, Rao XM, Zhou HM. Unassisted refolding of urea-denatured arginine kinase from shrimp Feneropenaeus chinensis: evidence for two equilibrium intermediates in the refolding pathway. Protein Sci 2005; 13:1892-901. [PMID: 15215531 PMCID: PMC2279925 DOI: 10.1110/ps.03464804] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The refolding process and the equilibrium intermediates of urea-denatured arginine kinase (AK) were investigated by 1-anilino-8-naphthalenesulfonate (ANS) intrinsic fluorescence, far-UV circular dichroism (CD), size-exclusion chromatography (SEC), and enzymatic activity. In dilute denaturant, two equilibrium refolding intermediates (I and N') were discovered, and a refolding scheme of urea-denatured AK was proposed. During the refolding of urea-denatured AK, the fluorescence intensity increased remarkably, accompanied by a significant blue shift of the emission maximum and a pronounced increase in molar ellipticity of CD at 222 nm. The first folding intermediate (I) was inactive in urea solution ranging between 2.4 and 3.0 M. The second (N') existed between a 0.4- and 0.8-M urea solution, with slightly increased activity. Neither the blue shift emission maximum nor the molar ellipticity of CD at 222 nm showed significant changes in these two regions. The two intermediates were characterized by monitoring the ANS binding ability in various residual urea solutions, and two peaks of the emission intensity were observed in urea solutions of 0.6 and 2.8 M, respectively. The SEC results indicated that a distribution coefficient (K(D)) platform existed in urea solutions ranging between 2.4 and 3.0 M urea, suggesting that there was a similarly apparent protein profile and size in the urea solution region. The refolding kinetics showed that the urea-denatured AK was in two-phase refolding. Proline isomerization occurred in the unfolding process of AK, which blocked the slow phase of refolding. These results suggested that the refolding process of urea-denatured AK contained at the least two equilibrium refolding intermediates.
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Affiliation(s)
- Ji-Cheng Pan
- Department of Biological Science and Biotechnology, School of Life Science and Engineering, Tsinghua University, Bejing, China
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35
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Mazon H, Marcillat O, Forest E, Vial C. Denaturant sensitive regions in creatine kinase identified by hydrogen/deuterium exchange. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:1461-8. [PMID: 15880663 DOI: 10.1002/rcm.1941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The GdmHCl-induced unfolding of creatine kinase (CK) has been studied by hydrogen/deuterium (H/D) exchange combined with mass spectrometry. MM-CK unfolded for various periods in different denaturant concentrations was pulsed-labeled with deuterium to identify different conformational intermediate states. For all denaturation times or GdmHCl concentrations, we observed variable proportions of only two species. The low-mass envelope of isotope peaks corresponds to a species that has gained about 10 deuteriums more than native CK, and the high-mass envelope to a completely deuterated species. To localize precisely the unfolded regions in the states highly populated during denaturation, the protein was digested with two proteases (pepsin and type XIII protease) after H/D exchange and rapid quenching of the reaction. The two sets of fragments obtained were analyzed by liquid chromatography coupled to mass spectrometry to determine the deuterium level in each fragment. Bimodal distributions of deuterium were found for most peptides, indicating that these regions were either folded or unfolded. This behavior is consistent with cooperative, localized unfolding. However, we observed a monomodal distribution of deuterium in two regions (1-12 and 162-186). We conclude that the increment of mass observed in the low-mass species of the intact protein (+10 Da) has its origin in these two segments. These regions, which are very sensitive to low GdmHCl concentrations, are involved in the monomer-monomer interface of CK and their perturbation is likely to weaken the dimeric structure. At higher denaturant concentration, this would induce dissociation of the dimer.
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Affiliation(s)
- Hortense Mazon
- UMR CNRS 5013, Biomembranes et enzymes associés, Université Claude Bernard Lyon I, 43, boulevard du 11 Novembre 1918, 69622 Villeurbanne cedex, France
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36
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Zhu L, Qin ZJ, Zhou JM, Kihara H. Unfolding kinetics of dimeric creatine kinase measured by stopped-flow small angle X-ray scattering. Biochimie 2004; 86:127-32. [PMID: 15016451 DOI: 10.1016/j.biochi.2003.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 12/15/2003] [Indexed: 11/26/2022]
Abstract
The unfolding kinetics of creatine kinase (CK) in various concentrations of urea or guanidine hydrochloride (GuHCl) was investigated by small angle X-ray scattering (SAXS) using synchrotron radiation, and compared with the results obtained by stopped-flow circular dichroism and stopped-flow fluorescence. Using the three methods, the unfolding kinetics of CK fits well to a single exponential function with similar apparent rate constants, and the amplitude of the monophasic kinetics covers the entire range of the equilibrium values. The results suggest that the unfolding time-course measured by integrated SAXS intensity corresponds to the intramolecular loss of globular structure. The refolding kinetics of 8 M urea-denatured CK was monitored in a stopped-flow apparatus by following the spectroscopic changes, and the final state of folding was investigated by SAXS. A substantial part of the ellipticity is recovered within a burst phase, indicating that the secondary structure forms at an early stage in refolding. The R(g) value of the final folded state was 33.6 A when the folding buffer contained 20% glycerol, which is characteristic of native-like compactness and globularity.
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Affiliation(s)
- Li Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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37
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Doyle SM, Bilsel O, Teschke CM. SecA folding kinetics: a large dimeric protein rapidly forms multiple native states. J Mol Biol 2004; 341:199-214. [PMID: 15312773 DOI: 10.1016/j.jmb.2004.06.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 06/01/2004] [Accepted: 06/01/2004] [Indexed: 11/25/2022]
Abstract
SecA, a 202 kDa dimeric protein, is the ATPase for the Sec-dependent translocase of precursor proteins in vivo. SecA must undergo conformational changes, which may involve dissociation into a monomer, as it translocates the precursor protein across the inner membrane. To better understand the dynamics of SecA in vivo, protein folding studies to probe the native, intermediate, and unfolded species of SecA in vitro have been done. SecA folds through a stable dimeric intermediate and dimerizes in the dead-time of a manual-mixing kinetic experiment ( approximately 5-7 seconds). Here, stopped-flow fluorescence and CD, as well as ultra-rapid continuous flow fluorescence techniques, were used to further probe the rapid folding kinetics of SecA. In the absence of urea, rapid, near diffusion-limited ( approximately 10(9)M(-1)s(-1)) SecA dimerization occurs following a rate-limiting unimolecular rearrangement of a rapidly formed intermediate. Multiple kinetic folding and unfolding phases were observed and SecA was shown to have multiple native and unfolded states. Using sequential-mixing stopped-flow experiments, SecA was determined to fold via parallel channels with sequential intermediates. These results confirm that SecA is a highly dynamic protein, consistent with the rapid, major conformational changes it must undergo in vivo.
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Affiliation(s)
- Shannon M Doyle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
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38
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Chatterjee M, Mandal DK. Kinetic analysis of subunit oligomerization of the legume lectin soybean agglutinin. Biochemistry 2003; 42:12217-22. [PMID: 14567683 DOI: 10.1021/bi034642l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reconstitution of soybean agglutinin (SBA), a tetrameric GalNAc/Gal-specific legume lectin, after denaturation in urea has been studied using fluorescence, far-UV CD, a hemagglutination assay, and chemical cross-linking with glutaraldehyde as a bifunctional reagent. The reconstituted protein exhibits similar quaternary structure and activity as of native lectin. The kinetics of subunit oligomerization has been determined from the cross-linking reaction of the reconstituting protein followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Monomers and tetramers could be quantitatively analyzed during reconstitution. Dimers are not detectable. The reassociation reaction follows second-order kinetics. The results are described by a kinetic mechanism in which the monomer-to-dimer association (characterized by a second-order rate constant (k(1)) of 1.4 x 10(4) M(-1) s(-1) at 37 degrees C) is involved in the rate-determining step of the oligomerization reaction.
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39
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Liang Y, Du F, Sanglier S, Zhou BR, Xia Y, Van Dorsselaer A, Maechling C, Kilhoffer MC, Haiech J. Unfolding of rabbit muscle creatine kinase induced by acid. A study using electrospray ionization mass spectrometry, isothermal titration calorimetry, and fluorescence spectroscopy. J Biol Chem 2003; 278:30098-105. [PMID: 12771138 DOI: 10.1074/jbc.m304050200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Electrospray ionization mass spectrometry, isothermal titration calorimetry (ITC), fluorescence spectroscopy, and glutaraldehyde cross-linking SDS-PAGE have been used to study the unfolding of rabbit muscle creatine kinase (MM-CK) induced by acid. The mass spectrometric experiments show that MM-CK is unfolded gradually when titrated with acid. MM-CK is a dimer (the native state) at pH 7.0 and becomes an equilibrium mixture of the dimer and a partially folded monomer (the intermediate) between pH 6.7 and 5.0. The dimeric protein becomes an equilibrium mixture of the intermediate and an unfolded monomer (the unfolded state) between pH 5.0 and 3.0 and is almost fully unfolded at pH 3.0 reached. The results from a "phase diagram" method of fluorescence show that the conformational transition between the native state and the intermediate of MM-CK occurs in the pH range of 7.0-5.2, and the transition between the intermediate and the unfolded state of the protein occurs between pH 5.2 and 3.0. The intrinsic molar enthalpy changes for formation of the unfolded state of MM-CK induced by acid at 15.0, 25.0, 30.0, and 37.0 degrees C have been determined by ITC. A large positive molar heat capacity change of the unfolding, 8.78 kcal mol-1 K-1, at all temperatures examined indicates that hydrophobic interaction is the dominant driving force stabilizing the native structure of MM-CK. Combining the results from these four methods, we conclude that the acid-induced unfolding of MM-CK follows a "three-state" model and that the intermediate state of the protein is a partially folded monomer.
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Affiliation(s)
- Yi Liang
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
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40
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Hahn HS, Park YD, Lee JR, Park KH, Kim TJ, Yang JM, Hahn MJ. Aggregation and folding of recombinant human creatine kinase. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:563-70. [PMID: 14703990 DOI: 10.1023/b:jopc.0000005506.98513.43] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The processes of aggregation and refolding of recombinant human creatine kinase (rHCK) were studied. Most of the rHCK expressed in E. coli was present in the insoluble traction and it could be solubilized in 6 M urea solution. Unfolding of rHCK in 6 M urea showed biphasic kinetic courses (kappa1 = 6.5 x 10(-3) s(-1); kappa2 = 0.54 x 10(-3) s(-1)) as observed by maximum fluorescence wavelength change. During refolding of the rHCK dissolved in urea, significant aggregation was noticed following first-order kinetics. Aggregation rate constants were influenced by the concentration of NaCl, which increased the difference in transition-free energy (deltadeltaG), showing that stabilization of folding intermediates by NaCl could efficiently reduce the formation of insoluble aggregates. Formations of aggregate were also reduced by adjusting temperature, pH, and concentration of rHCK. Refolding of rHCK under the optimized condition which prevented the aggregation also showed multi-kinetic phases (kappa1 = 3.0 x 10(-3) s(-1); kappa2 = 0.64 x 10(-3) s(-1)). Under optimized conditions applied in this study, rHCK could correctly refold retrieving the high specific enzymatic activity.
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Affiliation(s)
- Hwa-Sun Hahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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41
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Cheltsov AV, Guida WC, Ferreira GC. Circular permutation of 5-aminolevulinate synthase: effect on folding, conformational stability, and structure. J Biol Chem 2003; 278:27945-55. [PMID: 12736261 DOI: 10.1074/jbc.m207011200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The first and regulatory step of heme biosynthesis in mammals begins with the pyridoxal 5'-phosphate-dependent condensation reaction catalyzed by 5-aminolevulinate synthase. The enzyme functions as a homodimer with the two active sites at the dimer interface. Previous studies demonstrated that circular permutation of 5-aminolevulinate synthase does not prevent folding of the polypeptide chain into a structure amenable to binding of the pyridoxal 5'-phosphate cofactor and assembly of the two subunits into a functional enzyme. However, while maintaining a wild type-like three-dimensional structure, active, circularly permuted 5-aminolevulinate synthase variants possess different topologies. To assess whether the aminolevulinate synthase overall structure can be reached through alternative or multiple folding pathways, we investigated the guanidine hydrochloride-induced unfolding, conformational stability, and structure of active, circularly permuted variants in relation to those of the wild type enzyme using fluorescence, circular dichroism, activity, and size exclusion chromatography. Aminolevulinate synthase and circularly permuted variants folded reversibly; the equilibrium unfolding/refolding profiles were biphasic and, in all but one case, protein concentration-independent, indicating a unimolecular process with the presence of at least one stable intermediate. The formation of this intermediate was preceded by the disruption of the dimeric interface or dissociation of the dimer without significant change in the secondary structural content of the subunits. In contrast to the similar stabilities associated with the dimeric interface, the energy for the unfolding of the intermediate as well as the overall conformational stabilities varied among aminolevulinate synthase and variants. The unfolding of one functional permuted variant was protein concentration-dependent and had a potentially different folding mechanism. We propose that the order of the ALAS secondary structure elements does not determine the ability of the polypeptide chain to fold but does affect its folding mechanism.
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Affiliation(s)
- Anton V Cheltsov
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Florida, Tampa, Florida 33612, USA
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42
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Wójciak P, Mazurkiewicz A, Bakalova A, Kuciel R. Equilibrium unfolding of dimeric human prostatic acid phosphatase involves an inactive monomeric intermediate. Int J Biol Macromol 2003; 32:43-54. [PMID: 12719131 DOI: 10.1016/s0141-8130(03)00024-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Guanidine hydrochloride (GdnHCl)-induced unfolding of human prostatic acid phosphatase (hPAP), a homodimer of 50 kDa subunit molecular weight, was investigated with activity measurements, size exclusion HPLC, tryptophan fluorescence, 1-anilinonaphtalene-8-sulfonate (ANS) binding and reactivity with 2-(4'-maleimidoanilino)naphthalene-6-sulfonate (MIANS). Equilibrium analysis was performed to shed light on the role of dimerization in the folding and stability of the catalytically active oligomeric protein. Unfolding was reversible, as verified by activity measurements and tryptophan fluorescence. The noncoincidence of the unfolding curves obtained by different techniques suggests the occurrence of a multiphasic process. The reaction of hPAP inactivation is accompanied by dissociation of the dimer into two monomers. The midpoint of this transition is at 0.65 M GdnHCl with 4.24+/-0.12 kcalmol(-1) free energy change. Binding of ANS to the inactive phosphatase monomer, especially remarkable in the region from 0.8 to 1.25M GdnHCl, suggests that the hydrophobic probe indicates exposition of the intersubunit hydrophobic surface and a loosening of the monomer's tertiary structure. Strong fluorescence of thiol group derivatives, the products of their reaction with MIANS, appears in a limited range of GdnHCl concentrations (1.2-1.6M). This shows that in the relaxed structure of the intermediate, the reagent is allowed to penetrate into the hydrophobic environment of the partially hidden thiol groups. The equilibrium unfolding reaction of hPAP, as monitored by tryptophan fluorescence, does not depend on the protein concentration and displays a single transition curve with a midpoint at 1.7 M GdnHCl and value of DeltaG(unf)(H(2)O)=3.38+/-0.08 kcalmol(-1) per monomer, a result implying that this transition is related to the conformational change of the earlier dissociated and already inactive subunit of the protein.
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Affiliation(s)
- Paulina Wójciak
- Institute of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
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43
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Insight into structural transition, aggregation and folding of glycoprotein in the presence of chromium(III) complexes by spectroscopic, microscopic and kinetic studies. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(02)02049-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Luo JK, Hornby JAT, Wallace LA, Chen J, Armstrong RN, Dirr HW. Impact of domain interchange on conformational stability and equilibrium folding of chimeric class micro glutathione transferases. Protein Sci 2002; 11:2208-17. [PMID: 12192076 PMCID: PMC2373595 DOI: 10.1110/ps.0208002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Rat micro class glutathione transferases M1-1 and M2-2 are homodimers that share a 78% sequence identity but display differences in stability. M1-1 is more stable at the secondary and tertiary structural levels, whereas its quaternary structure is less stable. Each subunit in these proteins consists of two structurally distinct domains with intersubunit contacts occurring between domain 1 of one subunit and domain 2 of the other subunit. The chimeric subunit variants M(12), which has domain 1 of M1 and domain 2 of M2, and its complement M(21), were used to investigate the conformational stability of the chimeric homodimers M(12)-(12) and M(21)-(21) to determine the contribution of each domain toward stability. Exchanging entire domains between class micro GSTs is accommodated by the GST fold. Urea-induced equilibrium unfolding data indicate that whereas the class micro equilibrium unfolding mechanism (i.e., N(2) <--> 2I <--> 2U) is not altered, domain exchanges impact significantly on the conformational stability of the native dimers and monomeric folding intermediates. Data for the wild-type and chimeric proteins indicate that the order of stability for the native dimer (N(2)) is M2-2 > M(12)-(12) M1-1 approximately M(21)-(21), and that the order of stability of the monomeric intermediate (I) is M1 > M2 approximately M(12) > M(21). Interactions involving Arg 77, which is topologically conserved in GSTs, appear to play an important role in the stability of both the native dimeric and folding monomeric structures.
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Affiliation(s)
- Jiann-Kae Luo
- University Research Council Protein Structure-Function Research Programme, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
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45
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Kuznetsova IM, Stepanenko OV, Turoverov KK, Zhu L, Zhou JM, Fink AL, Uversky VN. Unraveling multistate unfolding of rabbit muscle creatine kinase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1596:138-55. [PMID: 11983429 DOI: 10.1016/s0167-4838(02)00212-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
GdmCl-induced unfolding of rabbit muscle creatine kinase, CK, has been studied by a variety of physico-chemical methods including near and far UV CD, SEC, intrinsic fluorescence (intensity, anisotropy and lifetime) as well as intensity and lifetime of bound ANS fluorescence. The formation of several stable unfolding intermediates, some of which were not observed previously, has been established. This was further confirmed by representation of fluorescence data in terms of "phase diagram", i.e. I(lambda1) versus I(lambda2) dependence, where I(lambda1) and I(lambda2) are fluorescence intensity values measured on wavelengths lambda(1) and lambda(2) under the different experimental conditions for a protein undergoing structural transformations. The unfolding behavior of CK was shown to be strongly affected by association of partially folded intermediates. A model of CK unfolding, which takes into account both structural perturbations and association of partially folded intermediates has been elaborated.
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Affiliation(s)
- Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
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46
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Perrett S, Zhou JM. Expanding the pressure technique: insights into protein folding from combined use of pressure and chemical denaturants. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:210-23. [PMID: 11983397 DOI: 10.1016/s0167-4838(01)00345-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The fundamental principles derived from in vitro protein folding experiments have practical application in understanding the pathology of diseases of protein misfolding and for the development of industrial processes to produce proteins as pharmaceuticals and biotechnological reagents. High pressure as a tool to denature or disaggregate proteins offers a number of unique advantages. The emphasis of this review is on how low concentrations of chemical denaturants can be used in combination with high pressure to extend the range and scope of this useful technique. This approach has already been used in a number of studies, which are discussed here in the context of the questions they address. These include: the origin of the volume change observed on protein unfolding, pressure-induced formation of partially structured intermediates, pressure-induced dissociation of oligomeric and aggregated proteins, and the use of volume changes to probe the structure of the transition state. Wider use of hydrostatic pressure as a denaturation tool, facilitated by combination with chemical denaturants, is likely to bring significant advances to our understanding of protein structure, stability and folding, particularly in relation to proteins associated with the amyloid and prion diseases.
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Affiliation(s)
- Sarah Perrett
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China
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47
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Zhou JM, Zhu L, Balny C, Perrett S. Pressure denaturation of the yeast prion protein Ure2. Biochem Biophys Res Commun 2001; 287:147-52. [PMID: 11549268 DOI: 10.1006/bbrc.2001.5556] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Denaturation of the Saccharomyces cerevisiae prion protein Ure2 was investigated using hydrostatic pressure. Pressures of up to 600 MPa caused only limited perturbation of the structure of the 40-kDa dimeric protein. However, nondenaturing concentrations of GdmCl in combination with high pressure resulted in complete unfolding of Ure2 as judged by intrinsic fluorescence. The free energy of unfolding measured by pressure denaturation or by GdmCl denaturation is the same, indicating that pressure does not induce dimer dissociation or population of intermediates in 2 M GdmCl. Pressure-induced changes in 5 M GdmCl suggest residual structure in the denatured state. Cold denaturation under pressure at 200 MPa showed that unfolding begins below -5 degrees C and Ure2 is more susceptible to cold denaturation at low ionic strength. Results obtained using two related protein constructs, which lack all or part of the N-terminal prion domain, were very similar.
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Affiliation(s)
- J M Zhou
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China 100101
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48
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Park YD, Ou WB, Yu TW, Zhou HM. Folding pathway for partially folded rabbit muscle creatine kinase. Biochem Cell Biol 2001. [DOI: 10.1139/o01-129] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Rabbit muscle creatine kinase (CK) was modified by 5,5'-dithio-bis(2-nitrobenzoic acid) accompanied by 3 M guanidine hydrochloride denaturation to produce a partially folded state with modified thiol groups. The partially folded CK was in a monomeric state detected by size exclusion chromatography, native-polyacrylamide gel electrophoresis, circular dichroism, and intrinsic fluorescence studies. After dithiothreitol (DTT) treatment, about 70% CK activity was regained with a two-phase kinetic course. Rate constants calculated for regaining of activity and refolding were compared with those for CK modified with various treatments to show that refolding and recovery of activity were synchronized. To further characterize the partially folded CK state and its folding pathway, the molecular chaperone GroEL was used to evaluate whether it can bind with partly folded CK during refolding, and 1-anilinonaphthalene-8-sulfonate was used to detect the hydrophobic surface of the monomeric state of CK. The monomeric state of CK did not bind with GroEL, although it had a larger area of hydrophobic surface relative to the native state. These results may provide different evidence for the structural requirement of GroEL recognition to the substrate protein compared with previously reported results that GroEL bound with substrate proteins mainly through hydrophobic surface. The present study provides data for a monomeric intermediate trapped by the modification of the SH groups during the refolding of CK. Schemes are given for explaining both the partial folding CK pathway and the refolding pathway.Key words: creatine kinase; partially folded state; reactivation; refolding; GroEL; intermediate.
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49
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Zhu L, Fan YX, Perrett S, Zhou JM. Relationship between kinetic and equilibrium folding intermediates of creatine kinase. Biochem Biophys Res Commun 2001; 285:857-62. [PMID: 11467829 DOI: 10.1006/bbrc.2001.5248] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Creatine kinase (CK) is a dimeric enzyme important in ATP regeneration in cells where energy demands are high. The folding of CK under equilibrium and transient conditions has been studied in detail and is found to be complex. At equilibrium in 0.8 M GuHCl, 90% of CK molecules are in the form of a partially structured, monomeric intermediate. We exploit this property to measure kinetics of refolding and unfolding to and from this equilibrium intermediate (EI), using far-UV circular dichroism and intrinsic fluorescence as structural probes. We are thus able to compare the properties of EI and the kinetic intermediate formed during the burst phase in refolding. Native CK and EI unfold with rate constants in seconds and milliseconds, respectively. As is observed for refolding of fully-denatured CK, refolding from EI to the native state shows a burst phase followed by two exponential phases. The burst phase refolding intermediate is inferred to have more structure and greater stability than the equilibrium intermediate. When refolding from the fully-denatured state in 0.8 M GuHCl, the equilibrium intermediate is formed within the dead-time of mixing in the stopped-flow apparatus. The equilibrium intermediate may thus represent a kinetic intermediate formed early during folding.
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Affiliation(s)
- L Zhu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
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50
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Meng F, Park Y, Zhou H. Role of proline, glycerol, and heparin as protein folding aids during refolding of rabbit muscle creatine kinase. Int J Biochem Cell Biol 2001; 33:701-9. [PMID: 11390278 DOI: 10.1016/s1357-2725(01)00048-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aggregation of 3 M guanidine hydrochloride denatured creatine kinase (ATP: creatine N-phosphotransferase, EC 2.7.3.2) occurs after dilution into the refolding solution. Proline, glycerol and heparin sodium act as folding aids which can effectively inhibit aggregation of creatine kinase during refolding. Proline at 1 M concentration, glycerol at 10% concentration and heparin at 25 mg/ml not only completely prevented creatine kinase aggregation but also enabled the creatine kinase to return to its native state as well as to recover most of its native activity. The reactivity after the aggregation was completely blocked by the presence of each folding aid reached 65-80% of the native activity. Results of turbidity, activity, intrinsic fluorescence and 1-anilinonaphthalene-8-sulfonate binding fluorescence measurements suggested that the effect of heparin differs from that of proline and glycerol in its artificial chaperone-like behavior. Heparin may bind with creatine kinase both in the native state and during the refolding course. The results showed that this heparin-creatine kinase complex favorably restored the creatine kinase reactivity.
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Affiliation(s)
- F Meng
- Department of Biological Science and Biotechnology, Tsinghua University, 100084, Beijing, PR China
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