1
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Khan S, Khan M, Lohani M, Ahmad S, Sherwani S, Bhagwath S, Khan MWA, Wahid M, Aqil F, Haque S. NADP/H binding nearly doubles the stability of a Mycobacterium drug target: an unfolding study. J Biomol Struct Dyn 2023; 41:8018-8025. [PMID: 36166625 DOI: 10.1080/07391102.2022.2127910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
Mycobacterium Aspartate beta semialdehyde dehydrogenase (ASADH) was studied using various spectroscopic techniques and size exclusion chromatography to examine the unfolding of free (apo) and NADP/H-bound (holo) forms of ASADH. Non-cooperative guanidinium chloride (GdnHCl)-induced unfolding of the apo ASADH was discovered, and no partially folded intermediate structures were stabilized. On the other hand, it was observed that GdnHCl's unfolding of holoenzyme was a cooperative process without any stable intermediate structure. The native form of holoenzyme is found to be stable against the lower concentration of GdnHCl only (namely up to 1.25 M GdnHCl). The tryptophan environment appears to unfold cooperatively in case of the holoenzyme and is in well coordination with the overall unfolding of the holoenzyme. The presence of NADP/H shows a stabilizing effect on the tryptophan environment as well as on the native NADP/H-bound enzyme. Δ G Solvent o values reveal nearly two-fold (∼1.9) conformationally more stable folded holoenzyme compared to its native apo state. The Cm for the apo and holo forms of ASADH are 1.3 and 1.9 M, respectively. Novel drug leads targeting the NADP/H binding domain of ASADH could offer promising drugs against extremely infective Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Mahvish Khan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saheem Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Subuhi Sherwani
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Sundeep Bhagwath
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Mohd Wajid A Khan
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Farrukh Aqil
- Department of Medicine and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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Varejão N, Reverter D. Using Intrinsic Fluorescence to Measure Protein Stability Upon Thermal and Chemical Denaturation. Methods Mol Biol 2023; 2581:229-241. [PMID: 36413321 DOI: 10.1007/978-1-0716-2784-6_16] [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] [Indexed: 06/16/2023]
Abstract
Understanding how point mutations affect the performance of protein stability has been the focus of several studies all over the years. Intrinsic fluorescence is commonly used to follow protein unfolding since during denaturation, progressive redshifts on tryptophan fluorescence emission are observed. Since the unfolding process (achieved by chemical or physical denaturants) can be considered as two-state N➔D, it is possible to utilize the midpoint unfolding curves (fU = 50%) as a parameter to evaluate if the mutation destabilizes wild-type protein. The idea is to determine the [D]1/2 or Tm values from both wild type and mutant and calculate the difference between them. Positive values indicate the mutant is less stable than wild type.
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Affiliation(s)
- Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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3
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Zhao X, Li G, Feng X, Cheng Q, Lu Z, Gu R, Lu J, Liu W. Physicochemical characterization and linear epitopes identification of arginine kinase allergen from Crassostrea gigas. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3435-3445. [PMID: 34837649 DOI: 10.1002/jsfa.11691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/10/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Molluscan shellfish, including oysters, often cause allergic reactions in sensitive people throughout the world. It has been demonstrated that arginine kinase (AK) is one of the major allergens of oyster. The present study aimed to evaluate the immunoreactivity and structure of oyster AK as affected by heat treatment, pH change, and in vitro digestion. What is more, the immunoglobulin E-binding epitopes of this allergen were also predicted and validated. RESULTS Thermal and pH assays revealed that AK was unstable at temperature >40 °C or pH ≤5.0 by sodium dodecyl sulfate polyacrylamide gel electrophoresis and circular dichroism, and the digestibility assays suggested that AK was more easily digested by pepsin than by trypsin and chymotrypsin. The potential epitopes were predicted through immunoinformatics tools, and seven linear epitopes were identified by indirect competition enzyme-linked immunosorbent assay with pooled sera and individual serum from oyster-allergic patients. The critical amino acids in each epitope were also confirmed using mutant peptides. These linear epitopes and critical amino acids were apt to distribute on the outer surface of homology-based AK model. Moreover, the three denaturants (sodium dodecyl sulfate, β-mercaptoethanol, and urea) can destroy the spatial structure of AK and increase or reduce its allergenicity by denaturation treatments. CONCLUSION Processing conditions lay the foundation for the variation of allergenicity. Seven linear epitopes and their critical amino acids were identified by indirect competitive enzyme-linked immunosorbent assay. These findings will be helpful in allergy diagnosis and development of hypoallergenic products in the near future. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Xiaohan Zhao
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Guoming Li
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Xiaowen Feng
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Qingli Cheng
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Zhihao Lu
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Ruizeng Gu
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Jun Lu
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
| | - Wenying Liu
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing, PR China
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4
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Sil P, Paul SS, Silvio ED, Travaglini-Allocatelli C, Chattopadhyay K. Studies of cytochrome c-551 unfolding using fluorescence correlation spectroscopy and other biophysical techniques. Phys Chem Chem Phys 2016; 18:24537-48. [DOI: 10.1039/c6cp04819f] [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
Fluorescence correlation spectroscopy studies with a bacterial cytochrome c labeled at different positions complement NMR hydrogen exchange results.
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Affiliation(s)
- Pallabi Sil
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Simanta Sarani Paul
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Eva Di Silvio
- Department of Biochemical Sciences
- University of Rome “La Sapienza”
- Rome
- Italy
| | | | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
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5
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Yang Y, Cao MJ, Alcocer M, Liu QM, Fei DX, Mao HY, Liu GM. Mapping and characterization of antigenic epitopes of arginine kinase of Scylla paramamosain. Mol Immunol 2015; 65:310-20. [DOI: 10.1016/j.molimm.2015.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 01/30/2023]
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6
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Stabilization Mechanism of Cytochromec552from a Moderately Thermophilic Bacterium,Hydrogenophilus thermoluteolus. Biosci Biotechnol Biochem 2014; 72:2103-9. [DOI: 10.1271/bbb.80187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Georgescauld F, Moynié L, Habersetzer J, Cervoni L, Mocan I, Borza T, Harris P, Dautant A, Lascu I. Intersubunit ionic interactions stabilize the nucleoside diphosphate kinase of Mycobacterium tuberculosis. PLoS One 2013; 8:e57867. [PMID: 23526954 PMCID: PMC3589492 DOI: 10.1371/journal.pone.0057867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/27/2013] [Indexed: 01/10/2023] Open
Abstract
Most nucleoside diphosphate kinases (NDPKs) are hexamers. The C-terminal tail interacting with the neighboring subunits is crucial for hexamer stability. In the NDPK from Mycobacterium tuberculosis (Mt) this tail is missing. The quaternary structure of Mt-NDPK is essential for full enzymatic activity and for protein stability to thermal and chemical denaturation. We identified the intersubunit salt bridge Arg80-Asp93 as essential for hexamer stability, compensating for the decreased intersubunit contact area. Breaking the salt bridge by the mutation D93N dramatically decreased protein thermal stability. The mutation also decreased stability to denaturation by urea and guanidinium. The D93N mutant was still hexameric and retained full activity. When exposed to low concentrations of urea it dissociated into folded monomers followed by unfolding while dissociation and unfolding of the wild type simultaneously occur at higher urea concentrations. The dissociation step was not observed in guanidine hydrochloride, suggesting that low concentration of salt may stabilize the hexamer. Indeed, guanidinium and many other salts stabilized the hexamer with a half maximum effect of about 0.1 M, increasing protein thermostability. The crystal structure of the D93N mutant has been solved.
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Affiliation(s)
- Florian Georgescauld
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Lucile Moynié
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Johann Habersetzer
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Laura Cervoni
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi “La Sapienza”, Roma, Italy
| | - Iulia Mocan
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
| | - Tudor Borza
- Laboratoire de Chimie Structurale des Macromolécules, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Pernile Harris
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alain Dautant
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
- * E-mail: (AD); (IL)
| | - Ioan Lascu
- IBGC, University Bordeaux, Bordeaux, France
- IBGC, CNRS UMR 5095, Bordeaux, France
- * E-mail: (AD); (IL)
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8
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Travaglini-Allocatelli C. Protein Machineries Involved in the Attachment of Heme to Cytochrome c: Protein Structures and Molecular Mechanisms. SCIENTIFICA 2013; 2013:505714. [PMID: 24455431 PMCID: PMC3884852 DOI: 10.1155/2013/505714] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/24/2013] [Indexed: 05/09/2023]
Abstract
Cytochromes c (Cyt c) are ubiquitous heme-containing proteins, mainly involved in electron transfer processes, whose structure and functions have been and still are intensely studied. Surprisingly, our understanding of the molecular mechanism whereby the heme group is covalently attached to the apoprotein (apoCyt) in the cell is still largely unknown. This posttranslational process, known as Cyt c biogenesis or Cyt c maturation, ensures the stereospecific formation of the thioether bonds between the heme vinyl groups and the cysteine thiols of the apoCyt heme binding motif. To accomplish this task, prokaryotic and eukaryotic cells have evolved distinctive protein machineries composed of different proteins. In this review, the structural and functional properties of the main maturation apparatuses found in gram-negative and gram-positive bacteria and in the mitochondria of eukaryotic cells will be presented, dissecting the Cyt c maturation process into three functional steps: (i) heme translocation and delivery, (ii) apoCyt thioreductive pathway, and (iii) apoCyt chaperoning and heme ligation. Moreover, current hypotheses and open questions about the molecular mechanisms of each of the three steps will be discussed, with special attention to System I, the maturation apparatus found in gram-negative bacteria.
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Affiliation(s)
- Carlo Travaglini-Allocatelli
- Department of Biochemical Sciences, University of Rome “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
- *Carlo Travaglini-Allocatelli:
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9
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Kannan K, Jasra RV. Designing of nitrile hydratase from alkaline protease using quanidine hydrochloride and cobalt metal ion. Catal Today 2012. [DOI: 10.1016/j.cattod.2012.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Molecular characterization of a novel trehalose-6-phosphate hydrolase, TreA, from Bacillus licheniformis. Int J Biol Macromol 2012; 50:459-70. [DOI: 10.1016/j.ijbiomac.2012.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/06/2012] [Accepted: 01/10/2012] [Indexed: 11/20/2022]
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11
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Kim S, Chung JK, Kwak K, Bowman SEJ, Bren KL, Bagchi B, Fayer MD. Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy. J Phys Chem B 2008; 112:10054-63. [PMID: 18646797 PMCID: PMC2671645 DOI: 10.1021/jp802246h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unfolded vs native CO-coordinated horse heart cytochrome c (h-cyt c) and a heme axial methionine mutant cyt c552 from Hydrogenobacter thermophilus ( Ht-M61A) are studied by IR absorption spectroscopy and ultrafast 2D-IR vibrational echo spectroscopy of the CO stretching mode. The unfolding is induced by guanidinium hydrochloride (GuHCl). The CO IR absorption spectra for both h-cyt c and Ht-M61A shift to the red as the GuHCl concentration is increased through the concentration region over which unfolding occurs. The spectra for the unfolded state are substantially broader than the spectra for the native proteins. A plot of the CO peak position vs GuHCl concentration produces a sigmoidal curve that overlays the concentration-dependent circular dichroism (CD) data of the CO-coordinated forms of both Ht-M61A and h-cyt c within experimental error. The coincidence of the CO peak shift curve with the CD curves demonstrates that the CO vibrational frequency is sensitive to the structural changes induced by the denaturant. 2D-IR vibrational echo experiments are performed on native Ht-M61A and on the protein in low- and high-concentration GuHCl solutions. The 2D-IR vibrational echo is sensitive to the global protein structural dynamics on time scales from subpicosecond to greater than 100 ps through the change in the shape of the 2D spectrum with time (spectral diffusion). At the high GuHCl concentration (5.1 M), at which Ht-M61A is essentially fully denatured as judged by CD, a very large reduction in dynamics is observed compared to the native protein within the approximately 100 ps time window of the experiment. The results suggest the denatured protein may be in a glassy-like state involving hydrophobic collapse around the heme.
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Affiliation(s)
- Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Kyungwon Kwak
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Biman Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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12
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Bhambhani A, Chah S, Hvastkovs EG, Jensen GC, Rusling JF, Zare RN, Kumar CV. Folding control and unfolding free energy of yeast iso-1-cytochrome c bound to layered zirconium phosphate materials monitored by surface plasmon resonance. J Phys Chem B 2008; 112:9201-8. [PMID: 18598069 DOI: 10.1021/jp7121642] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The free energy change (Delta G degrees ) for the unfolding of immobilized yeast iso-1-cytochrome c (Cyt c) at nanoassemblies was measured by surface plasmon resonance (SPR) spectroscopy. Data show that SPR is sensitive to protein conformational changes, and protein solid interface exerts a major influence on bound protein stability. First, Cyt c was self-assembled on the Au film via the single thiol of Cys-102. Then, crystalline sheets of layered alpha-Zr(O(3)POH)(2).H(2)O (alpha-ZrP) or Zr(O(3)PCH(2)CH(2)COOH)(2).xH(2)O (alpha-ZrCEP) were adsorbed to construct alpha-ZrP/Cyt c/Au or alpha-ZrCEP/Cyt c/Au nanoassemblies. The construction of each layer was monitored by SPR, in real time, and the assemblies were further characterized by atomic force microscopy and electrochemical studies. Thermodynamic stability of the protein nanoassembly was assessed by urea-induced unfolding. Surprisingly, unfolding is reversible in all cases studied here. Stability of Cyt c in alpha-ZrP/Cyt c/Au increased by approximately 4.3 kJ/mol when compared to the unfolding free energy of Cyt c/Au assembly. In contrast, the protein stability decreased by approximately 1.5 kJ/mol for alpha-ZrCEP/Cyt c/Au layer. Thus, OH-decorated surfaces stabilized the protein whereas COOH-decorated surfaces destabilized it. These data quantitate the role of specific functional groups of the inorganic layers in controlling bound protein stability.
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Affiliation(s)
- Akhilesh Bhambhani
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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13
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Michel LV, Bren KL. Submolecular unfolding units of Pseudomonas aeruginosa cytochrome c-551. J Biol Inorg Chem 2008; 13:837-45. [PMID: 18392863 DOI: 10.1007/s00775-008-0370-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 03/20/2008] [Indexed: 11/26/2022]
Abstract
Hydrogen exchange rates for backbone amide protons of oxidized Pseudomonas aeruginosa cytochrome c-551 (P. aeruginosa cytochrome c) have been measured in the presence of low concentrations of the denaturant guanidine hydrochloride. Analysis of the data has allowed identification of submolecular unfolding units known as foldons. The highest-energy foldon bears similarity to the proposed folding intermediate for P. aeruginosa cytochrome c. Parallels are seen to the foldons of the structurally homologous horse cytochrome c, although the heme axial methionine-bearing loop has greater local stability in P. aeruginosa cytochrome c, in accord with previous folding studies. Regions of low local stability are observed to correspond with regions that interact with redox partners, providing a link between foldon properties and function.
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Affiliation(s)
- Lea V Michel
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, 14642, USA
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14
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Garcia-Mira MM, Schmid FX. Key Role of Coulombic Interactions for the Folding Transition State of the Cold Shock Protein. J Mol Biol 2006; 364:458-68. [PMID: 17020767 DOI: 10.1016/j.jmb.2006.08.071] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 08/17/2006] [Accepted: 08/24/2006] [Indexed: 11/16/2022]
Abstract
The cold shock protein CspB shows a five-stranded beta-sheet structure, and it folds rapidly via a native-like transition state. A previous Phi value analysis showed that most of the residues with Phi values close to one reside in strand beta1, and two of them, Lys5 and Lys7 are partially exposed charged residues. To elucidate how coulombic interactions of these two residues contribute to the energetic organisation of the folding transition state we performed comparative folding experiments in the presence of an ionic denaturant (guanidinium chloride) and a non-ionic denaturant (urea) and a double-mutant analysis. Lys5 contributes 6.6 kJ mol(-1) to the stability of the transition state, and half of it originates from screenable coulombic interactions. Lys7 contributes 5.3 kJ mol(-1), and 3.4 kJ mol(-1) of it are screened by salt. In the folded protein Lys7 interacts with Asp25, and the screenable coulombic interaction between these two residues is fully formed in the transition state. This suggests that long-range coulombic interactions such as those originating from Lys5 and Lys7 of CspB can be important for organizing and stabilizing native-like structure early in protein folding.
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Affiliation(s)
- Maria M Garcia-Mira
- Laboratorium für Biochemie und Bayreuther Zentrum fürMolekulare Biowissenschaften, Universität Bayreuth, D-95440, Bayreuth, Germany.
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15
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Bonamore A, Ilari A, Giangiacomo L, Bellelli A, Morea V, Boffi A. A novel thermostable hemoglobin from the actinobacterium Thermobifida fusca. FEBS J 2005; 272:4189-201. [PMID: 16098200 DOI: 10.1111/j.1742-4658.2005.04831.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gene coding for a hemoglobin-like protein (Tf-trHb) has been identified in the thermophilic actinobacterium Thermobifida fusca and cloned in Escherichia coli for overexpression. The crystal structure of the ferric, acetate-bound derivative, was obtained at 2.48 A resolution. The three-dimensional structure of Tf-trHb is similar to structures reported for the truncated hemoglobins from Mycobacterium tuberculosis and Bacillus subtilis in its central domain. The complete lack of diffraction patterns relative to the N- and C-terminal segments indicates that these are unstructured polypeptides chains, consistent with their facile cleavage in solution. The absence of internal cavities and the presence of two water molecules between the bound acetate ion and the protein surface suggest that the mode of ligand entry is similar to that of typical hemoglobins. The protein is characterized by higher thermostability than the similar mesophilic truncated hemoglobin from B. subtilis, as demonstrated by far-UV CD melting experiments on the cyano-met derivatives. The ligand-binding properties of Tf-trHb, analyzed in stopped flow experiments, demonstrate that Tf-trHb is capable of efficient O2 binding and release between 55 and 60 degrees C, the optimal growth temperature for Thermobifida fusca.
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16
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Chah S, Kumar CV, Hammond MR, Zare RN. Denaturation and renaturation of self-assembled yeast iso-1-cytochrome c on Au. Anal Chem 2005; 76:2112-7. [PMID: 15053677 DOI: 10.1021/ac035416k] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We have made surface plasmon resonance (SPR) measurements of yeast iso-1-cytochrome c (Cyt c) on a gold surface. Angle-resolved SPR curves are recorded as a function of urea concentration before and after self-assembly of the Cyt c. Exposure to a urea solution causes denaturation of Cyt c, which shifts the minimum in the SPR curve to a larger angle and decreases the signal amplitude. The Gibbs free energy change for denaturation of the protein on Au is calculated from the change of the SPR signal amplitude with urea concentration. We find that (1) Cyt c can be reversibly denatured and renatured, depending on the urea concentration, and (2) the Gibbs free energy change for denaturation of Cyt c on Au surface in water, DeltaG degrees (water), is 1.5 kcal/mol, which is approximately 4 times less than that in bulk solution.
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Affiliation(s)
- Soonwoo Chah
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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17
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Brunori M, Bigotti MG, Cutruzzolà F, Gianni S, Travaglini-Allocatelli C. Cytochrome c(551) as a model system for protein folding. Biophys Chem 2003; 100:409-19. [PMID: 12646380 DOI: 10.1016/s0301-4622(02)00295-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable progress was made over the last few years in understanding the mechanism of folding of cytochrome c(551), a small acidic hemeprotein from Pseudomonas aeruginosa. Comparison of our results with those obtained by others on horse heart cytochrome c allows to draw some general conclusions on the structural features that are common determinants in the folding of members of the cytochrome c family.
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Affiliation(s)
- Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Università di Roma La Sapienza, P. le A. Moro 5, 00185 Roma, Italy.
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18
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Srimathi T, Kumar TKS, Kathir KM, Chi YH, Srisailam S, Lin WY, Chiu IM, Yu C. Structurally homologous all beta-barrel proteins adopt different mechanisms of folding. Biophys J 2003; 85:459-72. [PMID: 12829501 PMCID: PMC1303102 DOI: 10.1016/s0006-3495(03)74491-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2002] [Accepted: 01/15/2003] [Indexed: 11/15/2022] Open
Abstract
Acidic fibroblast growth factors from human (hFGF-1) and newt (nFGF-1) (Notopthalamus viridescens) are 16-kDa, all beta-sheet proteins with nearly identical three-dimensional structures. Guanidine hydrochloride (GdnHCl)-induced unfolding of hFGF-1 and nFGF-1 monitored by fluorescence and far-UV circular dichroism (CD) shows that the FGF-1 isoforms differ significantly in their thermodynamic stabilities. GdnHCl-induced unfolding of nFGF-1 follows a two-state (Native state to Denatured state(s)) mechanism without detectable intermediate(s). By contrast, unfolding of hFGF-1 monitored by fluorescence, far-UV circular dichroism, size-exclusion chromatography, and NMR spectroscopy shows that the unfolding process is noncooperative and proceeds with the accumulation of stable intermediate(s) at 0.96 M GdnHCl. The intermediate (in hFGF-1) populated maximally at 0.96 M GdnHCl has molten globule-like properties and shows strong binding affinity to the hydrophobic dye, 1-Anilino-8-naphthalene sulfonate (ANS). Refolding kinetics of hFGF-1 and nFGF-1 monitored by stopped-flow fluorescence reveal that hFGF-1 and nFGF-1 adopts different folding mechanisms. The observed differences in the folding/unfolding mechanisms of nFGF-1 and hFGF-1 are proposed to be either due to differential stabilizing effects of the charged denaturant (Gdn(+) Cl(-)) on the intermediate state(s) and/or due to differences in the structural interactions stabilizing the native conformation(s) of the FGF-1 isoforms.
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Schwehm JM, Fitch CA, Dang BN, García-Moreno E B, Stites WE. Changes in stability upon charge reversal and neutralization substitution in staphylococcal nuclease are dominated by favorable electrostatic effects. Biochemistry 2003; 42:1118-28. [PMID: 12549934 DOI: 10.1021/bi0266434] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single site mutations that reverse or neutralize a surface charge were made at 22 ionizable residues in staphylococcal nuclease. Unfolding free energies were obtained by guanidine hydrochloride denaturation. These data, in conjunction with previously obtained stabilities of the corresponding alanine mutants, unequivocally show that the dominant contribution to stability for virtually all of the wild-type side chains examined is the electrostatic effect associated with each residue's charged group. With only a few exceptions, these charges stabilize the native state, with an average loss of 0.5 kcal/mol of stability upon neutralization of a charge. When the charge is reversed, the average destabilization is doubled. Structure-based calculations of electrostatic free energy with the continuum method based on the finite difference solution to the linearized Poisson-Boltzmann equation reproduce the observed energetics when the polarizability in the protein interior is represented with a dielectric constant of 20. However, in some cases, large differences are found, giving insight into possible areas for improvement of the calculations. In particular, it appears that the assumptions made in the calculations about the absence of electrostatic interactions in the denatured state and the energetic consequences of dynamic fluctuations in the native state will have to be further explored.
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Affiliation(s)
- Jeffery M Schwehm
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701-1201, USA
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Del Vecchio P, Graziano G, Granata V, Barone G, Mandrich L, Rossi M, Manco G. Denaturing action of urea and guanidine hydrochloride towards two thermophilic esterases. Biochem J 2002; 367:857-63. [PMID: 12160466 PMCID: PMC1222942 DOI: 10.1042/bj20020695] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2002] [Revised: 07/25/2002] [Accepted: 08/02/2002] [Indexed: 11/17/2022]
Abstract
The stability of two thermophilic esterases, AFEST from Archaeoglobus fulgidus and EST2 from Alicyclobacillus acidocaldarius, against the denaturing action of urea and guanidine hydrochloride has been investigated by means of steady-state fluorescence and circular dichroism measurements. Experimental results indicate that the two enzymes, even though very resistant to temperature and urea, show a resistance to guanidine hydrochloride weaker than expected on the basis of data collected so far for a large set of globular proteins. Structural information available for AFEST and EST2 and ideas that emerged from studies on the molecular origin of the greater thermal stability of thermophiles allow the suggestion of a reliable rationale. The present results may be an indication that the optimization of charge-charge interactions on the protein surface is a key factor for the stability of the two esterases.
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Affiliation(s)
- Pompea Del Vecchio
- Department of Chemistry, University of Naples Federico II, Via Cintia, 45-80126 Naples, Italy.
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