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Alaei L, Moosavi-Movahedi AA. Stability of multi-subunit proteins and conformational lock. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 150:145-152. [DOI: 10.1016/j.pbiomolbio.2019.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022]
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Xiao BL, Ning YN, Niu NN, Li D, Moosavi-Movahedi AA, Sheibani N, Hong J. Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase. Sci Rep 2019; 9:4353. [PMID: 30867507 PMCID: PMC6416402 DOI: 10.1038/s41598-019-40892-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/25/2019] [Indexed: 01/01/2023] Open
Abstract
The conformational lock was a bio-thermodynamic theory to explain the characteristics of interfaces in oligomeric enzymes and their effects on catalytic activity. The previous studies on superoxide dismutases (Cu, Zn-SODs) showed that the dimeric structure contributed to the high catalytic efficiency and the stability. In this study, steered molecular dynamics simulations were used firstly to study the main interactions between two subunits of Cu, Zn-SODs. The decomposition process study showed that there were not only four pairs of hydrogen bonds but also twenty-five residue pairs participating hydrophobic interactions between A and B chains of SOD, and van der Waals interactions occupied a dominant position among these residue pairs. Moreover, the residue pairs of hydrogen bonds played a major role in maintaining the protein conformation. The analysis of the energy and conformational changes in the SMD simulation showed that there were two groups (two conformational locks) between A and B chains of SOD. The first group consisted of one hydrogen-bond residues pair and seven hydrophobic interactions residues pairs with a total average energy of −30.10 KJ/mol, and the second group of three hydrogen-bond residues pair and eighteen hydrophobic interactions residues pairs formed with a total average energy of −115.23 KJ/mol.
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Affiliation(s)
- Bao-Lin Xiao
- School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China
| | - Yan-Na Ning
- School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China
| | - Nan-Nan Niu
- School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China
| | - Di Li
- School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China
| | - Ali Akbar Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Enquelab Avenue, P.O. Box 13145-1384, Tehran, Iran
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences and Biomedical Engineering, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Jun Hong
- School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China. .,Henan Engineering Laboratory for Mammary Bioreactor, School of Life Sciences, Henan University JinMing Road, Kaifeng, 475000, China.
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Amani M, Moosavi-Movahedi AA, Kurganov BI. What can we get from varying scan rate in protein differential scanning calorimetry? Int J Biol Macromol 2017; 99:151-159. [DOI: 10.1016/j.ijbiomac.2017.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/25/2022]
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Amani M, Barzegar A, Mazani M. Osmolytic Effect of Sucrose on Thermal Denaturation of Pea Seedling Copper Amine Oxidase. Protein J 2017; 36:147-153. [PMID: 28315108 DOI: 10.1007/s10930-017-9706-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Protein stability is a subject of interest by many researchers. One of the common methods to increase the protein stability is using the osmolytes. Many studies and theories analyzed and explained osmolytic effect by equilibrium thermodynamic while most proteins undergo an irreversible denaturation. In current study we investigated the effect of sucrose as an osmolyte on the thermal denaturation of pea seedlings amine oxidase by the enzyme activity, fluorescence spectroscopy, circular dichroism, and differential scanning calorimetry. All experiments are in agreement that pea seedlings amine oxidase denaturation is controlled kinetically and its kinetic stability is increased in presence of sucrose. Differential scanning calorimetry experiments at different scanning rates showed that pea seedlings amine oxidase unfolding obeys two-state irreversible model. Fitting the differential scanning calorimetry data to two-state irreversible model showed that unfolding enthalpy and T *, temperature at which rate constant equals unit per minute, are increased while activation energy is not affected by increase in sucrose concentration. We concluded that osmolytes decrease the molecular oscillation of irreversible proteins which leads to decline in unfolding rate constant.
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Affiliation(s)
- Mojtaba Amani
- Department of Biochemistry, Faculty of Medicine, Ardabil University of Medical Sciences (ArUMS), Daneshgah Street, Ardabil, 5618985991, Iran.
| | - Aboozar Barzegar
- Department of Biochemistry, Faculty of Medicine, Ardabil University of Medical Sciences (ArUMS), Daneshgah Street, Ardabil, 5618985991, Iran
| | - Mohammad Mazani
- Department of Biochemistry, Faculty of Medicine, Ardabil University of Medical Sciences (ArUMS), Daneshgah Street, Ardabil, 5618985991, Iran
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Chebotareva NA, Roman SG, Kurganov BI. Dissociative mechanism for irreversible thermal denaturation of oligomeric proteins. Biophys Rev 2016; 8:397-407. [PMID: 28510015 PMCID: PMC5418479 DOI: 10.1007/s12551-016-0220-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/13/2016] [Indexed: 01/09/2023] Open
Abstract
Protein stability is a fundamental characteristic essential for understanding conformational transformations of the proteins in the cell. When using protein preparations in biotechnology and biomedicine, the problem of protein stability is of great importance. The kinetics of denaturation of oligomeric proteins may have characteristic properties determined by the quaternary structure. The kinetic schemes of denaturation can include the multiple stages of conformational transitions in the protein oligomer and stages of reversible dissociation of the oligomer. In this case, the shape of the kinetic curve of denaturation or the shape of the melting curve registered by differential scanning calorimetry can vary with varying the protein concentration. The experimental data illustrating dissociative mechanism for irreversible thermal denaturation of oligomeric proteins have been summarized in the present review. The use of test systems based on thermal aggregation of oligomeric proteins for screening of agents possessing anti-aggregation activity is discussed.
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Affiliation(s)
- Natalia A Chebotareva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia.
| | - Svetlana G Roman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia
| | - Boris I Kurganov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia
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Moosavi-Movahedi F, Saboury AA, Alijanvand HH, Bohlooli M, Salami M, Moosavi-Movahedi AA. Thermal inactivation and conformational lock studies on horse liver alcohol dehydrogenase: Structural mechanism. Int J Biol Macromol 2013; 58:66-72. [DOI: 10.1016/j.ijbiomac.2013.03.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/10/2013] [Accepted: 03/12/2013] [Indexed: 10/27/2022]
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Sattari Z, Pourfaizi H, Dehghan G, Amani M, Moosavi-Movahedi AA. Thermal inactivation and conformational lock studies on glucose oxidase. Struct Chem 2012. [DOI: 10.1007/s11224-012-0136-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Eronina TB, Chebotareva NA, Kleymenov SY, Roman SG, Makeeva VF, Kurganov BI. Effect of 2-hydroxypropyl-β-cyclodextrin on thermal stability and aggregation of glycogen phosphorylase b from rabbit skeletal muscle. Biopolymers 2010; 93:986-93. [PMID: 20540152 DOI: 10.1002/bip.21508] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The study of the kinetics of thermal aggregation of glycogen phosphorylase b (Phb) from rabbit skeletal muscles by dynamic light scattering at 48°C showed that 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) accelerated the aggregation process and induced the formation of the larger protein aggregates. The reason of the accelerating effect of HP-β-CD is destabilization of the protein molecule under action of HP-β-CD. This conclusion was supported by the data on differential scanning calorimetry and the kinetic data on thermal inactivation of Phb. It is assumed that destabilization of the Phb molecule is due to preferential binding of HP-β-CD to intermediates of protein unfolding in comparison with the original native state. The conclusion regarding the ability of the native Phb for binding of HP-β-CD was substantiated by the data on the enzyme inhibition by HP-β-CD. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 986-993, 2010.
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Affiliation(s)
- Tatyana B Eronina
- Department of Structural Biochemistry of Proteins, A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071, Russia.
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New Model for Polymerization of Oligomeric Alcohol Dehydrogenases into Nanoaggregates. Appl Biochem Biotechnol 2009; 160:1188-205. [DOI: 10.1007/s12010-009-8646-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 04/12/2009] [Indexed: 10/20/2022]
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Electroactive centers in Euphorbia latex and lentil seedling amine oxidases. Biosci Biotechnol Biochem 2008; 72:29-36. [PMID: 18175931 DOI: 10.1271/bbb.70299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The electrochemical behavior of redox centers in the active site of amine oxidases from lentil seedlings and Euphorbia characias latex was investigated using a mercury film electrode. Tyrosine-derived 6-hydroxydopa quinone (TPQ) and copper ions in the active site are redox centers of these amine oxidases. The enzymes undergo two reduction processes at negative potentials related to the reduction of the TPQ cofactor to the corresponding hydroquinones and the reduction of copper ions, (Cu(II)-->Cu(I)). Copper depleted enzymes, prepared by reduction with dithionite followed by dialysis against cyanide, undergo only one reduction process. Nyquist diagrams, recorded at potentials corresponding to the reduction of cofactors as dc-offset, represent charge transfer impedance followed by a Warburg-type line at low frequencies, indicating the occurrence of a diffusion controlled process in the rate-limiting step of the reduction process.
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Amani M, Moosavi-Movahedi AA, Floris G, Mura A, Kurganov BI, Ahmad F, Saboury AA. Two-state irreversible thermal denaturation of Euphorbia characias latex amine oxidase. Biophys Chem 2007; 125:254-9. [PMID: 16971037 DOI: 10.1016/j.bpc.2006.08.006] [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] [Received: 05/11/2006] [Revised: 08/07/2006] [Accepted: 08/17/2006] [Indexed: 11/26/2022]
Abstract
Thermal denaturation of Euphorbia latex amine oxidase (ELAO) has been studied by enzymatic activity, circular dichroism and differential scanning calorimetry. Thermal denaturation of ELAO is shown to be an irreversible process. Checking the validity of two-state it really describes satisfactorily the thermal denaturation of ELAO. Based on this model we obtain the activation energy, parameter T(*) (the absolute temperature at which the rate constant of denaturation is equal to 1 min(-1)), and total enthalpy of ELAO denaturation. HPLC experiments show that the thermal denatured enzyme conserves its dimeric state. The N(2)-->kD(2) model for thermal denaturation of ELAO is proposed: where N(2) and D(2) are the native and denatured dimer, respectively.
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Affiliation(s)
- Mojtaba Amani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Hong J, Ghourchian H, Moosavi–Movahedi AA. Direct electron transfer of redox proteins on a Nafion-cysteine modified gold electrode. Electrochem commun 2006. [DOI: 10.1016/j.elecom.2006.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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