Volume 9, Issue 3 (2018)
JMBS 2018, 9(3): 451-457 |
Back to browse issues page
1- Biophysics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
2- Biology Department, Science Faculty, University of Zanjan, Zanjan, Iran
3- Biochemistry Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
4- Tarbiat Modares University, Nasr Bridge, Jalal-Al-Ahmad Highway, Tehran, Iran ,ranjbarb@modares.ac.ir
2- Biology Department, Science Faculty, University of Zanjan, Zanjan, Iran
3- Biochemistry Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
4- Tarbiat Modares University, Nasr Bridge, Jalal-Al-Ahmad Highway, Tehran, Iran ,
Abstract: (5150 Views)
Aims: Studies based on thermal stability are considered as one of the methods for investigating the physicochemical properties of proteins in biotechnology. The aim of this study was to evaluate the effect of replacement of Arginine 39 amino acid with lysine on the heat denaturation of mnemiopsin photoprotein 1.
Materials and Methods: In the current experimental study, R39K mutated mnemiopsin was compared with wild protein (in which arginine 39 amino acid was converted to the lysine amino acid). In order to investigate the effect of mutation on the content of the secondary structure, a rotation interpolation method was used. To investigate the possible changes in the rate of thermal stability of mutated and wild proteins, heat denaturation measurements were performed by differential scanning calorimeter. Bioinformatics software were used to compare the structure of two types of proteins.
Findings: The mutated R39K compression decreased in comparison with wild protein. No significant change was observed in the values of thermodynamic parameters, especially Tm. The upward movement of arginine 187 amino acid in the mutated protein decreased the thermal stability of this protein. Increasing the accessible surface of lysine 188 in the mutated protein increased its stability.
Conclusion: In thermal stability of the R39K mutated protein, various factors are effective, including the molecular movements of amino acids, their accessible surface, and the content of the secondary structure of protein stabilizing. This mutation reduces the mutated R39K compression rather than the wild protein; increasing ASA related to Lys188 amino acid in the mutated R39K compared with wild protein increases protein stability, but reducing the amount of secondary structure in this mutated, accompanied by an increase in the molecular upward movement in the Arg187 amino acid serves to reduce the stability of this mutated.
Materials and Methods: In the current experimental study, R39K mutated mnemiopsin was compared with wild protein (in which arginine 39 amino acid was converted to the lysine amino acid). In order to investigate the effect of mutation on the content of the secondary structure, a rotation interpolation method was used. To investigate the possible changes in the rate of thermal stability of mutated and wild proteins, heat denaturation measurements were performed by differential scanning calorimeter. Bioinformatics software were used to compare the structure of two types of proteins.
Findings: The mutated R39K compression decreased in comparison with wild protein. No significant change was observed in the values of thermodynamic parameters, especially Tm. The upward movement of arginine 187 amino acid in the mutated protein decreased the thermal stability of this protein. Increasing the accessible surface of lysine 188 in the mutated protein increased its stability.
Conclusion: In thermal stability of the R39K mutated protein, various factors are effective, including the molecular movements of amino acids, their accessible surface, and the content of the secondary structure of protein stabilizing. This mutation reduces the mutated R39K compression rather than the wild protein; increasing ASA related to Lys188 amino acid in the mutated R39K compared with wild protein increases protein stability, but reducing the amount of secondary structure in this mutated, accompanied by an increase in the molecular upward movement in the Arg187 amino acid serves to reduce the stability of this mutated.
Keywords: Thermal Stability, Mnemiopsin, Molecular Movements, Accessible Surface, Differential Scaling Calorimetry
Article Type: Research Paper |
Subject:
Agricultural Biotechnology
Received: 2015/04/28 | Accepted: 2018/03/6 | Published: 2018/09/22
Received: 2015/04/28 | Accepted: 2018/03/6 | Published: 2018/09/22
References
1. Kumar S, Tsai CJ, Nussinov R. Factors enhancing protein thermostability. Protein Eng. 2000;13(3):179-91. [Link] [DOI:10.1093/protein/13.3.179]
2. Talluri S. Advances in engineering of proteins for thermal stability. Int J Adv Biotechnol Res. 2011;2(1):190-200. [Link]
3. Gill P, Tohidi Moghadam T, Ranjbar B. Differential scanning calorimetry techniques: Applications in biology and nanoscience. J Biomol Tech. 2010; 21(4):167-93. [Link]
4. Graziano G, Catanzano F, Giancola C, Barone G. DSC Study of the thermal stability of S-protein and S-peptide/S-protein complexes. Biochemistry. 1996;35(41):13386-92. [Link] [DOI:10.1021/bi960856+]
5. Protasevich I, Ranjbar B, Lobachov V, Makarov A, Gilli R, Briand C, et al. Conformation and thermal denaturation of apocalmodulin: Role of electrostatic mutations. Biochemistry. 1997;36(8)2017-24. [Link] [DOI:10.1021/bi962538g]
6. Tsuji FI, Ohmiya Y, Fagan TF, Toh H, Inouye S. Molecular evolution of the Ca2+-binding photoproteins of the Hydrozoa. Photochem Photobiol. 1995;62(4):657-61. [Link] [DOI:10.1111/j.1751-1097.1995.tb08713.x]
7. Aghamaali MR1, Jafarian V, Sariri R, Molakarimi M, Rasti B, Taghdir M, et al. Cloning, sequencing, expression and structural investigation of mnemiopsin from Mnemiopsis leidyi: An attempt toward understanding ca2+-regulated photoproteins. Protein J. 2011;30(8):566-74. [Link] [DOI:10.1007/s10930-011-9363-8]
8. Moncrief ND, Kretsinger RH, Goodman M. Evolution of EF-hand calcium-modulated proteins: I. relationships based on amino acid sequences. J Mol Evol. 1990;30(6):522-62. [Link] [DOI:10.1007/BF02101108]
9. Gonzalez JE, Tsien RY. Improved indicators of cell membrane potential that use fluorescence resonance energy transfer. Chem Biol. 1997;4(4):269-77. [Link] [DOI:10.1016/S1074-5521(97)90070-3]
10. Blinks JR. Use of photoproteins as intracellular calcium indicators. Environ Health Perspect. 1990;84:75-81. [Link] [DOI:10.1289/ehp.908475]
11. Lewis CJ, Daunert S. Photoproteins as luminescent labels in binding assays. Fresenius J Anal Chem. 2000;366(6-7):760-8. [Link] [DOI:10.1007/s002160051570]
12. Stepanyuk GA, Liu ZJ, Burakova LP, Lee J, Rose J, Vysotski ES, et al. Spatial structure of the novel light-sensitive photoprotein berovin from the ctenophore Beroe abyssicola in the Ca2+-loaded apoprotein conformation state. Biochim Biophys Acta. 2013;1834(10)2139-46. [Link] [DOI:10.1016/j.bbapap.2013.07.006]
13. Ward WW, Seliger HH. Properties of mnemiopsin and berovin, calcium-activated photoproteins from the Ctenophores Mnemiopsis species and Beroe ovata. Biochemistry. 1974;13(7):1500-10. [Link] [DOI:10.1021/bi00704a028]
14. Ward WW, Seliger HH. Extraction and purification of calcium-activated photoproteins from the ctenophores Mnemiopsis species and Beroe ovata. Biochemistry. 1974;13(7):1491-9. [Link] [DOI:10.1021/bi00704a027]
15. Takenaka Y, Yamaguchi A, Tsuruoka N, Torimura M, Gojobori T, Shigeri Y. Evolution of bioluminescence in marine planktonic copepods. Mol Biol Evol. 2006;29(6):1669-81. [Link] [DOI:10.1093/molbev/mss009]
16. Liu ZJ, Stepanyuk GA, Vysotski ES, Lee J, Markova SV, Malikova NP, et al. Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state. Proc Natl Acad Sci USA. 2006;103(8);2570-5. [Link] [DOI:10.1073/pnas.0511142103]
17. Deng L, Vysotski ES, Markova SV, Liu ZJ, Lee J, Rose, et al. All three Ca2+-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obeli. Protein Sci. 2005;14(2):663-75. [Link] [DOI:10.1110/ps.041142905]
18. Head JF, Inouye S, Teranishi K, Shimomura O. The crystal structure of the photoprotein aequorin at 2.3 A resolution. Nature. 2000;405(6784):372-76. [Link] [DOI:10.1038/35012659]
19. Dikici E, Qu X, Rowe L, Millner L, Logue C, Deo SK, et al. Aequorin variants with improved bioluminescence properties. Protein Eng Des Sel. 2009;22(4):243-8. [Link] [DOI:10.1093/protein/gzn083]
20. Mahdavi A, Sajedi RH, Hosseinkhani S, Taghdir M, Sariri R. Site-directed mutagenesis of photoprotein mnemiopsin: Implication of some conserved residues in bioluminescence properties. Photochem Photobiol Sci. 2013;12(3):467-78. [Link] [DOI:10.1039/C2PP25320H]
21. Jafarian V, Sariri R, Hosseinkhani S, Aghamaali MR, Sajedi RH, Taghdir M, et al. A unique EF-hand motif in mnemiopsin photoprotein from Mnemiopsis leidyi: Implication for its low calcium sensitivity. Biochem Biophys Res Commun. 2011;413(2):164-70. [Link] [DOI:10.1016/j.bbrc.2011.08.022]
22. Mahdavi A, Sajedi RH, Hosseinkhani S, Taghdir M. Hyperactive Arg39Lys mutated mnemiopsin: Implication of positively charged residue in chromophore binding cavity. Photochem Photobiol Sci. 2015;14(4):792-800. [Link] [DOI:10.1039/C4PP00191E]
23. Ranjbar B, Gill P. Circular dichroism techniques: Biomolecular and nanostructural analyses- a review. Chem Biol Drug Des. 2009;74(2):101-20. [Link] [DOI:10.1111/j.1747-0285.2009.00847.x]
24. Wang W, Malcolm BA. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange Site-Directed Mutagenesis. Biotechniques. 1999;26(4):680-2. [Link] [DOI:10.2144/99264st03]
25. Chen YH, Yang JT, Martinez HM. Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. Biochemistry. 1972;11(22):4120-31. [Link] [DOI:10.1021/bi00772a015]
26. Maghami P, Ranjbar B, Hosseinkhani S, Ghasemi A, Moradi A, Gill P. Relationship between stability and bioluminescence color of firefly luciferase. Photochem Photobiol Sci. 2010;9(3):376-83. [Link] [DOI:10.1039/b9pp00161a]
27. Hakiminia F, Rnjbar B, Khalifeh Kh, Khajeh Kh. Kinetic and thermodynamic properties of Pseudomonas fluorescence lipase upon addition of proline. Int J Biolo Macromol. 2013;55:123-6. [Link] [DOI:10.1016/j.ijbiomac.2012.12.046]
28. Freire E, Biltonen RL. Statistical mechanical deconvolution of thermal transitions in macromolecules. I. Theory and application to homogeneous systems. biopolymers. 1978;17(2):463-79. [Link] [DOI:10.1002/bip.1978.360170212]
29. Protein Structure Modeling With MODELLER. Current protocols in bioinformatics. John Wiley& Sons Inc; 2006. 15:5.6.1-5.6.30. [Link]
30. Smith CA, Kortemme T. Backrub-like Backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol. 2008;380(4):742-56. [Link] [DOI:10.1016/j.jmb.2008.05.023]
31. Tina KG, Bhadra R, Srinivasan N. PIC: Protein interactions calculator. Nucleic Acids Res. 2007;35:473-6. [Link] [DOI:10.1093/nar/gkm423]
32. Willard L, Ranjan A, Zhang H, Monzavi H, Boyko RF, Sykes BD, et al. VADAR: A web server for quantitative evaluation of protein structure quality. Nucleic Acids Res. 2003;31(13):3316-9. [Link] [DOI:10.1093/nar/gkg565]
33. Bornot A, Etchebest C, De Brevern AG. Predicting protein flexibility through the prediction of local structures. Proteins. 2011;79(3):839-52. [Link] [DOI:10.1002/prot.22922]
34. De Brevern AG, Bornot A, Craveur P, Etchebest C, Gelly JC. PredyFlexy: flexibility and local structure prediction from sequenc. 2012;40: 317-22. [Link]
35. Serdyuk IN, Zaccai NR, Zaccai J. Methods in molecular biophysics: Structure, dynamics, function. Cambridge: Cambridge University Press; 2007. [Link] [DOI:10.1017/CBO9780511811166]
36. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 157(1):105-32. [Link] [DOI:10.1016/0022-2836(82)90515-0]
| Rights and permissions | |
 |
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |