Triple mutated antibody scFv2F3 with high GPx activity: Insights from MD, docking, MDFE, and MM-PBSA simulation

Amino Acids

Volumn 44, Issue 3, 2013, Pages 1009-1019

  Luo, Quan ^a   Zhang, Chunqiu ^a   Miao, Lu ^a   Zhang, Dongmei ^a   Bai, Yushi ^a   Hou, Chunxi ^a   Liu, Junqiu ^a   Yan, Fei ^b   Mu, Ying ^b   Luo, Guimin ^b  

^a Jilin University   (China)

^b JILIN UNIVERSITY   (China)

Author keywords

Abzyme; Docking; GPx mimic; MD simulation; MDFE simulation; MM PBSA

Indexed keywords

GLUTAMINE; GLUTATHIONE PEROXIDASE; PHENYLALANINE; SERINE; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY; SINGLE CHAIN FRAGMENT VARIABLE F3 ANTIBODY; UNCLASSIFIED DRUG; VALINE;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; CHEMICAL INTERACTION; CHEMICAL MODIFICATION; CONFORMATION; CONTROLLED STUDY; DIPOLE; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; MOLECULAR BIOLOGY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MEDICINE; MOLECULAR STABILITY; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ANTIBODIES, CATALYTIC; CATALYTIC DOMAIN; GLUTATHIONE PEROXIDASE; KINETICS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS, SITE-DIRECTED; MUTATION; SINGLE-CHAIN ANTIBODIES; THERMODYNAMICS;

EID: 84878361518     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-012-1435-3     Document Type: Article

References (37)

1. Bashford D, Case DA (2000) Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem 51:129-152
2. Battin EE, Brumaghim JL (2009) Antioxidant activity of sulfur and selenium: a review of reactive oxygen species scavenging, glutathione peroxidase, and metal-binding antioxidant mechanisms. Cell Biochem Biophys 55:1-23
3. Bhabak KP, Mugesh G (2010) Functional mimics of glutathione peroxidase: bioinspired synthetic antioxidants. Acc Chem Res 43:1408-1419
4. Braman J, Papworth C, Greener A (1996) Site-directed mutagenesis using double-stranded plasmid DNA templates. Methods Mol Biol 57:31-44
5. Devasagayam TP, Tilak JC, Boloor KK, Sane KS, Ghaskadbi SS, Lele RD (2004) Free radicals and antioxidants in human health: current status and future prospects. J Assoc Physicians India 52:794-804
6. Esworthy RS, Swiderek KM, Ho YS, Chu FF (1998) Selenium-dependent glutathione peroxidase-GI is a major glutathione peroxidase activity in the mucosal epithelium of rodent intestine. Biochim Biophys Acta 1381:213-226
7. Frisch MJ, Trucks GW, Schlegel HB (2003) Gaussian 03 (Revision A.1) Gaussian Pittsburgh
8. Fujiwara S, Amisaki T (2008) Identification of high affinity fatty acid binding sites on human serum albumin by MM-PBSA method. Biophys J 94:95-103
9. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723
10. Huang X, Liu XM, Luo Q, Liu JQ, Shen JC (2011) Artificial selenoenzymes: designed and redesigned. Chem Soc Rev 40:1171-1184
11. Huber RE, Criddle RS (1967) Comparison of the chemical properties of selenocysteine and selenocystine with their sulfur analogs. Arch Biochem Biophys 122:164-173
12. Hummer G, Szabo A (1996) Calculation of free-energy differences from computer simulations of initial and final states. J Chem Phys 105:2004-2010
13. Kollman P (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Reviews 93:2395-2417
14. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE III (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889-897
15. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291
16. Li LW, Uversky NV, Dunker K, Meroueh SO (2007) A computational investigation of allostery in the catabolite activator protein. J Am Chem Soc 129:15668-15676
17. Liu JQ, Luo GM, Mu Y (2012) Selenoproteins and mimics. Springer, Berlin
18. Lu SY, Jiang YJ, Zou JW, Wu TX (2012) Effect of double mutations K214/A-E215/Q of FRATide on GSK3β: insights from molecular dynamics simulation and normal mode analysis. Amino Acids 43:267-277
19. Luo Q, Han WW, Zhou YH, Yao Y, Li ZS (2008) The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies. J Mol Model 14:559-569
20. Luo Q, Zhou YH, Yao Y, Li ZS (2010) Theoretical design of catalytic domain of abzyme Se-scFv2F3 by introducing a catalytic triad. Chem Res Chin Univ 26:118-121
21. Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83-85
22. Maiorino M, Aumann KD, Brigelius-Flohé R, Doria D, van den Heuvel J, McCarthy J, Roveri A, Ursini F, Flohé L (1995) Probing the presumed catalytic triad of selenium-containing peroxidases by mutational analysis of phospholipid hydroperoxide glutathione peroxidase (PHGPx). Biol Chem Hoppe-Seyler 376:651-660
23. Maiorino M, Aumann KD, Brigelius-Flohé R, Doria D, van den Heuvel J, McCarthy J, Roveri A, Ursini F, Flohé L (1998) Probing the presumed catalytic triad of selenium-containing peroxidases by mutational analysis. Z Ernahrungswiss 37:118-121
24. Matés JM, Pérez-Gómez C, Núñez de Castro I (1999) Antioxidant enzymes and human diseases. Clin Biochem 32:595-603
25. Pastor RW, Brooks BR, Szabo A (1988) An analysis of the accuracy of Langevin and molecular dynamics algorithms. A Mol Phys 65:1409-1419
26. Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Prot Chem 66:27-85
27. Ren X, Gao S, You D, Huang H, Liu Z, Mu Y, Liu J, Zhang Y, Yan G, Luo G, Yang T, Shen J (2001) Cloning and expression of a single-chain catalytic antibody that acts as a glutathione peroxidase mimic with high catalytic efficiency. Biochem J 359:369-374
28. Scheerer P, Borchert A, Krauss N, Wessner H, Gerth C, Höhne W, Kuhn H (2007) Structural basis for catalytic activity and enzyme polymerization of phospholipid hydroperoxide glutathione peroxidase-4 (GPx4). Biochemistry 46:9041-9049
29. Simmerling C, Strockbine B, Roitberg AE (2002) All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 124:11258-11259
30. Simonson T, Carlsson J, Case DA (2004) Proton binding to proteins: pKa calculations with explicit and implicit solvent models. J Am Chem Soc 126:4167-4180
31. Stanfield RL, Wilson IA (1994) Antigen-induced conformational changes in antibodies: a problem for structural prediction and design. Trends Biotechnol 12:275-279
32. Thannickal VJ, Fanburg BL (2000) Reactive oxygen species in cell signaling. Am J Physiol Lung Cell Mol Physiol 279:L1005-L1028
33. Thomas JP, Maiorino M, Ursing F, Girutti AW (1990) Protective action of phospholipid hydroperoxide glutathione peroxidase against membrane-damaging lipid peroxidation. In situ reduction of phospholipid and cholesterol hydroperoxides. J Biol Chem 265:454-461
34. Toppo S, Flohé L, Ursini F, Vanin S, Maiorino M (2009) Catalytic mechanisms and specificities of glutathione peroxidases: variations of a basic scheme. Biochim Biophys Acta 1790:1486-1500
35. Tuccinardi T, Manetti F, Schenone S, Martinelli A, Botta M (2007) Construction and validation of a RET TK Catalytic domain by homology modeling. J Chem Inf Model 47:644-655
36. Wilson SR, Zucker PA, Huang RRC, Spector A (1989) Development of synthetic compounds with glutathione peroxidase activity. J Am Chem Soc 111:5936-5939
37. Wu ZP, Hilvert B (1990) Selenosubtilisin as a glutathione peroxidase mimic. J Am Chem Soc 112:5647-5648