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New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

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Abstract

Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

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References

  1. Madigan MT, Marrs BL (1997) Extremophiles. Sci Am 276(4):82–87

    Article  CAS  Google Scholar 

  2. Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008) Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol 9 (4):R70.

  3. Eisenberg H (1995) Life in unusual environments: progress in understanding the structure and function of enzymes from extreme halophilic bacteria. Arch Biochem Biophys 318(1):1–5

    Article  CAS  Google Scholar 

  4. Pieper U, Kapadia G, Mevarech M, Herzberg O (1998) Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. Structure 6(1):75–88

    Article  CAS  Google Scholar 

  5. Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8(6):738–748

    Article  CAS  Google Scholar 

  6. Joo WA, Kim CW (2005) Proteomics of halophilic archaea. J Chromatogr B Anal Technol Biomed Life Sci 815(1–2):237–250

    Article  CAS  Google Scholar 

  7. Rasiah IA, Rehm BH (2009) One-step production of immobilized alpha-amylase in recombinant Escherichia coli. Appl Environ Microbiol 75(7):2012–2016

    Article  CAS  Google Scholar 

  8. Ghollasi M, Khajeh K, Naderi-Manesh H, Ghasemi A (2010) Engineering of a Bacillus alpha-amylase with improved thermostability and calcium independency. Appl Biochem Biotechnol 162(2):444–459

    Article  CAS  Google Scholar 

  9. Hutcheon GW, Vasisht N, Bolhuis A (2005) Characterisation of a highly stable alpha-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 9(6):487–495

    Article  CAS  Google Scholar 

  10. Prakash O, Jaiswal N (2010) Alpha-amylase: an ideal representative of thermostable enzymes. Appl Biochem Biotechnol 160(8):2401–2414

    Article  Google Scholar 

  11. Qian M, Haser R, Buisson G, Duee E, Payan F (1994) The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution. Biochemistry 33(20):6284–6294

    Article  CAS  Google Scholar 

  12. van der Maarel M, van der Veen B, Uitdehaag J, Leemhuis H, Dijkhuizen L (2002) Properties and applications of starch-converting enzymes of the alpha-amylase family. J Biotechnol 94(2):137–155

    Article  Google Scholar 

  13. Aghajari N, Feller G, Gerday C, Haser R (1998) Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level. Structure 6(12):1503–1516

    Article  CAS  Google Scholar 

  14. Gilles C, Astier JP, Marchis-Mouren G, Cambillau C, Payan F (1996) Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose. Eur J Biochem 238(2):561–569

    Article  CAS  Google Scholar 

  15. Swift HJ, Brady L, Derewenda ZS, Dodson EJ, Dodson GG, Turkenburg JP, Wilkinson AJ (1991) Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method. Acta Crystallogr B 47(Pt 4):535–544

    Article  Google Scholar 

  16. Kagawa M, Fujimoto Z, Momma M, Takase K, Mizuno H (2003) Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose. J Bacteriol 185(23):6981–6984

    Article  CAS  Google Scholar 

  17. Linden A, Mayans O, Meyer-Klaucke W, Antranikian G, Wilmanns M (2003) Differential regulation of a hyperthermophilic alpha-amylase with a novel (Ca, Zn) two-metal center by zinc. J Biol Chem 278(11):9875–9884

    Article  CAS  Google Scholar 

  18. Elcock AH, McCammon JA (1998) Electrostatic contributions to the stability of halophilic proteins. J Mol Biol 280(4):731–748

    Article  CAS  Google Scholar 

  19. Mevarech M, Frolow F, Gloss LM (2000) Halophilic enzymes: proteins with a grain of salt. Biophys Chem 86(2–3):155–164

    Article  CAS  Google Scholar 

  20. Siglioccolo A, Paiardini A, Piscitelli M, Pascarella S (2011) Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface. BMC Struct Biol 11:50

    Article  CAS  Google Scholar 

  21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  Google Scholar 

  22. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31(13):3320–3323

    Article  CAS  Google Scholar 

  23. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815

    Article  CAS  Google Scholar 

  24. Sivakumar N, Li N, Tang JW, Patel BK, Swaminathan K (2006) Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly-extreme condition. FEBS Lett 580(11):2646–2652

    Article  CAS  Google Scholar 

  25. Watanabe K, Hata Y, Kizaki H, Katsube Y, Suzuki Y (1997) The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 A resolution: structural characterization of proline-substitution sites for protein thermostabilization. J Mol Biol 269(1):142–153

    Article  CAS  Google Scholar 

  26. Bekker H, Berndsen HJC, Dijkstra EJ, Achterop S, Van Drunen R, Van Der Spoel D, Sijbers A, Keegstra H, Reitsma B, Renardus MKR (1993) Gromacs: a parallel computer for molecular dynamics simulations. Phys Comput 92:252–256

    Google Scholar 

  27. Melo F, Devos D, Depiereux E, Feytmans E (1997) ANOLEA: a www server to assess protein structures. Proc Int Conf Intell Syst Mol Biol 5:187–190

    CAS  Google Scholar 

  28. Khemili S, Kwasigroch JM, Hamadouche T, Gilis D (2012) Modelling and bioinformatics analysis of the dimeric structure of house dust mite allergens from families 5 and 21: Der f 5 could dimerize as Der p 5. J Biomol Struct Dyn 29(4):663–675

    Article  CAS  Google Scholar 

  29. Dietmann S, Holm L (2001) Identification of homology in protein structure classification. Nat Struct Biol 8(11):953–957

    Article  CAS  Google Scholar 

  30. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577–2637

    Article  CAS  Google Scholar 

  31. Delano WL (2002) The pymol molecular graphics system. DeLano Scientific

  32. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98(18):10037–10041

    Article  CAS  Google Scholar 

  33. Tina KG, Bhadra R, Srinivasan N (2007) PIC: protein interactions calculator. Nucleic Acids Res 35(Web Server issue):W473–W476

    Article  CAS  Google Scholar 

  34. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599

    Article  CAS  Google Scholar 

  35. Kastritis PL, Papandreou NC, Hamodrakas SJ (2007) Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs. Int J Biol Macromol 41(4):447–453

    Article  CAS  Google Scholar 

  36. Chagnot C, Zorgani MA, Astruc T, Desvaux M (2013) Proteinaceous determinants of surface colonization in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective. Front Microbiol 4:303

    Article  Google Scholar 

  37. Desvaux M, Hebraud M, Talon R, Henderson IR (2009) Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol 17(4):139–145

    Article  CAS  Google Scholar 

  38. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR (2004) The general secretory pathway: a general misnomer? Trends Microbiol 12(7):306–309

    Article  CAS  Google Scholar 

  39. Sawaya MR, Kraut J (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 36(3):586–603

    Article  CAS  Google Scholar 

  40. Karlin S, Brocchieri L, Bergman A, Mrazek J, Gentles AJ (2002) Amino acid runs in eukaryotic proteomes and disease associations. Proc Natl Acad Sci USA 99(1):333–338

    Article  CAS  Google Scholar 

  41. Costantini S, Colonna G, Facchiano AM (2006) Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Commun 342(2):441–451

    Article  CAS  Google Scholar 

  42. Bieger B, Essen LO, Oesterhelt D (2003) Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum. Structure 11(4):375–385

    Article  CAS  Google Scholar 

  43. Muller-Santos M, de Souza EM, Pedrosa Fde O, Mitchell DA, Longhi S, Carriere F, Canaan S, Krieger N (2009) First evidence for the salt-dependent folding and activity of an esterase from the halophilic archaea Haloarcula marismortui. Biochim Biophys Acta 1791(8):719–729

    Article  Google Scholar 

  44. Ebrahimie E, Ebrahimi M, Sarvestani NR (2011) Protein attributes contribute to halo-stability, bioinformatics approach. Saline Syst 7(1):1

    Article  CAS  Google Scholar 

  45. Dym O, Mevarech M, Sussman JL (1995) Structural features that stabilize halophilic malate dehydrogenase from an archaebacterium. Science 267(5202):1344–1346

    Article  CAS  Google Scholar 

  46. Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K (2003) Unique amino acid composition of proteins in halophilic bacteria. J Mol Biol 327(2):347–357

    Article  CAS  Google Scholar 

  47. Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK (2004) Protein flexibility and intrinsic disorder. Protein Sci 13(1):71–80

    Article  CAS  Google Scholar 

  48. Tadeo X, Lopez-Mendez B, Trigueros T, Lain A, Castano D, Millet O (2009) Structural basis for the aminoacid composition of proteins from halophilic archea. PLoS Biol 7(12):e1000257. doi:10.1371/journal.pbio.1000257

    Article  Google Scholar 

  49. Eisenberg D, Schwarz E, Komaromy M, Wall R (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 179(1):125–142

    Article  CAS  Google Scholar 

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Correspondence to Mohamed Amine Zorgani.

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Zorgani, M.A., Patron, K. & Desvaux, M. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface. J Comput Aided Mol Des 28, 721–734 (2014). https://doi.org/10.1007/s10822-014-9754-y

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