Influence of antifreeze proteins on local waters structure dynamics in presence of osmolytes

• Autorzy: Krishnamoorthy A. N.
• Języki publikacji: EN

Abstrakty

EN

Antifreeze proteins are synthesized by various organisms to enable their cells to survive subzero environment in the arctic and polar regions. These proteins produce a difference between the melting and freezing points termed as thermal hysteresis. The main objective of this study is to examine the dynamics of water molecules and hydrogen bonds at the protein-water interface of antifreeze protein using atomistic molecular dynamics simulations using GROMACS. For this work a prototype of AFP (antifreeze protein) from antarctic notothenioids (ala-ala-thr repeats) and a mutant which is not antifreeze active were generated using PRODRG server. The hydration dynamics results revealed that the retarded water dynamics in the AFP compared to its mutant was responsible for the antifreeze activity. Furthermore a considerable increase in antifreeze activity were observed for the AFP in presence of osmolytes. The mechanism of action were tested using preferential binding parameter derived from Kirkwood-Buff integerals.

Słowa kluczowe

EN

hydration dynamics; hydrogen bond lifetime; osmolytes; Kirkwood-Buff integrals; prefential binding parameter

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2013
• Tom: Vol.17, No 1-2
• Strony: 5--42
• Opis fizyczny: Bibliogr. 50 poz., rys., tab.

Twórcy

autor

Krishnamoorthy A. N.

• Institute for Computational Physics, Universitat Stuttgart

Bibliografia

• [1] www.rcsb.org/pdb/101/motm.do?momID=120
• [2] De Vries A L and Wohlsclag D E 1969 Science 163 1073
• [3] Jorov A, Zhorov B S and Yang D S 2004 Protein Sci. 13 (6) 1524
• [4] Smiatek J, Harishchandra R K, Rnbner O, Galla H-J and Heuer A 2012 Biophys. Chem. 160 62
• [5] Collins K D, Neilson G W and Enderby J E 2007 Biophys. Chem. 128 95
• [6] Marshall C B, Daley M E, Graham L A, Skyes B D and Davies P L 2002 FEBS Lett. 529 (2-3) 261
• [7] Ebbinghaus S, Meister K, Brn B, De Vries A L, Gruebele M and Havenith M 2010 J ACS Chem. 132 12210
• [8] Fletcher G L, Hew C L and Davies P L 2001 Annu. Rev. Physiol. 63 359
• [9] Capicciotti C J, Doshi M and Ben R N 2013 Ice Recrystallization Inhibitors: From Biological Antifreezes to Small Molecules, Department of Chemistry, D’Iorio Hall. University of Ottawa, Ottawa, ON, Canada
• [10] Raymond J A and De Vries A L 1977 Proc. Natl. Acad. Sei. USA 74 (6) 2589
• [11] Schüttelkopf A W and van Aalten D M F 2004 Acta Crystal. D60 1355
• [12] Greiner W, Neise L and Stöcker H 2001 Thermodynamics and Statistical Mechanics, Springer
• [13] Hunenberger P H 2005 Adv. Polymer. Sci. 173 105
• [14] Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A and Haak J R 1984 J. Chem. Phys. 81 (8) 3684
• [15] Karatsas I and Shreve S 1997 Broumian Motion and Stochastic Calculus, 2nd Ed., New York, Springer-Verlag
• [16] Hess B. Kutzner C, van der Spoel D and Lindahl E 2008 J. Chem. Theory Comput. 4 (3) 435
• [17] Amornwittawat N, Wang S and Banatlao J 2009 Biochim. Biophys. Acta 1794 3-11
• [18] Meister K, Ebbinghaus S, Xu Y, Duman J G, De Vries A L, Gruebele M, Leitner D M and Havenith M 2012 Proc. Natl. Acad. Sei. USA, doi:10.1073/pnas.l214911110
• [19] Makhatadze G I and Privalov P L 1995 Adv. Protein Chem. 47 307
• [20] Marcus Y 2009 Chem. Rev. 109 1346
• [21] Wiggins P M 2001 Cell. Mol. Biol. 47 735
• [22] De Xammar Oro J R 2001 J. Biol. Phys. 27 73
• [23] Hua L, Zhou R, Thirumalai D and Berne B J 2008 Proc. Natl. Acad. Sei. USA 105 (44) 16928
• [24] Smiatek J, Harishchandra R K, Rubner O, Galla H-J and Heuer A 2012 Bwphys. Chem. 160 62
• [25] Robinson D and Jencks W 1965 J. Am. Chem. Soc. 87 2462
• [26] Arakawa T and Timasheff S N 1985 Bwphys. J. 47 411
• [27] Timasheff S N 2002 Biochemistry 41 13473
• [28] Lemkul .1 A, Allen W J and Bevan D R 2010 J. Chem. Inf. Model. 50 (12) 2221
• [29] Luzar A and Chandler D 1996 Hydrogen Bond Kinetics in Liquid Water, Department of Chemistry, University of California, USA
• [30] Luzar A 2000 J. Chem. Phys. 113 10663
• [31] Yu I, Jindo Y and Nagaoka M 2007 J. Phys. Chem. B111 10231
• [32]Baynes B M, Wang D I C and Trout B L 2004 Proteins in Mixed Solvents: A Molecular-Level Perspective, Department of Chemical Engineering, M.I.T., Cambridge, USA
• [33] Kirkwood J G and Buff F P 1951 J. Chem. Phys. 19 774
• [34] Ben-Naim A 1992 Statistical Thermodynamics for Chemists and Biochemists, Plenum Press, New York
• [35] Canchi D R and Garcia A E 2013 Anna. Rev. Phys. Chem. 64 273
• [36] Bencivenga F, Cimatorihus A, Gessini A, Izzo M G and Masciovecchio C 2009 J. Chem.Phys. 131 1445021
• [37] Richmond T J 1984 J. Mol. Biol. 178 63
• [38] Eisenhaber F, Lijnzaad P, Argcxs P. Sander C and Scharf M 1995 J. Comp. Chem. 16 273
• [39] Ebbinghaus S, Kim S J, Heyden M, Yu X, Heugen U, Gruebele M, Leitner D M and Havenith M 2007 Proc. Natl. Acad. Sei. USA 104 (52) 20749
• [40] Nicodemus-Johnson J, Silic S. Ghigliotti L, Pisano E and Cheng C-H C 2011 Genomics 98 194
• [41] Zangi R, Zhou R and Berne B ,J 2009 .J. Am. Chem. Soc. 131 (4) 1535
• [42] Luzar A and Chandler D 1996 Nature 379 55
• [43] Li N, Andorfer C and Duman J 1998 J. Exp. Biol. 201 2243
• [44] Amornwittawat N, Wang S, Duman J G and Wen X 2008 Biochim. Biophys. Acta 1784 1942
• [45] Jorov A, Zhorov B S and Yang DSC 2004 Protein Sci. 13 1524
• [46] Raymond J A and De Vries A L 1977 Proc. Natl. Acad. Sci. USA 74 2589
• [47] Stanley C and Rau D C 2008 Biochemistry 47 6711
• [48] Balasubramaniam S, Bandyopadhyay S, Pal S and Bagchi B 2003 Current Science 85 1571
• [49] Wan S, Stote R H and Karplus M 2004 J. Chem. Phys. 121 (19) 9539
• [50] Shirts M R, Pitera J W, Swope W C and Pande V S 2003 J. Chem. Phys. 119 5740