Molecular dynamics simulation to investigate the impact of disulfide bond formation on conformational stability of chicken cystatin I66Q mutant

Reference

• Abkevich , V.I. and Shakhnovich , E.I. 2000 . What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis . Journal of Molecular Biology , 300 : 975 – 985 .
   PubMed Web of Science ®Google Scholar
• Abrahamson , M. 1996 . Molecular basis for amyloidosis related to hereditary brain hemorrhage . Scandinavian Journal of Clinical and Laboratory Investigation , 226 ( Supplement ) : 47 – 56 .
   Google Scholar
• Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. Intermolecular forces, 11(supplement 1), 331–338.
   Google Scholar
• Bjork , I. and Ylinenjarvi , K. 1992 . Different roles of the two disulfide bonds of the cysteine proteinase inhibitor, chicken cystatin, for the conformation of the active protein . Biochemistry , 31 : 8597 – 8602 .
   PubMed Web of Science ®Google Scholar
• Bobek , L.A. and Levine , M.J. 1992 . Cystatins-inhibitors of cysteine proteinases . Critical Reviews in Oral Biology and Medicine , 3 : 307 – 332 .
   PubMedGoogle Scholar
• Bode , W. , Engh , R. , Musil , D. , Thiele , U. , Huber , R. , Karshikov , A. , … and Turk , V. 1988 . The 2.0 A X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases . EMBO Journal , 7 : 2593 – 2599 .
   PubMed Web of Science ®Google Scholar
• Day , R. , Bennion , B.J. , Ham , S. and Daggett , V. 2002 . Increasing temperature accelerates protein unfolding without changing the pathway of unfolding . Journal of Molecular Biology , 322 : 189 – 203 .
   PubMed Web of Science ®Google Scholar
• Ekiel , I. , Abrahamson , M. , Fulton , D.B. , Lindahl , P. , Storer , A.C. , Levadoux , W. , … and Gehring , K. 1997 . NMR structural studies of Human Cystatin C dimers and monomers . Journal of Molecular Biology , 271 : 266 – 277 .
   PubMed Web of Science ®Google Scholar
• Engh , R.A. , Dieckmann , T. , Bode , W. , Auerswald , E.A. , Turk , V. , Huber , R. and Oschkinat , H. 1993 . Conformational variability of chicken cystatin. Comparison of structures determined by X-ray diffraction and NMR spectroscopy . Journal of Molecular Biology , 234 : 1060 – 1069 .
   PubMed Web of Science ®Google Scholar
• Essmann , U. , Perera , L. , Berkowitz , M.L. , Darden , T. , Lee , H.J. and Pedersen , L.G. 1995 . A smooth particle mesh Ewald potential . Journal of Chemical Physics , 103 : 8577 – 8592 .
   Web of Science ®Google Scholar
• Grana-Montes , R. , de Groot , N.S. , Castillo , V. , Sancho , J. , Velazquez-Campoy , A. and Ventura , S. 2012 . Contribution of disulfide bonds to stability, folding, and amyloid fibril formation: The PI3-SH3 domain case . Antioxidants & Redox Signaling , 16 : 1 – 15 .
   PubMed Web of Science ®Google Scholar
• Grubb , A. , Jensson , O. , Gudmundsson , G. , Arnason , A. , Lofberg , H. and Malm , J. 1984 . Abnormal metabolism of gamma-trace alkaline microprotein. The basic defect in hereditary cerebral hemorrhage with amyloidosis . New England Journal of Medicine , 311 : 1547 – 1549 .
   PubMed Web of Science ®Google Scholar
• He , J. , Song , Y. , Ueyama , N. , Harada , A. , Azakami , H. and Kato , A. 2005 . Characterization of recombinant amyloidogenic chicken cystatin mutant I66Q expressed in yeast . Journal of Biochemistry , 137 : 477 – 485 .
   PubMed Web of Science ®Google Scholar
• He , J. , Song , Y. , Ueyama , N. , Saito , A. , Azakami , H. and Kato , A. 2006 . Prevention of amyloid fibril formation of amyloidogenic chicken cystatin by site-specific glycosylation in yeast . Protein Science , 15 : 213 – 222 .
   PubMed Web of Science ®Google Scholar
• Hess , B. , Kutzner , C. , Van Der Spoel , D. and Lindahl , E. 2008 . GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation . Journal of Chemical Theory and Computation , 4 : 435 – 447 .
   PubMed Web of Science ®Google Scholar
• Ivanova , M.I. , Sawaya , M.R. , Gingery , M. , Attinger , A. and Eisenberg , D. 2004 . An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril . Proceedings of National Academy Sciences USA , 101 : 10584 – 10589 .
   PubMed Web of Science ®Google Scholar
• Janowski , R. , Kozak , M. , Jankowska , E. , Grzonka , Z. , Grubb , A. , Abrahamson , M. and Jaskolski , M. 2001 . Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping . Natural Structural Biology , 8 : 316 – 320 .
   PubMedGoogle Scholar
• Jerala , R. and Zerovnik , E. 1999 . Accessing the global minimum conformation of stefin a dimer by annealing under partially denaturing conditions . Journal of Molecular Biology , 291 : 1079 – 1089 .
   PubMed Web of Science ®Google Scholar
• Kabsch , W. and Sander , C. 1983 . Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features . Biopolymers , 22 : 2577 – 2637 .
   PubMed Web of Science ®Google Scholar
• Kaeser , S.A. , Herzig , M.C. , Coomaraswamy , J. , Kilger , E. , Selenica , M.L. , Winkler , D.T. , … and Jucker , M. 2007 . Cystatin C modulates cerebral beta-amyloidosis . Nature Genetics , 39 : 1437 – 1439 .
   PubMed Web of Science ®Google Scholar
• Kato , A. , Tanimoto , S. , Muraki , Y. , Kobayashi , K. and Kumagai , I. 1992 . Structural and functional properties of hen egg-white lysozyme deamidated by protein engineering . Bioscience, Biotechnology, and Biochemistry , 56 : 1424 – 1428 .
   PubMed Web of Science ®Google Scholar
• Kibria , F.M. and Lees , W.J. 2008 . Balancing conformational and oxidative kinetic traps during the folding of bovine pancreatic trypsin inhibitor (BPTI) with glutathione and glutathione disulfide . Journal of the American Chemical Society , 130 : 796 – 797 .
   PubMed Web of Science ®Google Scholar
• Knaus , K.J. , Morillas , M. , Swietnicki , W. , Malone , M. , Surewicz , W.K. and Yee , V.C. 2001 . Crystal structure of the human prion protein reveals a mechanism for oligomerization . Natural Structural Biology , 8 : 770 – 774 .
   PubMedGoogle Scholar
• Kolodziejczyk , R. , Michalska , K. , Hernandez-Santoyo , A. , Wahlbom , M. , Grubb , A. and Jaskolski , M. 2010 . Crystal structure of Human Cystatin C stabilized against amyloid formation . FEBS Journal , 277 : 1726 – 1737 .
   PubMed Web of Science ®Google Scholar
• Mi , W. , Pawlik , M. , Sastre , M. , Jung , S.S. , Radvinsky , D.S. , Klein , A.M. , … and Levy , E. 2007 . Cystatin C inhibits amyloid-beta deposition in Alzheimer’s disease mouse models . Nature Genetics , 39 : 1440 – 1442 .
   PubMed Web of Science ®Google Scholar
• Olafsson , I. and Grubb , A. 2000 . Hereditary cystatin C amyloid angiopathy . Amyloid , 7 : 70 – 79 .
   PubMed Web of Science ®Google Scholar
• Pechmann , S. , Levy , E.D. , Tartaglia , G.G. and Vendruscolo , M. 2009 . Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins . Proceedings of National Academy of Sciences USA , 106 : 10159 – 10164 .
   PubMed Web of Science ®Google Scholar
• Rodziewicz-Motowidlo , S. , Wahlbom , M. , Wang , X. , Lagiewka , J. , Janowski , R. , Jaskolski , M. , … and Grzonka , Z. 2006 . Checking the conformational stability of cystatin C and its L68Q variant by molecular dynamics studies: Why is the L68Q variant amyloidogenic? . Journal of Structural Biology , 154 : 68 – 78 .
   PubMed Web of Science ®Google Scholar
• Sanders , A. , Jeremy Craven , C. , Higgins , L.D. , Giannini , S. , Conroy , M.J. , Hounslow , A.M. , … and Staniforth , R.A. 2004 . Cystatin forms a tetramer through structural rearrangement of domain-swapped dimers prior to amyloidogenesis . Journal of Molecular Biology , 336 : 165 – 178 .
   PubMed Web of Science ®Google Scholar
• Santiveri , C.M. , Leon , E. , Rico , M. and Jimenez , M.A. 2008 . Context-dependence of the contribution of disulfide bonds to beta-hairpin stability . Chemistry , 14 : 488 – 499 .
   PubMed Web of Science ®Google Scholar
• Schagger , H. 2006 . Tricine–SDS-PAGE . Nature Protocols , 1 : 16 – 22 .
   PubMed Web of Science ®Google Scholar
• Schirra , H.J. , Guarino , R.F. , Anderson , M.A. and Craik , D.J. 2010 . Selective removal of individual disulfide bonds within a potato type II serine proteinase inhibitor from Nicotiana alata reveals differential stabilization of the reactive-site loop . Journal of Molecular Biology , 395 : 609 – 626 .
   PubMed Web of Science ®Google Scholar
• Scott , W.R.P. , Hünenberger , P.H. , Tironi , I.G. , Mark , A.E. , Billeter , S.R. , Fennen , J. , … and van Gunsteren , W.F. 1998 . The GROMOS biomolecular simulation program package . Journal of Physical Chemistry A , 103 : 3596 – 3407 .
   Web of Science ®Google Scholar
• Staniforth , R.A. , Giannini , S. , Higgins , L.D. , Conroy , M.J. , Hounslow , A.M. , Jerala , R. , … and Waltho , J.P. 2001 . Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily . EMBO Journal , 20 : 4774 – 4781 .
   PubMed Web of Science ®Google Scholar
• Venkatraman , J. , Nagana Gowda , G.A. and Balaram , P. 2002 . Design and construction of an open multistranded beta-sheet polypeptide stabilized by a disulfide bridge . Journal of the American Chemical Society , 124 : 4987 – 4994 .
   PubMed Web of Science ®Google Scholar
• Wu , D. , Ma , D. , Hao , Y.Y. , Chu , J. , Wang , Y.H. , Zhuang , Y.P. and Zhang , S.L. 2010 . Incomplete formation of intramolecular disulfide bond triggers degradation and aggregation of human consensus interferon-alpha mutant by Pichia pastoris . Applied Microbiology and Biotechnology , 85 : 1759 – 1767 .
   PubMed Web of Science ®Google Scholar
• Yu , Y. , Liu , X. , He , J. , Zhang , M. , Li , H. , Wei , D. and Song , Y. 2012 . Appendant structure plays an important role in amyloidogenic cystatin dimerization prior to domain swapping . Journal of Biomolecular Structure & Dynamics , 30 : 102 – 112 .
   PubMed Web of Science ®Google Scholar
• Yu , Y. , Wang , Y. , He , J. , Liu , Y. , Li , H. , Zhang , H. and Song , Y. 2010 . Structural and dynamic properties of a new amyloidogenic chicken cystatin mutant I108T . Journal of Biomolecular Structure & Dynamics , 27 : 641 – 649 .
   PubMed Web of Science ®Google Scholar
• Zerovnik , E. , Stoka , V. , Mirtic , A. , Guncar , G. , Grdadolnik , J. , Staniforth , R.A. , … and Turk , V. 2011 . Mechanisms of amyloid fibril formation–focus on domain-swapping . FEBS Journal , 278 : 2263 – 2282 .
   PubMed Web of Science ®Google Scholar
• Zhao , J.H. , Liu , H.L. , Liu , Y.F. , Lin , H.Y. , Fang , H.W. , Ho , Y. and Tsai , W.B. 2009 . Molecular dynamics simulations to investigate the aggregation behaviors of the Abeta(17–42) oligomers . Journal of Biomolecular Structure & Dynamics , 26 : 481 – 490 .
   PubMed Web of Science ®Google Scholar