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Research Article

Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability

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Pages 867-873 | Received 01 Aug 2014, Accepted 15 Oct 2014, Published online: 03 Feb 2015

References

  • Dufton MJ. Could domain movements be involved in the mechanism of trypsin-like serine proteases? FEBS Lett 1990;271:9–13
  • Dror RO, Green HF, Valant C, et al. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature 2013;503:295–9
  • Atilgan C, Atilgan AR. Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Comput Biol 2009;5: e1000544
  • Atilgan C, Gerek ZN, Ozkan SB, Atilgan AR. Manipulation of conformational change in proteins by single-residue perturbations. Biophys J 2010;99:933–43
  • Ikeguchi M, Ueno J, Sato M, Kidera A. Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 2005;94:078102
  • Klibanov AM. Improving enzymes by using them in organic solvents. Nature 2001;409:241–6
  • Atilgan AR, Aykut AO, Atilgan C. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J Chem Phys 2011;135:155102
  • Price ES, DeVore MS, Johnson CK. Detecting intramolecular dynamics and multiple forster resonance energy transfer states by fluorescence correlation spectroscopy. J Phys Chem B 2010;114:5895–902
  • Aykut AO, Atilgan AR, Atilgan C. Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin. PLoS Comput Biol 2013;9:e1003366
  • Negi S, Aykut AO, Atilgan AR, Atilgan C. Calmodulin readily switches conformation upon protonating high pK(a) acidic residues. J Phys Chem B 2012;116:7145–53
  • Bolia A, Gerek ZN, Ozkan SB. BP-Dock: a flexible docking scheme for exploring protein ligand interactions based on unbound structures. J Chem Inform Model 2014;54:913–25
  • Döring K, Surrey T, Nollert P, Jähnig F. Effects of ligand binding on the internal dynamics of maltose-binding protein. Eur J Biochem 1999;266:477–83
  • Plunkett G, Senear DF, Zuroske G, Ryan CA. Proteinase inhibitors I and II from leaves of wounded tomato plants: purification and properties. Arch Biochem Biophys 1982;213:463–72
  • Pagán M, Solá RJ, Griebenow K. On the role of protein structural dynamics in the catalytic activity and thermostability of serine protease subtilisin Carlsberg. Biotechnol Bioeng 2009;103:77–84
  • Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW. Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteinases. Protein Eng 1991;4:719–37
  • Bontemps Y, Scamuffa N, Calvo F, Khatib AM. Potential opportunity in the development of new therapeutic agents based on endogenous and exogenous inhibitors of the proprotein convertases. Med Res Rev 2007;27:631–48
  • Braxton S, Wells JA. Incorporation of a stabilizing calcium-binding loop into subtilisin BPN'. Biochemistry 1992;31:7796–801
  • Bryan P, Pantoliano MW, Quill SG, et al. Site-directed mutagenesis and the role of the oxyanion hole in subtilisin. Proc Natl Acad Sci USA 1986;83:3743–5
  • Santos AM, Clemente IM, Barletta G, Griebenow K. Activation of serine protease subtilisin Carlsberg in organic solvents: combined effect of methyl-β-cyclodextrin and water. Biotechnol Lett 1999;21:1113–8
  • Chen K, Arnold FH. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc Natl Acad Sci USA 1993;90:5618–22
  • Atilgan AR, Atilgan C. Local motifs in proteins combine to generate global functional moves. Brief Funct Genomics 2012;11:479–88
  • Atilgan C, Okan OB, Atilgan AR. Network-based models as tools hinting at nonevident protein functionality. Annu Rev Biophys 2012;41:205–25
  • Barrette-Ng IH, Ng KK-S, Cherney MM, et al. Structural basis of inhibition revealed by a 1:2 complex of the two-headed tomato inhibitor-II and subtilisin Carlsberg. J Biol Chem 2003;278:24062–71
  • Barrette-Ng IH, Ng KK-S, Cherney MM, et al. Unbound form of tomato inhibitor-II reveals interdomain flexibility and conformational variability in the reactive site loops. J Biol Chem 2003;278:31391–400
  • Richardson M. The proteinase inhibitors of plants and micro-organisms. Phytochemistry 1977;16:159–69
  • Yilmaz LS, Atilgan AR. Identifying the adaptive mechanism in globular proteins: fluctuations in densely packed regions manipulate flexible parts. J Chem Phys 2000;113:4454–64
  • Atilgan AR, Durell SR, Jernigan RL, et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001;80:505–15
  • Ben-Avraham D. Vibrational normal-mode spectrum of globular proteins. Phys Rev B 1993;47:14559–60
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33–8
  • Brooks BR, Bruccoleri RE, Olafson BD, et al. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187–217
  • Buck M, Bouguet-Bonnet S, Pastor RW, MacKerell Jr AD. Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J 2006;90:L36–8
  • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781–802
  • Darden T, Perera L, Li LP, Pedersen L. New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure 1999;7:R55–60
  • Pereira PJB, Lozanov V, Patthy A, et al. Specific inhibition of insect α-amylases: yellow meal worm α-amylase in complex with the Amaranth α-amylase inhibitor at 2.0 Å resolution. Structure 1999;7:1079–88
  • Neidhart DJ, Petsko GA. The refined crystal structure of subtilisin Carlsberg at 2.5 Å resolution. Protein Eng 1988;2:271–6
  • Hedstrom L. Serine protease mechanism and specificity. Chem Rev 2002;102:4501–24
  • Atilgan C, Okan OB, Atilgan AR. How orientational order governs collectivity of folded proteins. Proteins Struct FunctBioinform 2010;78:3363–75
  • Zhao HM, Arnold FH. Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng 1999;12:47–53
  • Strausberg SL, Ruan B, Fisher KE, et al. Directed coevolution of stability and catalytic activity in calcium-free subtilisin. Biochemistry 2005;44:3272–9
  • Celniker G, Nimrod G, Ashkenazy H, et al. ConSurf: using evolutionary data to raise testable hypotheses about protein function. Israel J Chem 2013;53:199–206
  • Rao SN, Singh UC, Bash PA, Kollman PA. Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin. Nature 1987;328:551–4
  • Solá RJ, Rodríguez-Martínez JA, Griebenow K. Modulation of protein biophysical properties by chemical glycosylation: biochemical insights and biomedical implications. Cell Mol Life Sci 2007;64:2133–52

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