Observation of Solvent Penetration during Cold Denaturation of E. coli Phosphofructokinase-2

Biophysical Journal - Tập 104 - Trang 2254-2263 - 2013
César A. Ramírez-Sarmiento1, Mauricio Baez2, Christian A.M. Wilson1, Jorge Babul1, Elizabeth A. Komives3, Victoria Guixé1
1Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
2Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
3Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California

Tài liệu tham khảo

Matthews, 1993, Pathways of protein folding, Annu. Rev. Biochem., 62, 653, 10.1146/annurev.bi.62.070193.003253 Privalov, 1990, Cold denaturation of proteins, Crit. Rev. Biochem. Mol. Biol., 25, 281, 10.3109/10409239009090612 Privalov, 1986, Cold denaturation of myoglobin, J. Mol. Biol., 190, 487, 10.1016/0022-2836(86)90017-3 Privalov, 1988, Stability of protein structure and hydrophobic interaction, Adv. Protein Chem., 39, 191, 10.1016/S0065-3233(08)60377-0 Damaschun, 1993, Cold denaturation-induced conformational changes in phosphoglycerate kinase from yeast, Biochemistry, 32, 7739, 10.1021/bi00081a019 Richardson, 2000, Difference in the mechanisms of the cold and heat induced unfolding of thioredoxin h from Chlamydomonas reinhardtii: spectroscopic and calorimetric studies, Biochemistry, 39, 11154, 10.1021/bi000610b Adrover, 2010, Understanding cold denaturation: the case study of Yfh1, J. Am. Chem. Soc., 132, 16240, 10.1021/ja1070174 Lopez, 2008, Mechanistic elements of protein cold denaturation, J. Phys. Chem. B, 112, 5961, 10.1021/jp075928t Mandell, 1998, Identification of protein-protein interfaces by decreased amide proton solvent accessibility, Proc. Natl. Acad. Sci. USA, 95, 14705, 10.1073/pnas.95.25.14705 Hughes, 2001, Phosphorylation causes subtle changes in solvent accessibility at the interdomain interface of methylesterase CheB, J. Mol. Biol., 307, 967, 10.1006/jmbi.2001.4523 Truhlar, 2006, Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB, Proc. Natl. Acad. Sci. USA, 103, 18951, 10.1073/pnas.0605794103 Baez, 2012, Expanded monomeric intermediate upon cold and heat unfolding of phosphofructokinase-2 from Escherichia coli, Biophys. J., 103, 2187, 10.1016/j.bpj.2012.09.043 Griko YuV, 1994, Differences in the processes of beta-lactoglobulin cold and heat denaturations, Biophys. J., 67, 356, 10.1016/S0006-3495(94)80488-6 Mizuguchi, 2000, Cold denaturation of alpha-lactalbumin, Proteins, 38, 407, 10.1002/(SICI)1097-0134(20000301)38:4<407::AID-PROT6>3.0.CO;2-# Kunugi, 2002, Cold denaturation of proteins under high pressure, Biochim. Biophys. Acta, 1595, 329, 10.1016/S0167-4838(01)00354-5 Azuaga, 1992, Heat and cold denaturation of beta-lactoglobulin B, FEBS Lett., 309, 258, 10.1016/0014-5793(92)80784-E Chen, 1989, Low-temperature unfolding of a mutant of phage T4 lysozyme. 2. Kinetic investigations, Biochemistry, 28, 691, 10.1021/bi00428a042 Chen, 1989, Low-temperature unfolding of a mutant of phage T4 lysozyme. 1. Equilibrium studies, Biochemistry, 28, 685, 10.1021/bi00428a041 Dias, 2008, Microscopic mechanism for cold denaturation, Phys. Rev. Lett., 100, 118101, 10.1103/PhysRevLett.100.118101 Babul, 1978, Phosphofructokinases from Escherichia coli. Purification and characterization of the nonallosteric isozyme, J. Biol. Chem., 253, 4350, 10.1016/S0021-9258(17)34726-9 Bradford, 1976, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal. Biochem., 72, 248, 10.1016/0003-2697(76)90527-3 Brown, 2006, Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation, Biophys. J., 90, 4651, 10.1529/biophysj.106.081372 Houtman, 2007, Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein complexes in cell signaling, Protein Sci., 16, 30, 10.1110/ps.062558507 Schuck, 2003, On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation, Anal. Biochem., 320, 104, 10.1016/S0003-2697(03)00289-6 Baez, 2009, Reversible unfolding of dimeric phosphofructokinase-2 from Escherichia coli reveals a dominant role of inter-subunit contacts for stability, FEBS Lett., 583, 2054, 10.1016/j.febslet.2009.05.034 Mandell, 1998, Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry, Anal. Chem., 70, 3987, 10.1021/ac980553g Wales, 2008, High-speed and high-resolution UPLC separation at zero degrees Celsius, Anal. Chem., 80, 6815, 10.1021/ac8008862 Bai, 1993, Primary structure effects on peptide group hydrogen exchange, Proteins, 17, 75, 10.1002/prot.340170110 Croy, 2004, Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution, Protein Sci., 13, 1767, 10.1110/ps.04731004 Pometun, 2006, Cold denaturation of encapsulated ubiquitin, J. Am. Chem. Soc., 128, 10652, 10.1021/ja0628654 Luan, 2013, Cooperative cold denaturation: the case of the C-terminal domain of the ribosomal protein L9, Biochemistry, 52, 2402, 10.1021/bi3016789 Li, 2007, The cold denatured state is compact but expands at low temperatures: hydrodynamic properties of the cold denatured state of the C-terminal domain of L9, J. Mol. Biol., 368, 256, 10.1016/j.jmb.2007.02.011 Shan, 2010, The cold denatured state of the C-terminal domain of protein L9 is compact and contains both native and non-native structure, J. Am. Chem. Soc., 132, 4669, 10.1021/ja908104s Romero-Romero, 2011, Highly anomalous energetics of protein cold denaturation linked to folding-unfolding kinetics, PLoS ONE, 6, e23050, 10.1371/journal.pone.0023050 Zhang, 1993, Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation, Protein Sci., 2, 522, 10.1002/pro.5560020404 Engen, 1997, Identification and localization of slow, natural, cooperative unfolding in the hematopoietic cell kinase SH3 domain by amide hydrogen exchange and mass spectrometry, Biochemistry, 36, 14384, 10.1021/bi971635m Engen, 1999, Hydrogen exchange shows peptide binding stabilizes motions in Hck SH2, Biochemistry, 38, 8926, 10.1021/bi982611y Weber, 1993, Thermodynamics of the association and the pressure dissociation of oligomeric proteins, J. Phys. Chem., 97, 7108, 10.1021/j100129a031 Foguel, 1994, Cold denaturation of a repressor-operator complex: the role of entropy in protein-DNA recognition, Proc. Natl. Acad. Sci. USA, 91, 8244, 10.1073/pnas.91.17.8244 Baez, 2011, Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization, FEBS Lett., 585, 2158, 10.1016/j.febslet.2011.05.041 Oshima, 2009, A theoretical analysis on characteristics of protein structures induced by cold denaturation, J. Chem. Phys., 131, 205102, 10.1063/1.3265985 Das, 2012, Direct characterization of hydrophobic hydration during cold and pressure denaturation, J. Phys. Chem. B, 116, 5342, 10.1021/jp211832c Panick, 1998, Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle X-ray scattering and Fourier-transform infrared spectroscopy, J. Mol. Biol., 275, 389, 10.1006/jmbi.1997.1454 Davidovic, 2009, Protein cold denaturation as seen from the solvent, J. Am. Chem. Soc., 131, 1025, 10.1021/ja8056419 Levy, 2006, Water mediation in protein folding and molecular recognition, Annu. Rev. Biophys. Biomol. Struct., 35, 389, 10.1146/annurev.biophys.35.040405.102134 Parducci, 2006, Evidence for a catalytic Mg2+ ion and effect of phosphate on the activity of Escherichia coli phosphofructokinase-2: regulatory properties of a ribokinase family member, Biochemistry, 45, 9291, 10.1021/bi060026o Bork, 1993, Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases, Protein Sci., 2, 31, 10.1002/pro.5560020104