References
- Alkaabi , KM , Yafea , A and Ashraf , SS . 2005 . “Effect of pH on thermal‐and chemical‐induced denaturation of GFP.” . Appl. Biochem. Biotechnol. , 126 : 149 – 156 .
- Andrews , BT , Schoenfish , AR , Roy , M , Waldo , G and Jennings , PA . 2007 . “The rough energy landscape of superfolder GFP is linked to the chromophore.” . J. Mol. Biol. , 373 : 476 – 490 .
- Bai , Y , Milne , JS , Mayne , L and Englander , SW . 1993 . “Primary structure effects on peptide group hydrogen exchange.” . Proteins , 17 : 75 – 86 .
- Bai , Y , Milne , JS , Mayne , L and Englander , SW . 1994 . “Protein stability parameters measured by hydrogen exchange.” . Proteins , 20 : 4 – 14 .
- Bai , Y , Sosnick , TR , Mayne , L and Englander , SW . 1995 . “Protein folding intermediates: native‐state hydrogen exchange.” . Science , 269 : 192 – 197 .
- Bhavesh , NS , Juneja , J , Udgaonkar , JB and Hosur , RV . 2004 . “Native and nonnative conformational preferences in the urea‐unfolded state of barstar.” . Protein Sci. , 13 : 3085 – 3091 .
- Bhavesh , NS , Panchal , SC , Mittal , R and Hosur , RV . 2001 . “NMR identification of local structural preferences in HIV‐1 protease tethered heterodimer in 6 M guanidine hydrochloride.” . FEBS Lett. , 509 : 218 – 224 .
- Bhavesh , NS , Sinha , R , Mohan , PM and Hosur , RV . 2003 . “NMR elucidation of early folding hierarchy in HIV‐1 protease.” . J. Biol. Chem. , 278 : 19980 – 19985 .
- Bhutani , N and Udgaonkar , JB . 2003 . “Folding subdomains of thioredoxin characterized by native‐state hydrogen exchange.” . Protein Sci. , 12 : 1719 – 1731 .
- Bowler , BE . 2007 . “Thermodynamics of protein denatured states.” . Mol. Biosyst. , 3 : 88 – 99 .
- Chamberlain , AK , Handel , TM and Marqusee , S . 1996 . “Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH.” . Nat. Struct. Biol. , 3 : 782 – 787 .
- Chatterjee , A , Mridula , P , Mishra , RK , Mittal , R and Hosur , RV . 2005 . “Folding regulates autoprocessing of HIV‐1 protease precursor.” . J. Biol. Chem. , 280 : 11369 – 11378 .
- Clarke , J and Itzhaki , LS . 1998 . “Hydrogen exchange and protein folding.” . Curr. Opin. Struct. Biol. , 8 : 112 – 118 .
- Clarke , J , Itzhaki , LS and Fersht , AR . 1997 . “Hydrogen exchange at equilibrium: a short cut for analysing protein‐folding pathways?” . Trends Biochem. Sci. , 22 : 284 – 287 .
- Connelly , GP , Bai , Y , Jeng , MF and Englander , SW . 1993 . “Isotope effects in peptide group hydrogen exchange.” . Proteins , 17 : 87 – 92 .
- Delaglio , F , Grzesiek , S , Vuister , GW , Zhu , G , Pfeifer , J and Bax , A . 1995 . “NMRPipe: a multidimensional spectral processing system based on UNIX pipes.” . J. Biomol. NMR , 6 : 277 – 293 .
- Dempsey , CE . 2001 . “Hydrogen exchange in peptides and proteins using NMR‐spectroscopy.” . Prog. Nucl. Magn. Reson. Spectrosc. , 39 : 135 – 170 .
- Dietz , H and Rief , M . 2004 . “Exploring the energy landscape of GFP by single‐molecule mechanical experiments.” . Proc. Natl. Acad. Sci. U.S.A. , 101 : 16192 – 16197 .
- Dyson , HJ and Wright , PE . 2004 . “Unfolded proteins and protein folding studied by NMR.” . Chem. Rev. (Washington, D.C.) , 104 : 3607 – 3622 .
- Englander , SW . 2000 . “Protein folding intermediates and pathways studied by hydrogen exchange.” . Annu. Rev. Biophys. Biomol. Struct. , 29 : 213 – 238 .
- Englander , SW and Kallenbach , NR . 1983 . “Hydrogen‐exchange and structural dynamics of proteins and nucleic‐acids.” . Q. Rev. Biophys. , 16 : 521 – 655 .
- Englander , SW , Mayne , L and Krishna , MMG . 2007 . “Protein folding and misfolding: mechanism and principles.” . Q. Rev. Biophys. , 40 : 287 – 326 .
- Enoki , S , Maki , K , Inobe , T , Takahashi , K , Kamagata , K , Oroguchi , T , Nakatani , H , Tomoyori , K and Kuwajima , K . 2006 . “The equilibrium unfolding intermediate observed at pH 4 and its relationship with the kinetic folding intermediates in green fluorescent protein.” . J. Mol. Biol. , 361 : 969 – 982 .
- Enoki , S , Saeki , K , Maki , K and Kuwajima , K . 2004 . “Acid denaturation and refolding of green fluorescent protein.” . Biophys. J. , 43 : 14238 – 14248 .
- See EPAPS Document No. E‐HJFOA5–2‐001807 for supplemental material. This document can be reached through a direct link in the online article's HTML reference Section or via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html).
- Ferraro , DM , Lazo , ND and Robertson , AD . 2004 . “EX1 hydrogen exchange and protein folding.” . Biophys. J. , 43 : 587 – 594 .
- Fukuda , H , Arai , M and Kuwajima , K . 2000 . “Folding of green fluorescent protein and the cycle3 mutant.” . Biophys. J. , 39 : 12025 – 12032 .
- Grzesiek , S and Bax , A . 1993 . “Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N‐enriched proteins.” . J. Biomol. NMR , 3 : 185 – 204 .
- Helms , V , Straatsma , TP and McCammon , JA . 1999 . “Internal dynamics of green fluorescent protein.” . J. Phys. Chem. B , 103 : 3263 – 3269 .
- Huang , JR , Craggs , TD , Christodoulou , J and Jackson , SE . 2007 . “Stable intermediate states and high energy barriers in the unfolding of GFP.” . J. Mol. Biol. , 370 : 356 – 371 .
- Huyghues‐Despointes , BM , Scholtz , JM and Pace , CN . 1999 . “Protein conformational stabilities can be determined from hydrogen exchange rates.” . Nat. Struct. Biol. , 6 : 910 – 912 .
- Hvidt , A and Nielsen , SO . 1966 . “Hydrogen exchange in proteins.” . Adv. Protein Chem. , 21 : 287 – 386 .
- Iimura , S . 2007 . “Characterization of the denatured structure of pyrrolidone carboxyl peptidase from a hyperthermophile under nondenaturing conditions: role of the C‐terminal alpha‐helix of the protein in folding and stability.” . Biophys. J. , 46 : 3664 – 3672 .
- Jackson , SE , Craggs , TD and Huang , JR . 2006 . “Understanding the folding of GFP using biophysical techniques.” . Expert Rev. Proteomics , 3 : 545 – 559 .
- Johnson , BA and Blevins , RA . 1994 . “NMR view—a computer‐program for the visualization and analysis of NMR data.” . J. Biomol. NMR , 4 : 603 – 614 .
- Karplus , M and McCammon , JA . 1981 . “The internal dynamics of globular proteins.” . Crit. Rev. Biochem. , 9 : 293 – 349 .
- Khan , F , Kuprov , I , Craggs , TD , Hore , PJ and Jackson , SE . 2006 . “(19)F NMR studies of the native and denatured states of green fluorescent protein.” . J. Am. Chem. Soc. , 128 : 10729 – 10737 .
- Klein‐Seetharaman , J . 2002 . “Long‐range interactions within a nonnative protein.” . Science , 295 : 1719 – 1722 .
- Krishna , MM , Hoang , L , Lin , Y and Englander , SW . 2004 . “Hydrogen exchange methods to study protein folding.” . Methods , 34 : 51 – 64 .
- Linderstrom‐Lang , K . 1958 . “Deuterium exchange and protein structure.” . In Symposium of Protein Structure , Edited by: Neuberger , A . 23 – 24 . London : Methuen .
- Mayo , SL and Baldwin , RL . 1993 . “Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A.” . Science , 262 : 873 – 876 .
- Miller , DW and Dill , KA . 1995 . “A statistical mechanical model for hydrogen exchange in globular proteins.” . Methods , 4 : 1860 – 1873 .
- Mohana‐Borges , R , Goto , NK , Kroon , GJ , Dyson , HJ and Wright , PE . 2004 . “Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings.” . J. Mol. Biol. , 340 : 1131 – 1142 .
- Nakanishi , M , Tsuboi , M and Ikegami , A . 1973 . “Fluctuation of the lysozyme structure. II. Effects of temperature and binding of inhibitors.” . J. Mol. Biol. , 75 : 673 – 682 .
- Oliveberg , M and Fersht , AR . 1996 . “Thermodynamics of transient conformations in the folding pathway of barnase: reorganization of the folding intermediate at low pH.” . Biophys. J. , 35 : 2738 – 2749 .
- Ormo , M , Cubitt , AB , Kallio , K , Gross , LA , Tsien , RY and Remington , SJ . 1996 . “Crystal structure of the Aequorea victoria green fluorescent protein.” . Science , 273 : 1392 – 1395 .
- Otting , G , Liepinsh , E and Wuthrich , K . 1991 . “Protein hydration in aqueous solution.” . Science , 254 : 974 – 980 .
- Pace , CN , Laurents , DV and Erickson , RE . 1992 . “Urea denaturation of barnase: pH dependence and characterization of the unfolded state.” . Biophys. J. , 31 : 2728 – 2734 .
- Palmer , AG , Cavanagh , J , Wright , PE and Rance , M . 1991 . “Sensitivity improvement in proton‐detected 2‐dimensional heteronuclear correlation NMR‐spectroscopy.” . J. Mater. Res. , 93 : 151 – 170 .
- Reid , BG and Flynn , GC . 1997 . “Chromophore formation in green fluorescent protein.” . Biophys. J. , 36 : 6786 – 6791 .
- Religa , TL , Markson , JS , Mayor , U , Freund , SM and Fersht , AR . 2005 . “Solution structure of a protein denatured state and folding intermediate.” . Nature (London) , 437 : 1053 – 1056 .
- Robic , S , Guzman‐Casado , M , Sanchez‐Ruiz , JM and Marqusee , S . 2003 . “Role of residual structure in the unfolded state of a thermophilic protein.” . Proc. Natl. Acad. Sci. U.S.A. , 100 : 11345 – 11349 .
- Schanda , P and Brutscher , B . 2005 . “Very fast two‐dimensional NMR spectroscopy for real‐time investigation of dynamic events in proteins on the time scale of seconds.” . J. Am. Chem. Soc. , 127 : 8014 – 8015 .
- Schleucher , J , Schwendinger , M , Sattler , M , Schmidt , P , Schedletzky , O , Glaser , SJ , Sorensen , OW and Griesinger , C . 1994 . “A general enhancement scheme in heteronuclear multidimensional NMR employing pulsed field gradients.” . J. Biomol. NMR , 4 : 301 – 306 .
- Seifert , MH , Georgescu , J , Ksiazek , D , Smialowski , P , Rehm , T , Steipe , B and Holak , TA . 2003 . “Backbone dynamics of green fluorescent protein and the effect of histidine 148 substitution.” . Biophys. J. , 42 : 2500 – 2512 .
- Shortle , D and Ackerman , MS . 2001 . “Persistence of native‐like topology in a denatured protein in 8 M urea.” . Science , 293 : 487 – 489 .
- Shortle , D , Chan , HS and Dill , KA . 1992 . “Modeling the effects of mutations on the denatured states of proteins.” . Protein Sci. , 1 : 201 – 215 .
- Takei , J , Pei , W , Vu , D and Bai , Y . 2002 . “Populating partially unfolded forms by hydrogen exchange‐directed protein engineering.” . Biophys. J. , 41 : 12308 – 12312 .
- Tsien , RY . 1998 . “The green fluorescent protein.” . Annu. Rev. Biochem. , 67 : 509 – 544 .
- Wagner , G and Wuthrich , K . 1982 . “Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution.” . J. Mol. Biol. , 160 : 343 – 361 .
- Wirmer , J , Schlorb , C , Klein‐Seetharaman , J , Hirano , R , Ueda , T , Imoto , T and Schwalbe , H . 2004 . “Modulation of compactness and long‐range interactions of unfolded lysozyme by single point mutations.” . Angew. Chem., Int. Ed. , 43 : 5780 – 5785 .
- Woodward , C , Simon , I and Tuchsen , E . 1982 . “Hydrogen exchange and the dynamic structure of proteins.” . Mol. Cell. Biochem. , 48 : 135 – 160 .
- Yan , S , Kennedy , SD and Koide , S . 2002 . “Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native‐state hydrogen exchange.” . J. Mol. Biol. , 323 : 363 – 375 .
- Yang , F , Moss , LG and Phillips , GN Jr. 1996 . “The molecular structure of green fluorescent protein.” . Nat. Biotechnol. , 14 : 1246 – 1251 .
- Zhang , X , Xu , Y , Zhang , J , Wu , J and Shi , Y . 2005 . “Structural and dynamic characterization of the acid‐unfolded state of hUBF HMG box 1 provides clues for the early events in protein folding.” . Biophys. J. , 44 : 8117 – 8125 .
- Zhang , Y‐Z and Roder , H . “SPHERE: a server program for hydrogen exchange rate estimation.” Zimmer, M 2002 “Green fluorescent protein (GFP): applications structure, and related photophysical behavior.” . Chem. Rev. (Washington, D.C.) , 102 759 – 781 .