Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Bio-Algorithms and Med-Systems

Editor-in-Chief: Roterman-Konieczna , Irena

CiteScore 2018: 0.29

SCImago Journal Rank (SJR) 2018: 0.129
Source Normalized Impact per Paper (SNIP) 2018: 0.324

See all formats and pricing
More options …

Fast closure of long loops at the initiation of the folding transition of globular proteins studied by time-resolved FRET-based methods

Tomer Orevi / Gil Rahamim / Sivan Shemesh / Eldad Ben Ishay / Dan Amir / Elisha Haas
Published Online: 2014-11-27 | DOI: https://doi.org/10.1515/bams-2014-0018


The protein folding problem would be considered “solved” when it will be possible to “read genes”, i.e., to predict the native fold of proteins, their dynamics, and the mechanism of fast folding based solely on sequence data. The long-term goal should be the creation of an algorithm that would simulate the stepwise mechanism of folding, which constrains the conformational space and in which random search for stable interactions is possible. Here, we focus attention on the initial phases of the folding transition starting with the compact disordered collapsed ensemble, in search of the initial sub-domain structural biases that direct the otherwise stochastic dynamics of the backbone. Our studies are designed to test the “loop hypothesis”, which suggests that fast closure of long loop structures by non-local interactions between clusters of mainly non-polar residues is an essential conformational step at the initiation of the folding transition of globular proteins. We developed and applied experimental methods based on time-resolved resonance excitation energy transfer (trFRET) measurements combined with fast mixing methods and studied the initial phases of the folding of Escherichia coli adenylate kinase (AK). A series of AK mutants were prepared, in which the ends of selected backbone segments that form long closed loops or secondary structure elements were labeled by donors and acceptors of excitation energy. The end-to-end distance distributions of such segments were determined under equilibrium and during the fast folding transitions. These experiments show that three out of seven long loops that were labeled in the AK molecule are closed very early in the transition. The N terminal 26-residue loop (loop I) is closed in <200 μs after the initiation of folding, while the β strand included in loop I is still disordered. The closure of the second 44-residue loop (loop II, which starts at the end of loop I) is also complete within <300 μs. Four other loops as well as five secondary structures of the CORE domain of AK (an α helix and four β strands) are formed at a late step, at a rate of 0.5±0.3 s–1, the rate of the cooperative folding of the molecule. These experiments reveal a hierarchically ordered pathway of folding of the AK molecule, ranging from microseconds to seconds. The results reviewed here, obtained mainly from studying a small number of model proteins, support the counterintuitive mechanism whereby non-local interactions are effective in the initiation of the folding pathways. The experiments presented demonstrate the importance of mapping the rates of sub-domain structural transitions along the folding transition, in situ, in the context of the other sections of the chain, whether folded or disordered. These experiments also show the power of the time-resolved FRET measurements in achieving this goal. A large body of data obtained by theoretical and experimental studies that support, or can accommodate, the loop hypothesis is reviewed. We suggest that mapping multiple sub-domain structural transitions during the refolding transition of many proteins using the approach presented here will refine the conclusions and help reveal some common principles of the initiation of the folding. To achieve this goal, the trFRET measurements should be combined with mutagenesis experiments where the role of selected residue clusters will be tested by perturbation mutations. Nevertheless, the solution of the protein folding problem depends on the application of many additional approaches, both experimental and theoretical, while the approach presented here is only a small section of the big puzzle.

Keywords: FRET; globular proteins; long loops; loop closure; protein folding


  • 1.

    Anfinsen CB, Haber E, Sela M, White FH, Jr. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci USA 1961;47:1309–14.CrossrefGoogle Scholar

  • 2.

    Anfinsen CB. Principles that govern folding of protein chains. Science 1973;181:223–30.Google Scholar

  • 3.

    Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Optimal protein-folding codes from spin-glass theory. Proc Natl Acad Sci USA 1992;89:4918–22.CrossrefGoogle Scholar

  • 4.

    Shakhnovich EI, Gutin AM. A new approach to the design of stable proteins. Protein Eng 1993;6:793–800.CrossrefGoogle Scholar

  • 5.

    Shakhnovich EI, Gutin AM. Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA 1993;90:7195–9.CrossrefGoogle Scholar

  • 6.

    Anfinsen CB, Scheraga HA. Experimental and theoretical aspects of protein folding. Adv Protein Chem 1975;29:205–300.CrossrefGoogle Scholar

  • 7.

    Shakhnovich EI. Proteins with selected sequences fold into unique native conformation. Phys Rev Lett 1994;72:3907–10.CrossrefGoogle Scholar

  • 8.

    Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature 1994;369:248–51.Google Scholar

  • 9.

    Ptitsyn OB. Stages in the mechanism of self-organization of protein molecules. Dokl Akad Nauk SSSR 1973;210:1213–5.Google Scholar

  • 10.

    Shortle D, Meeker AK. Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry 1989;28:936–44.CrossrefGoogle Scholar

  • 11.

    Kim PS, Baldwin RL. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 1982;51:459–89.CrossrefGoogle Scholar

  • 12.

    Karplus M, Weaver DL. Protein-folding dynamics. Nature 1976;260:404–6.Google Scholar

  • 13.

    Sosnick TR, Mayne L, Hiller R, Englander SW. The barriers in protein folding. Nat Struct Biol 1994;1:149–56.CrossrefGoogle Scholar

  • 14.

    Krantz BA, Mayne L, Rumbley J, Englander SW, Sosnick TR. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol 2002;324:359–71.Google Scholar

  • 15.

    Ionescu RM, Matthews CR. Folding under the influence. Nat Struct Biol 1999;6:304–7.Google Scholar

  • 16.

    Sosnick TR, Barrick, D. The folding of single domain proteins— have we reached a consensus? Curr Opin Struct Biol 2011;21:12–24.CrossrefGoogle Scholar

  • 17.

    Govindarajan S, Goldstein RA. The foldability landscape of model proteins. Biopolymers 1997;42:427–38.CrossrefGoogle Scholar

  • 18.

    Sosnick TR, Krantz BA, Dothager RS, Baxa M. Characterizing the protein folding transition state using psi analysis. Chem Rev 2006;106:1862–76.CrossrefGoogle Scholar

  • 19.

    Uversky VN, Narizhneva NV, Ivanova TV, Tomashevski AY. Rigidity of human alpha-fetoprotein tertiary structure is under ligand control. Biochemistry 1997;36:13638–45.CrossrefGoogle Scholar

  • 20.

    Mason JM, Bendall DS, Howe CJ, Worrall JA. The role of a disulfide bridge in the stability and folding kinetics of Arabidopsis thaliana cytochrome c(6A). Biochim Biophys Acta 2012;1824:311–8.Google Scholar

  • 21.

    Berezovsky IN, Trifonov EN. Loop fold nature of globular proteins. Protein Eng 2001;14:403–7.CrossrefGoogle Scholar

  • 22.

    Berezovsky IN, Trifonov EN. Van der Waals locks: loop-n-lock structure of globular proteins. J Molec Biol 2001;307:1419–26.Google Scholar

  • 23.

    Hubner IA, Edmonds KA, Shakhnovich EI. Nucleation and the transition state of the SH3 domain. J Mol Biol 2005;349:424–34.Google Scholar

  • 24.

    Lindorff-Larsen K, Vendruscolo M, Paci E, Dobson CM. Transition states for protein folding have native topologies despite high structural variability. Nat Struct Mol Biol 2004;11:443–9.CrossrefGoogle Scholar

  • 25.

    Lindorff-Larsen K, Rogen P, Paci E, Vendruscolo M, Dobson CM. Protein folding and the organization of the protein topology universe. Trends Biochem Sci 2005;30:13–9.CrossrefGoogle Scholar

  • 26.

    Paci E, Clarke J, Steward A, Vendruscolo M, Karplus M. Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain. Proc Natl Acad Sci USA 2003;100:394–9.CrossrefGoogle Scholar

  • 27.

    Geierhaas CD, Paci E, Vendruscolo M, Clarke J. Comparison of the transition states for folding of two Ig-like proteins from different superfamilies. J Mol Biol 2004;343:1111–23.Google Scholar

  • 28.

    Lappalainen I, Hurley MG, Clarke J. Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain. J Mol Biol 2008;375:547–59.Google Scholar

  • 29.

    Sosnick TR, Dothager RS, Krantz BA. Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc Natl Acad Sci USA 2004;101:17377–82.CrossrefGoogle Scholar

  • 30.

    Krantz BA, Dothager RS, Sosnick TR. Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J Mol Biol 2004;337:463–75.Google Scholar

  • 31.

    Tsong TY, Hu CK, Wu MC. Hydrophobic condensation and modular assembly model of protein folding. Biosystems 2008;93:78–89.CrossrefGoogle Scholar

  • 32.

    Fulton KF, Main ER, Daggett V, Jackson SE. Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J Mol Biol 1999;291:445–61.Google Scholar

  • 33.

    Samatova EN, Katina NS, Balobanov VA, Melnik BS, Dolgikh DA, Bychkova VE, et al. How strong are side chain interactions in the folding intermediate? Protein Sci 2009;18:2152–9.CrossrefGoogle Scholar

  • 34.

    Rader AJ, Yennamalli RM, Harter AK, Sen TZ. A rigid network of long-range contacts increases thermostability in a mutant endoglucanase. J Biomol Struct Dyn 2012;30:628–37.CrossrefGoogle Scholar

  • 35.

    Go N, Taketomi H. Respective roles of short- and long-range interactions in protein folding. Proc Natl Acad Sci USA 1978;75:559–63.CrossrefGoogle Scholar

  • 36.

    Taketomi H, Ueda Y, Go N. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 1975;7:445–59.Google Scholar

  • 37.

    Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 1995;252:460–71.Google Scholar

  • 38.

    Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Identifying the protein folding nucleus using molecular dynamics. J Mol Biol 2000;296:1183–8.Google Scholar

  • 39.

    Hubner IA, Oliveberg M, Shakhnovich EI. Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc Natl Acad Sci USA 2004;101:8354–9.Google Scholar

  • 40.

    Hubner IA, Shimada J, Shakhnovich EI. Commitment and nucleation in the protein G transition state. J Mol Biol 2004;336: 745–61.Google Scholar

  • 41.

    Abkevich VI, Gutin AM, Shakhnovich EI. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 1994;33:10026–36.CrossrefGoogle Scholar

  • 42.

    Juraszek J, Bolhuis PG. Sampling the multiple folding mechanisms of Trp-cage in explicit solvent. Proc Natl Acad Sci USA 2006;103:15859–64.CrossrefGoogle Scholar

  • 43.

    Zhang Z, Chan HS. Transition paths, diffusive processes, and preequilibria of protein folding. Proc Natl Acad Sci USA 2013;109:20919–24.Google Scholar

  • 44.

    Papandreou N, Berezovsky IN, Lopes A, Eliopoulos E, Chomilier J. Universal positions in globular proteins. Eur J Biochem 2004;271:4762–8.Google Scholar

  • 45.

    Lonquety M, Chomilier J, Papandreou N, Lacroix, Z. Prediction of stability upon point mutation in the context of the folding nucleus. OMICS 2010;14:151–6.CrossrefGoogle Scholar

  • 46.

    Prudhomme N, Chomilier J. Prediction of the protein folding core: application to the immunoglobulin fold. Biochimie 2009;91:1465–74.CrossrefGoogle Scholar

  • 47.

    Lonquety M, Chomilier J, Papandreou N, Lacroix Z. Prediction of stability upon point mutation in the context of the folding nucleus. OMICS 2009;14:151–6.Google Scholar

  • 48.

    Lonquety M, Lacroix Z, Chomilier J. Evaluation of the stability of folding nucleus upon mutation. In: Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics. Melbourne, Australia: Springer-Verlag, 2008:54–65.Google Scholar

  • 49.

    Peter EK, Shea JE. A hybrid MD-kMC algorithm for folding proteins in explicit solvent. Phys Chem Chem Phys 2014;16:6430–40.CrossrefGoogle Scholar

  • 50.

    Harrison SC, Durbin R. Is there a single pathway for the folding of a polypeptide chain? Proc Natl Acad Sci USA 1985;82:4028–30.CrossrefGoogle Scholar

  • 51.

    Rooman MJ, Kocher JP, Wodak SJ. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry 1992;31:10226–38.CrossrefGoogle Scholar

  • 52.

    Wright PE, Dyson HJ, Lerner RA. Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry 1988;27:7167–75.CrossrefGoogle Scholar

  • 53.

    Dill KA, Fiebig KM, Chan HS. Cooperativity in protein-folding kinetics. Proc Natl Acad Sci USA 1993;90:1942–6.CrossrefGoogle Scholar

  • 54.

    Weikl TR, Dill KA. Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol 2003;329:585–98.Google Scholar

  • 55.

    Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 1973;70:697–701.CrossrefGoogle Scholar

  • 56.

    Kihara D. The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci 2005;14:1955–63.CrossrefGoogle Scholar

  • 57.

    Daggett V, Fersht AR. Is there a unifying mechanism for protein folding? Trends Biochem Sci 2003;28:18–25.CrossrefGoogle Scholar

  • 58.

    Gilis D, Rooman M. Identification and ab initio simulations of early folding units in proteins. Proteins-Structure Function and Bioinformatics 2001;42:164–76.Google Scholar

  • 59.

    Aurora R, Creamer TP, Srinivasan R, Rose GD. Local interactions in protein folding: lessons from the alpha-helix. J Biol Chem 1997;272:1413–6.Google Scholar

  • 60.

    Baldwin RL, Rose GD. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem Sci 1999;24:77–83.CrossrefGoogle Scholar

  • 61.

    Baldwin RL, Rose GD. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 1999;24:26–33.CrossrefGoogle Scholar

  • 62.

    Dadlez M. Folding initiation sites and protein folding. Acta Biochim Pol 1999;46:487–508.Google Scholar

  • 63.

    Skwierawska A, Rodziewicz-Motowidlo S, Oldziej S, Liwo A, Scheraga HA. Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Biopolymers 2008;89:1032–44.CrossrefGoogle Scholar

  • 64.

    Simon I, Glasser L, Scheraga HA. Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1991;88:3661–5.CrossrefGoogle Scholar

  • 65.

    Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209–25.Google Scholar

  • 66.

    Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992;226:507–33.Google Scholar

  • 67.

    Bowie JU, Eisenberg D. An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 1994;91:4436–40.CrossrefGoogle Scholar

  • 68.

    Lee J, Liwo A, Scheraga HA. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10–55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci USA 1999;96:2025–30.CrossrefGoogle Scholar

  • 69.

    Chikenji G, Fujitsuka Y, Takada S. Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc Natl Acad Sci USA 2006;103:3141–6.CrossrefGoogle Scholar

  • 70.

    Haspel N, Tsai CJ, Wolfson H, Nussinov R. Reducing the computational complexity of protein folding via fragment folding and assembly. Protein Sci 2003;12:1177–87.CrossrefGoogle Scholar

  • 71.

    Haspel N, Tsai CJ, Wolfson H, Nussinov R. Hierarchical protein folding pathways: a computational study of protein fragments. Proteins 2003;51:203–15.CrossrefGoogle Scholar

  • 72.

    Ozkan SB, Wu GA, Chodera JD, Dill KA. Protein folding by zipping and assembly. Proc Natl Acad Sci USA 2007;104:11987–92.CrossrefGoogle Scholar

  • 73.

    Dill KA, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annu Rev Biophys 2008;37:289–316.CrossrefGoogle Scholar

  • 74.

    Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA. Blind test of physics-based prediction of protein structures. Biophys J 2009;96:917–24.CrossrefGoogle Scholar

  • 75.

    Fersht AR, Daggett V. Protein folding and unfolding at atomic resolution. Cell 2002;108:573–82.CrossrefGoogle Scholar

  • 76.

    Cavagnero S, Dyson HJ, Wright PE. Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin. J Molec Biol 1999;285:269–82.Google Scholar

  • 77.

    Cavagnero S, Nishimura C, Schwarzinger S, Dyson HJ, Wright PE. Conformational and dynamic characterization of the molten globule state of an apomyoglobin mutant with an altered folding pathway. Biochemistry 2001;40:14459–67.CrossrefGoogle Scholar

  • 78.

    Gulotta M, Gilmanshin R, Buscher TC, Callender RH, Dyer RB. Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape. Biochemistry 2001;40:5137–43.CrossrefGoogle Scholar

  • 79.

    Kay MS, Ramos CH, Baldwin RL. Specificity of native-like interhelical hydrophobic contacts in the apomyoglobin intermediate. Proc Natl Acad Sci USA 1999;96:2007–12.CrossrefGoogle Scholar

  • 80.

    Felitsky DJ, Lietzow MA, Dyson HJ, Wright PE. Modeling transient collapsed states of an unfolded protein to provide insights into early folding events. Proc Natl Acad Sci USA 2008;105:6278–83.CrossrefGoogle Scholar

  • 81.

    Martinez JC, Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol 1999;6:1010–6.Google Scholar

  • 82.

    Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 1999;6:1016–24.Google Scholar

  • 83.

    Northey JG, Di Nardo AA, Davidson AR. Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Biol 2002;9:126–30.CrossrefGoogle Scholar

  • 84.

    Northey JG, Maxwell KL, Davidson AR. Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J Molec Biol 2002;320:389–402.Google Scholar

  • 85.

    Dasgupta A, Udgaonkar JB. Evidence for initial non-specific polypeptide chain collapse during the refolding of the SH3 domain of PI3 kinase. J Molec Biol 2010;403:430–45.Google Scholar

  • 86.

    Zarrine-Afsar A, Dahesh S, Davidson AR. Protein folding kinetics provides a context-independent assessment of beta-strand propensity in the Fyn SH3 domain. J Molec Biol 2007;373:764–74.Google Scholar

  • 87.

    Demarest SJ, Horng JC, Raleigh DP. A protein dissection study demonstrates that two specific hydrophobic clusters play a key role in stabilizing the core structure of the molten globule state of human alpha-lactalbumin. Proteins 2001;42:237–42.CrossrefGoogle Scholar

  • 88.

    Demarest SJ, Boice JA, Fairman R, Raleigh DP. Defining the core structure of the alpha-lactalbumin molten globule state. J Molec Biol 1999;294:213–21.Google Scholar

  • 89.

    Knowling S, Bartlett AI, Radford SE. Dissecting key residues in folding and stability of the bacterial immunity protein 2011;7. Protein Eng Des Sel 24:517–23.CrossrefGoogle Scholar

  • 90.

    Knowling SE, Figueiredo AM, Whittaker SB, Moore GR, Radford SE. Amino acid insertion reveals a necessary three-helical intermediate in the folding pathway of the colicin E7 immunity protein Im7. J Molec Biol 2009;392:1074–86.Google Scholar

  • 91.

    O’Neill JC, Jr., Robert Matthews C. Localized, stereochemically sensitive hydrophobic packing in an early folding intermediate of dihydrofolate reductase from Escherichia coli. J Molec Biol 2000;295:737–44.Google Scholar

  • 92.

    Niggemann M, Steipe B. Exploring local and non-local interactions for protein stability by structural motif engineering. J Molec Biol 2000;296:181–95.Google Scholar

  • 93.

    Bolen DW, Rose GD. Structure and energetics of the hydrogen-bonded backbone in protein folding. Annu Rev Biochem 2008;77:339–62.CrossrefGoogle Scholar

  • 94.

    Teufel DP, Johnson CM, Lum JK, Neuweiler H. Backbone-driven collapse in unfolded protein chains. J Mol Biol 2011;409: 250–62.Google Scholar

  • 95.

    Finkelstein AV, Shakhnovich EI. Theory of cooperative transitions in protein molecules: II. Phase diagram for a protein molecule in solution. Biopolymers 1989;28:1681–94.CrossrefGoogle Scholar

  • 96.

    Ziv G, Thirumalai D, Haran G. Collapse transition in proteins. Phys Chem Chem Phys 2009;11:83–93.CrossrefGoogle Scholar

  • 97.

    Haran G. How, when and why proteins collapse: the relation to folding. Curr Opin Struct Biol 2012;22:14–20.CrossrefGoogle Scholar

  • 98.

    Ben-Naim A. Myths and verities in protein folding theories: from Frank and Evans iceberg-conjecture to explanation of the hydrophobic effect. J Chem Phys 2014;139:165105.Google Scholar

  • 99.

    Udgaonkar JB. Polypeptide chain collapse and protein folding. Arch Biochem Biophys 2013;531:24–33.Google Scholar

  • 100.

    Amir D, Haas E. Estimation of intramolecular distance distributions in bovine pancreatic trypsin inhibitor by site-specific labeling and nonradiative excitation energy-transfer measurements. Biochemistry 1987;26:2162–75.CrossrefGoogle Scholar

  • 101.

    Haas E, Katchalski-Katzir E, Steinberg IZ. Brownian motion of the ends of oligopeptide chains in solution as estimated by energy transfer between the chain ends. Biopolymers 1978;17:11–31.CrossrefGoogle Scholar

  • 102.

    Haas E. Fluorescence resonance energy transfer (FRET) and single molecule fluorescence detection studies of the mechanism of protein folding and unfolding. In: Kiefhaber JB (editor). Protein folding handbook. Weinheim, Germany: Wiley-VCH, 2004: 573–633.Google Scholar

  • 103.

    Bilsel O, Matthews CR. Molecular dimensions and their distributions in early folding intermediates. Curr Opin Struct Biol 2006;16:86–93.CrossrefGoogle Scholar

  • 104.

    Wu P, Brand L. Conformational flexibility in a staphylococcal nuclease mutant K45C from time-resolved resonance energy transfer measurements. Biochemistry 1994;33:10457–62.CrossrefGoogle Scholar

  • 105.

    Sinha KK, Udgaonkar JB. Dependence of the size of the initially collapsed form during the refolding of barstar on denaturant concentration: Evidence for a continuous transition. J Molec Biol 2005;353:704–18.Google Scholar

  • 106.

    Orevi T, Lerner E, Rahamim G, Amir D, Haas E. Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics. Methods Mol Biol 2014;1076:113–69.Google Scholar

  • 107.

    Haas E. The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. Chemphyschem 2005;6:858–70.CrossrefGoogle Scholar

  • 108.

    Beechem JM, Haas E. Simultaneous determination of intramolecular distance distributions and conformational dynamics by global analysis of energy transfer measurements. Biophys J 1989;55:1225–36.CrossrefGoogle Scholar

  • 109.

    Ratner V, Sinev M, Haas E. Determination of intramolecular distance distribution during protein folding on the millisecond timescale. J Mol Biol 2000;299:1363–71.Google Scholar

  • 110.

    Ratner V, Amir D, Kahana E, Haas E. Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase. J Mol Biol 2005;352:683–99.CrossrefGoogle Scholar

  • 111.

    Ben Ishay E, Rahamim G, Orevi T, Hazan G, Amir D, Haas E. Fast subdomain folding prior to the global refolding transition of E. coli adenylate kinase: a double kinetics study. J Mol Biol 2012;423:613–23.Google Scholar

  • 112.

    Bilsel O, Kayatekin C, Wallace LA, Matthews CR. A microchannel solution mixer for studying microsecond protein folding reactions. Rev Sci Instrum 2005;76:014302-1–7.CrossrefGoogle Scholar

  • 113.

    Ben Ishay E, Hazan G, Rahamim G, Amir D, Haas E. An instrument for fast acquisition of fluorescence decay curves at picosecond resolution designed for “double kinetics” experiments: Application to FRET study of protein folding Rev Sci Instrum 2012;83:084301.CrossrefGoogle Scholar

  • 114.

    Ratner V, Haas E. An instrument for time resolved monitoring of fast chemical transitions: application to the kinetics of refolding of a globular protein. Rev Sci Instrum 1998;69:2147–54.CrossrefGoogle Scholar

  • 115.

    Teilum K, Maki K, Kragelund BB, Poulsen FM, Roder H. Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing. Proc Natl Acad Sci USA 2002;99:9807–12.CrossrefGoogle Scholar

  • 116.

    Welker E, Maki K, Shastry MC, Juminaga D, Bhat R, Scheraga HA, et al. Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A. Proc Natl Acad Sci USA 2004;101:17681–6.CrossrefGoogle Scholar

  • 117.

    Kathuria SV, Guo L, Graceffa R, Barrea R, Nobrega RP, Matthews CR, et al. Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering. Biopolymers 2011;95:550–8.CrossrefGoogle Scholar

  • 118.

    Huber R, Kukla D, Bode W, Schwager P, Bartels K, Deisenhofer J, et al. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor: II. Crystallographic refinement at 1.9 A resolution. J Molec Biol 1974;89:73–101.Google Scholar

  • 119.

    Ittah V, Haas E. Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. Biochemistry 1995;34:4493–506.CrossrefGoogle Scholar

  • 120.

    Eaton WA, Munoz V, Hagen SJ, Jas GS, Lapidus LJ, Henry ER, et al. Fast kinetics and mechanisms in protein folding. Annu Rev Biophys Biomol Struct 2000;29:327–59.CrossrefGoogle Scholar

  • 121.

    Lapidus LJ, Eaton WA, Hofrichter J. Measuring the rate of intramolecular contact formation in polypeptides. Proc Natl Acad Sci USA 2000;97:7220–5.CrossrefGoogle Scholar

  • 122.

    Krieger F, Fierz B, Bieri O, Drewello M, Kiefhaber T. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J Mol Biol 2003;332:265–74.Google Scholar

  • 123.

    Buscaglia M, Schuler B, Lapidus LJ, Eaton WA, Hofrichter J. Kinetics of intramolecular contact formation in a denatured protein. J Mol Biol 2003;332:9–12.Google Scholar

  • 124.

    Neuweiler H, Schulz A, Bohmer M, Enderlein J, Sauer M. Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level. J Am Chem Soc 2003;125:5324–30.CrossrefGoogle Scholar

  • 125.

    Kubelka J, Henry ER, Cellmer T, Hofrichter J, Eaton WA. Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci USA 2008;105:18655–62.CrossrefGoogle Scholar

  • 126.

    Zhu L, Kurt N, Choi J, Lapidus LJ, Cavagnero S. Sub-millisecond chain collapse of the Escherichia coli globin ApoHmpH. J Phys Chem B 2013;117:7868–77.CrossrefGoogle Scholar

  • 127.

    Camacho CJ, Thirumalai D. Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins 1995;22:27–40.CrossrefGoogle Scholar

  • 128.

    Wang L, Rivera EV, Benavides-Garcia MG, Nall BT. Loop entropy and cytochrome c stability. J Mol Biol 2005;353:719–29.CrossrefGoogle Scholar

  • 129.

    Scalley-Kim M, Minard P, Baker D. Low free energy cost of very long loop insertions in proteins. Protein Sci 2003;12:197–206.CrossrefGoogle Scholar

  • 130.

    Fersht AR. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc Natl Acad Sci USA 1995;92:10869–73.CrossrefGoogle Scholar

  • 131.

    Fersht AR. Nucleation mechanisms in protein folding. Curr Opin Struct Biol 1997;7:3–9.CrossrefGoogle Scholar

  • 132.

    Mirny L, Shakhnovich E. Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct 2001;30:361–96.CrossrefGoogle Scholar

  • 133.

    Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985–94.Google Scholar

  • 134.

    Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV. Contact order revisited: influence of protein size on the folding rate. Protein Sci 2003;12:2057–62.CrossrefGoogle Scholar

  • 135.

    Weikl TR. Loop-closure principles in protein folding. Arch Biochem Biophys 2008;469:67–75.Google Scholar

  • 136.

    Plaxco KW, Baker D. Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proc Natl Acad Sci USA 1998;95:13591–6.CrossrefGoogle Scholar

  • 137.

    Berezovsky IN, Grosberg AY, Trifonov EN. Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett 2000;466:283–6.Google Scholar

  • 138.

    Berezovsky IN, Kirzhner VM, Kirzhner A, Rosenfeld VR, Trifonov EN. Closed loops: persistence of the protein chain returns. Protein Eng 2002;15:955–7.CrossrefGoogle Scholar

  • 139.

    Berezovsky IN, Kirzhner VM, Kirzhner A, Trifonov EN. Protein folding: looping from hydrophobic nuclei. Proteins 2001;45:346–50.CrossrefGoogle Scholar

  • 140.

    Chintapalli SV, Yew BK, Illingworth CJ, Upton GJ, Reeves PJ, Parkes KE, et al. Closed loop folding units from structural alignments: experimental foldons revisited. J Comput Chem 2010;31:2689–701.CrossrefGoogle Scholar

  • 141.

    Chintapalli SV, Illingworth CJ, Upton GJ, Sacquin-Mora S, Reeves PJ, Mohammedali HS, et al. Assessing the effect of dynamics on the closed-loop protein-folding hypothesis. J R Soc Interface 2014;11:20130935.Google Scholar

  • 142.

    Bai Y, Sosnick TR, Mayne L, Englander SW. Protein folding intermediates: native-state hydrogen exchange. Science 1995;269:192–7.Google Scholar

  • 143.

    Englander SW, Mayne L, Krishna MM. Protein folding and misfolding: mechanism and principles. Q Rev Biophys 2007;40:287–326.Google Scholar

  • 144.

    Hoang L, Maity H, Krishna MM, Lin Y, Englander SW. Folding units govern the cytochrome c alkaline transition. J Molec Biol 2003;331:37–43.Google Scholar

  • 145.

    Unger R, Moult J. Local interactions dominate folding in a simple protein model. J Mol Biol 1996;259:988–94.Google Scholar

  • 146.

    Moult J, Unger R. An analysis of protein folding pathways. Biochemistry 1991;30:3816–24.CrossrefGoogle Scholar

  • 147.

    Yew BK, Chintapalli SV, Upton GG, Reynolds CA. Conservation of closed loops. J Mol Graph Model 2007;26:652–5.CrossrefGoogle Scholar

  • 148.

    Noivirt-Brik O, Hazan G, Unger R, Ofran Y. Non-local residue-residue contacts in proteins are more conserved than local ones. Bioinformatics 2013;29:331–7.CrossrefGoogle Scholar

  • 149.

    Magg C, Kubelka J, Holtermann G, Haas E, Schmid FX. Specificity of the initial collapse in the folding of the cold shock protein. J Molec Biol 2006;360:1067–80.Google Scholar

  • 150.

    Nettels D, Gopich IV, Hoffmann A, Schuler B. Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc Natl Acad Sci USA 2007;104:2655–60.CrossrefGoogle Scholar

  • 151.

    Sinha KK, Udgaonkar JB. Dissecting the non-specific and specific components of the initial folding reaction of barstar by multi-site FRET measurements. J Molec Biol 2007;370:385–405.Google Scholar

  • 152.

    Orevi T, Rahamim G, Hazan G, Amir D, Haas E. The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways. Biophys Rev 2013;5:85–98.CrossrefGoogle Scholar

  • 153.

    Creighton TE. Experimental studies of protein folding and unfolding. Prog Biophys Molec Biol 1978;33:231–97.Google Scholar

  • 154.

    Gussakovsky EE, Haas E. The compact state of reduced bovine pancreatic trypsin inhibitor is not the compact molten globule. FEBS Lett 1992;308:146–8.Google Scholar

  • 155.

    Baldwin RL. Making a network of hydrophobic clusters. Science 2002;295:1657–8.Google Scholar

  • 156.

    Klein-Seetharaman J, Oikawa M, Grimshaw SB, Wirmer J, Duchardt E, Ueda T, et al. Long-range interactions within a nonnative protein. Science 2002;295:1719–22.Google Scholar

  • 157.

    Lattman EE, Rose GD. Protein folding—what’s the question? Proc Natl Acad Sci USA 1993;90:439–41.CrossrefGoogle Scholar

  • 158.

    Buckler DR, Haas E, Scheraga HA. Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved nonradiative dynamic excitation energy transfer between site-specific extrinsic probes. Biochemistry 1995;34:15965–78.CrossrefGoogle Scholar

  • 159.

    Navon A, Ittah V, Landsman P, Scheraga HA, Haas E. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry 2001;40:105–18.CrossrefGoogle Scholar

  • 160.

    Schuler B, Eaton WA. Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 2008;18:16–26.CrossrefGoogle Scholar

  • 161.

    Ferreon AC, Deniz AA. Protein folding at single-molecule resolution. Biochim Biophys Acta 2011;1814:1021–9.Google Scholar

  • 162.

    Merchant KA, Best RB, Louis JM, Gopich IV, Eaton WA. Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations. Proc Natl Acad Sci USA 2007;104:1528–33.CrossrefGoogle Scholar

  • 163.

    Sherman E, Haran G. Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci USA 2006;103:11539–43.CrossrefGoogle Scholar

  • 164.

    Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, et al. De novo structure prediction and experimental characterization of folded peptoid oligomers. Proc Natl Acad Sci USA 2012;109:14320–5.CrossrefGoogle Scholar

  • 165.

    Yoo TY, Meisburger SP, Hinshaw J, Pollack L, Haran G, Sosnick TR, et al. Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state. J Molec Biol 2012;418:226–36.Google Scholar

  • 166.

    Kathuria SV, Kayatekin C, Barrea R, Kondrashkina E, Graceffa R, Guo L, et al. Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS. J Molec Biol 2014;426:1980–94.Google Scholar

  • 167.

    Mok YK, Kay CM, Kay LE, Forman-Kay J. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions. J Molec Biol 1999;289:619–38.Google Scholar

  • 168.

    Pashley CL, Morgan GJ, Kalverda AP, Thompson GS, Kleanthous C, Radford SE. Conformational properties of the unfolded state of Im7 in nondenaturing conditions. J Molec Biol 2012;416:300–18.Google Scholar

  • 169.

    Chen Y, Wedemeyer WJ, Lapidus LJ. A general polymer model of unfolded proteins under folding conditions. J Phys Chem B 2010;114:15969–75.CrossrefGoogle Scholar

  • 170.

    Förster T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann Phys 1948;437:55–75.Google Scholar

  • 171.

    Steinberg IZ. Long-range nonradiative transfer of electronic excitation energy in proteins and polypeptides. Ann Rev Biochem 1971;40:83–114.CrossrefGoogle Scholar

  • 172.

    Edelhoch H, Brand L, Wilchek M. Fluorescence studies with tryptophyl peptides. Biochemistry 1967;6:547–59.CrossrefGoogle Scholar

  • 173.

    Chan CK, Hu Y, Takahashi S, Rousseau DL, Eaton WA, Hofrichter J. Submillisecond protein folding kinetics studied by ultrarapid mixing. Proc Natl Acad Sci USA 1997;94:1779–84.CrossrefGoogle Scholar

  • 174.

    Nishimura C, Lietzow MA, Dyson HJ, Wright PE. Sequence determinants of a protein folding pathway. J Mol Biol 2005;351:383–92.Google Scholar

  • 175.

    Lapidus LJ, Yao S, McGarrity KS, Hertzog DE, Tubman E, Bakajin O. Protein hydrophobic collapse and early folding steps observed in a microfluidic mixer. Biophys J 2007;93:218–24.CrossrefGoogle Scholar

  • 176.

    Kato S, Kamikubo H, Hirano S, Yamazaki Y, Kataoka M. Nonlocal interactions are responsible for tertiary structure formation in staphylococcal nuclease. Biophys J 2010;98:678–86.CrossrefGoogle Scholar

  • 177.

    Meisner WK, Sosnick TR. Fast folding of a helical protein initiated by the collision of unstructured chains. Proc Natl Acad Sci USA 2004;101:13478–82.CrossrefGoogle Scholar

  • 178.

    Anil B, Sato S, Cho JH, Raleigh DP. Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing. J Mol Biol 2005;354:693–705.Google Scholar

  • 179.

    Munson M, Anderson KS, Regan L. Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude. Fold Des 1997;2:77–87.CrossrefGoogle Scholar

  • 180.

    Steward A, McDowell GS, Clarke J. Topology is the principal determinant in the folding of a complex all-alpha Greek key death domain from human FADD. J Mol Biol 2009;389:425–37.Google Scholar

  • 181.

    Behe MJ, Lattman EE, Rose GD. The protein-folding problem: the native fold determines packing, but does packing determine the native fold? Proc Natl Acad Sci USA 1991;88: 4195–9.CrossrefGoogle Scholar

  • 182.

    Beechem JM, Sherman MA, Mas MT. Sequential domain unfolding in phosphoglycerate kinase: fluorescence intensity and anisotropy stopped-flow kinetics of several tryptophan mutants. Biochemistry 1995;34:13943–8.CrossrefGoogle Scholar

  • 183.

    Kimura T, Lee JC, Gray HB, Winkler JR. Site-specific collapse dynamics guide the formation of the cytochrome c’ four-helix bundle. Proc Natl Acad Sci USA 2007;104:117–22.CrossrefGoogle Scholar

  • 184.

    Arai M, Kondrashkina E, Kayatekin C, Matthews CR, Iwakura M, Bilsel O. Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein. J Molec Biol 2007;368:219–29.Google Scholar

  • 185.

    Wu Y, Kondrashkina E, Kayatekin C, Matthews CR, Bilsel O. Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein. Proc Natl Acad Sci USA 2008;105:13367–72.CrossrefGoogle Scholar

  • 186.

    Millett IS, Doniach S, Plaxco KW. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv Protein Chem 2002;62:241–62.CrossrefGoogle Scholar

  • 187.

    Voelz VA, Jager M, Yao S, Chen Y, Zhu L, Waldauer SA, et al. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. J Am Chem Soc 2012;134:12565–77.CrossrefGoogle Scholar

  • 188.

    Daidone I, Neuweiler H, Doose S, Sauer M, Smith JC. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains. PLoS Comput Biol 2010;6:e1000645.CrossrefGoogle Scholar

  • 189.

    Nobrega RP, Arora K, Kathuria SV, Graceffa R, Barrea RA, Guo L, et al. Modulation of frustration in folding by sequence permutation. Proc Natl Acad Sci USA 2014;111:10562–7.CrossrefGoogle Scholar

  • 190.

    Mizukami T, Xu M, Cheng H, Roder H, Maki K. Nonuniform chain collapse during early stages of staphylococcal nuclease folding detected by fluorescence resonance energy transfer and ultrarapid mixing methods. Protein Sci 2013;22:1336–48.Google Scholar

  • 191.

    Huang F, Lerner E, Sato S, Amir D, Haas E, Fersht AR. Time-resolved fluorescence resonance energy transfer study shows a compact denatured state of the B domain of protein A. Biochemistry 2009;48:3468–76.CrossrefGoogle Scholar

  • 192.

    Fixman M, Stockmayer WH. Polymer conformation and dynamics in solution. Annu Rev Phys Chem 1970;21:407–28.CrossrefGoogle Scholar

  • 193.

    Flory PJ. Moments of the end-to-end vector of a chain molecule, its persistence and distribution. Proc Natl Acad Sci USA 1973;70:1819–23.CrossrefGoogle Scholar

  • 194.

    Camacho CJ, Thirumalai D. Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1995;92:1277–81.CrossrefGoogle Scholar

  • 195.

    Muller CW, Schulz GE. Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1,P5-di(adenosine-5′-)pentaphosphate. J Molec Biol 1988;202:909–12.Google Scholar

  • 196.

    Muller CW, Schulz GE. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state. J Molec Biol 1992;224:159–77.Google Scholar

  • 197.

    Noda L, Schulz GE, Von Zabern I. Crystalline adenylate kinase from carp muscle. Eur J Biochem 1975;51:229–35.CrossrefGoogle Scholar

  • 198.

    Schulz GE, Muller CW, Diederichs K. Induced-fit movements in adenylate kinases. J Mol Biol 1990;213:627–30.Google Scholar

  • 199.

    Jacob MH, Amir D, Ratner V, Gussakowsky E, Haas E. Predicting reactivities of protein surface cysteines as part of a strategy for selective multiple labeling. Biochemistry 2005;44:13664–72.CrossrefGoogle Scholar

  • 200.

    Gennes PG. Scaling concepts in polymer physics. Ithaca, NY: Cornel University Press, 1979.Google Scholar

  • 201.

    Orevi T, Ben Ishay E, Gershanov SL, Dalak MB, Amir D, Haas E. Fast closure of N-terminal long loops but slow formation of beta strands precedes the folding transition state of Escherichia coli adenylate kinase. Biochemistry 2014;53:3169–78.CrossrefGoogle Scholar

  • 202.

    Beals JM, Haas E, Krausz S, Scheraga HA. Conformational studies of a peptide corresponding to a region of the C-terminus of ribonuclease A: implications as a potential chain-folding initiation site. Biochemistry 1991;30:7680–92.CrossrefGoogle Scholar

  • 203.

    Bergasa-Caceres F, Ronneberg TA, Rabitz H. Sequential collapse model for protein folding pathways. J Phys Chem B 1999;103:9749–58.CrossrefGoogle Scholar

  • 204.

    Bergasa-Caceres F, Rabitz HA. Low entropic barrier to the hydrophobic collapse of the prion protein: effects of intermediate states and conformational flexibility. J Phys Chem A 2010;114:6978–82.CrossrefGoogle Scholar

  • 205.

    Mukherjee A, Bagchi B. Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid. J Chem Phys 2004;120:1602–12.CrossrefGoogle Scholar

  • 206.

    Banerjee S, Roy S, Bagchi B. Enhanced pair hydrophobicity in the water-dimethylsulfoxide (DMSO) binary mixture at low DMSO concentrations. J Phys Chem B 2010;114:12875–82.CrossrefGoogle Scholar

  • 207.

    Hu W, Walters BT, Kan ZY, Mayne L, Rosen LE, Marqusee S, et al. Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry. Proc Natl Acad Sci USA 2013;110:7684–89.CrossrefGoogle Scholar

  • 208.

    Englander SW, Mayne L. Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struct 1992;21:243–65.CrossrefGoogle Scholar

  • 209.

    Elove GA, Chaffotte AF, Roder H, Goldberg ME. Early steps in cytochrome-c folding probed by time-resolved circular-dichroism and fluorescence spectroscopy. Biochemistry 1992;31:6876–83.CrossrefGoogle Scholar

  • 210.

    Aznauryan M, Nettels D, Holla A, Hofmann H, Schuler B. Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteins. J Am Chem Soc 2013;135:14040–3.CrossrefGoogle Scholar

  • 211.

    Nilsson I, Lara P, Hessa T, Johnson AE, von Heijne G, Karamyshev AL. The code for directing proteins for translocation across ER membrane: SRP cotranslationally recognizes specific features of a signal sequence. J Molec Biol 2014 (in press).Google Scholar

  • 212.

    Johnson AE. Fluorescence approaches for determining protein conformations, interactions and mechanisms at membranes. Traffic 2005;6:1078–92.CrossrefGoogle Scholar

  • 213.

    Johnson AE. The co-translational folding and interactions of nascent protein chains: a new approach using fluorescence resonance energy transfer. FEBS Lett 2005;579:916–20.Google Scholar

  • 214.

    Miyake-Stoner SJ, Miller AM, Hammill JT, Peeler JC, Hess KR, Mehl RA, et al. Probing protein folding using site-specifically encoded unnatural amino acids as FRET donors with tryptophan. Biochemistry 2009;48:5953–62.CrossrefGoogle Scholar

  • 215.

    Waldauer SA, Wu L, Yao S, Bakajin O, Lapidus LJ. Microfluidic mixers for studying protein folding. J Vis Exp 2012;(62):e3976.Google Scholar

About the article

Corresponding author: Elisha Haas, The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel, Phone: +972 546270012, E-mail:

Received: 2014-09-18

Accepted: 2014-10-24

Published Online: 2014-11-27

Published in Print: 2014-12-19

Citation Information: Bio-Algorithms and Med-Systems, Volume 10, Issue 4, Pages 169–193, ISSN (Online) 1896-530X, ISSN (Print) 1895-9091, DOI: https://doi.org/10.1515/bams-2014-0018.

Export Citation

©2014 by De Gruyter.Get Permission

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Fernando Bergasa-Caceres, Elisha Haas, and Herschel A. Rabitz
The Journal of Physical Chemistry B, 2019, Volume 123, Number 21, Page 4463
Igor N. Berezovsky, Enrico Guarnera, and Zejun Zheng
Progress in Biophysics and Molecular Biology, 2017, Volume 128, Page 85

Comments (0)

Please log in or register to comment.
Log in