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MD + QM Correlations with Tryptophan Fluorescence Spectral Shifts and Lifetimes

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Fluorescence Spectroscopy and Microscopy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1076))

Abstract

Principles behind quenching of tryptophan (Trp) fluorescence are updated and extended in light of recent 100-ns and 1-μs molecular dynamics (MD) trajectories augmented with quantum mechanical (QM) calculations that consider electrostatic contributions to wavelength shifts and quenching. Four studies are summarized, including (1) new insight into the single exponential decay of NATA, (2) a study revealing how unsuspected rotamer transitions affect quenching of Trp when used as a probe of protein folding, (3) advances in understanding the origin of nonexponential decay from 100-ns simulations on 19 Trps in 16 proteins, and (4) the correlation of wavelength with lifetime for decay-associated spectra (DAS). Each study strongly reinforces the concept that—for Trp—electron transfer-based quenching is controlled much more by environment electrostatic factors affecting the charge transfer (CT) state energy than by distance dependence of electronic coupling. In each case, water plays a large role in unexpected ways.

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References

  1. Warshel A (1991) Computer modeling of chemical reactions in enzymes and solutions. Wiley-Interscience, New York

    Google Scholar 

  2. Johnson ET, Parson WW (2002) Electrostatic interactions in an integral membrane protein. Biochemistry 41:6483–6494

    PubMed  CAS  Google Scholar 

  3. Warshel A, Sharma PK, Kato M et al (2006) Modeling electrostatic effects in proteins. Biochim Biophys Acta 1764:1647–1676

    PubMed  CAS  Google Scholar 

  4. Olsson MHM, Parson WW, Warshel A (2006) Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 106:1737–1756

    PubMed  CAS  Google Scholar 

  5. McGeagh JD, Ranaghan KE, Mulholland AJ (2011) Protein dynamics and enzyme catalysis: insights from simulations. Biochim Biophys Acta 1814:1077–1092

    PubMed  CAS  Google Scholar 

  6. Muino PL, Harris D, Berryhill J et al (1992) Simulation of solvent dynamics effects on the fluorescence of 3-methylindole in water. Proc SPIE Int Soc Opt Eng 1640:240–250

    CAS  Google Scholar 

  7. Muiño PL, Callis PR (1994) Hybrid simulations of solvation effects on electronic spectra: indoles in water. J Chem Phys 100:4093–4109

    Google Scholar 

  8. Callis PR (1997) 1La and 1Lb transitions of tryptophan: applications of theory and experimental observations to fluorescence of proteins. Methods Enzymol 278:113–150

    PubMed  CAS  Google Scholar 

  9. Callis PR, Burgess BK (1997) Tryptophan fluorescence shifts in proteins from hybrid simulations: an electrostatic approach. J Phys Chem 101:9429–9432

    CAS  Google Scholar 

  10. Vivian JT, Callis PR (2001) Mechanisms of tryptophan fluorescence shifts in proteins. Biophys J 80:2093–2109

    PubMed  CAS  Google Scholar 

  11. Callis PR, Vivian JT (2003) Understanding the variable fluorescence quantum yield of tryptophan in proteins using QM-MM simulations. Quenching by charge transfer to the peptide backbone. Chem Phys Lett 369:409–414

    CAS  Google Scholar 

  12. Callis PR, Liu T (2004) Quantitative prediction of fluorescence quantum yields for tryptophan in proteins. J Phys Chem B 108:4248–4259

    CAS  Google Scholar 

  13. Kurz LC, Fite B, Jean J et al (2005) Photophysics of tryptophan fluorescence: link with the catalytic strategy of the citrate synthase from Thermoplasma acidophilum. Biochemistry 44:1394–1413

    PubMed  CAS  Google Scholar 

  14. Chen JJ, Flaugh SL, Callis PR et al (2006) Mechanism of the highly efficient quenching of tryptophan fluorescence in human gamma D-crystallin. Biochemistry 45:11552–11563

    PubMed  CAS  Google Scholar 

  15. Callis PR, Liu TQ (2006) Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins. Chem Phys 326:230–239

    CAS  Google Scholar 

  16. Xu JH, Toptygin D, Graver KJ et al (2006) Ultrafast fluorescence dynamics of tryptophan in the proteins monellin and IIA(Glc). J Am Chem Soc 128:1214–1221

    PubMed  CAS  Google Scholar 

  17. Pan CP, Callis PR, Barkley MD (2006) Dependence of tryptophan emission wavelength on conformation in cyclic hexapeptides. J Phys Chem B 110:7009–7016

    PubMed  CAS  Google Scholar 

  18. Callis PR, Petrenko A, Muino PL et al (2007) Ab initio prediction of tryptophan fluorescence quenching by protein electric field enabled electron transfer. J Phys Chem B 111:10335–10339

    PubMed  CAS  Google Scholar 

  19. Muiño PL, Callis PR (2009) Solvent effects on the fluorescence quenching of tryptophan by amides via electron transfer. Experimental and computational studies. J Phys Chem B 113:2572–2577

    PubMed  Google Scholar 

  20. Xu J, Chen J, Toptygin D et al (2009) Femtosecond fluorescence spectra of tryptophan in human gamma-crystallin mutants: site-dependent ultrafast quenching. J Am Chem Soc 131:16751–16757

    PubMed  CAS  Google Scholar 

  21. Chen J, Callis PR, King J (2009) Mechanism of the very efficient quenching of tryptophan fluorescence in human gamma D- and gamma S-crystallins: the gamma-crystallin fold may have evolved to protect tryptophan residues from ultraviolet photodamage. Biochemistry 48:3708–3716

    PubMed  CAS  Google Scholar 

  22. Callis PR (2009) Exploring the electrostatic landscape of proteins with tryptophan fluorescence. In: Geddes CD (ed) Reviews in fluorescence 2007, vol 4. Springer, New York, pp 199–248

    Google Scholar 

  23. Callis PR (2011) Predicting fluorescence lifetimes and spectra of biopolymers. Methods Enzymol 487:1–38

    PubMed  CAS  Google Scholar 

  24. Pan CP, Muino PL, Barkley MD et al (2011) Correlation of tryptophan fluorescence spectral shifts and lifetimes arising directly from heterogeneous environment. J Phys Chem B 115:3245–3253

    PubMed  CAS  Google Scholar 

  25. Tusell JR, Callis PR (2012) Simulations of tryptophan fluorescence dynamics during folding of the villin headpiece. J Phys Chem B 116:2586–2594

    PubMed  CAS  Google Scholar 

  26. Luo GB, Andricioaei I, Xie XS et al (2006) Dynamic distance disorder in proteins is caused by trapping. J Phys Chem B 110:9363–9367

    PubMed  CAS  Google Scholar 

  27. Warshel A, Sharma PK, Kato M et al (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210–3235

    PubMed  CAS  Google Scholar 

  28. Prakash MK, Marcus RA (2007) An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations. Proc Natl Acad Sci USA 104:15982–15987

    PubMed  CAS  Google Scholar 

  29. Prakash MK, Marcus RA (2008) Dielectric dispersion interpretation of single enzyme dynamic disorder, spectral diffusion, and radiative fluorescence lifetime. J Phys Chem B 112:399–404

    PubMed  CAS  Google Scholar 

  30. Shaw DE, Maragakis P, Lindorff-Larsen K et al (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341–346

    PubMed  CAS  Google Scholar 

  31. Vendruscolo M, Dobson CM (2011) Protein dynamics: Moore’s law in molecular biology. Curr Biol 21:R68–R70

    PubMed  CAS  Google Scholar 

  32. Zhong DP, Pal SK, Zewail AH (2011) Biological water: a critique. Chem Phys Lett 503:1–11

    CAS  Google Scholar 

  33. Tusell JR. Computation of fluorescence quenching by amide and histidine. Ph.D. Dissertation, Montana State University, Bozeman; 2011.

    Google Scholar 

  34. Tusell JR, Callis PR (2012) Computational predictions of exponential and non-exponential tryptophan fluorescence decay in NATA, the villin headpiece subdomain, and other proteins. Biophys J 102:217a

    Google Scholar 

  35. Broos J, Tveen-Jensen K, de Waal E et al (2007) The emitting state of tryptophan in proteins with highly blue-shifted fluorescence. Angew Chem Int Ed Engl 46:5137–5139

    PubMed  CAS  Google Scholar 

  36. Jensen TJ, Strambini G, Gonnelli G et al (2008) Mutations in transhydrogenase change the fluorescence emission state of trp-72 from 1La to 1Lb. Biophys J 95(7):3419–3428

    CAS  Google Scholar 

  37. Chen Y, Barkley MD (1998) Toward understanding tryptophan fluorescence in proteins. Biochemistry 37:9976–9982

    PubMed  CAS  Google Scholar 

  38. Jimenez R, Fleming GR, Kumar PV et al (1994) Femtosecond solvation dynamics of water. Nature 369:471–473

    CAS  Google Scholar 

  39. Boens N, Andriessen R, Ameloot M et al (1992) Kinetics and identifiability of intramolecular 2-state excited-state processes—global compartmental analysis of the fluorescence decay surface. J Phys Chem 96:6331–6342

    CAS  Google Scholar 

  40. Vandommelen L, Boens N, Ameloot M et al (1993) Species-associated spectra and upper and lower bounds on the rate constants of reversible intramolecular 2-state excited-state processs with added quencher—global compartmental analysis of the fluorescence decay surface. J Phys Chem 97:11738–11753

    CAS  Google Scholar 

  41. Van Dommelen L, Boens N, Ameloot M (1998) Time-resolved fluorescence of glucagon studied by global compartmental analysis. J Phys Chem B 102:3287–3294

    Google Scholar 

  42. Ameloot M, Beechem JM, Brand L (1986) Compartmental modeling of excited-state reactions—identifiability of the rate constants from fluorescence decay surfaces. Chem Phys Lett 129:211–219

    CAS  Google Scholar 

  43. Lofroth JE (1986) Time-resolved emission-spectra, decay-associated spectra, and species-associated spectra. J Phys Chem 90:1160–1168

    Google Scholar 

  44. Petrich JW, Chang MC, McDonald DB et al (1983) On the origin of nonexponential fluorescence decay in tryptophan and its derivatives. J Am Chem Soc 105:3824–3832

    CAS  Google Scholar 

  45. Bushueva TL, Busel EP, Burstein EA (1975) The interaction of protein functional groups with indole chromophore III. Amine, amide, and thiol groups. Stud Biophys Berlin 52:41–52

    CAS  Google Scholar 

  46. Ricci RW, Nesta JM (1976) Inter- and intramolecular quenching of indole fluorescence by carbonyl compounds. J Phys Chem 80:974–980

    CAS  Google Scholar 

  47. Froehlich PM, Nelson K (1978) Fluorescence quenching of indoles by amides. J Phys Chem 82:2401–2403

    CAS  Google Scholar 

  48. Chen Y, Liu B, Yu H-T et al (1996) The peptide bond quenches indole fluorescence. J Am Chem Soc 118:9271–9278

    CAS  Google Scholar 

  49. Rolinski OJ, Scobie K, Birch DJS (2009) Protein fluorescence decay: A gamma function description of thermally induced interconversion of amino acid rotamers. Phys Rev E 79(5 Pt 1):050901

    Google Scholar 

  50. Buchner GS, Murphy RD, Buchete NV et al (2011) Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory. Biochim Biophys Acta 1814:1001–1020

    PubMed  CAS  Google Scholar 

  51. Kubelka J, Henry ER, Cellmer T et al (2008) Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci USA 105:18655–18662

    PubMed  CAS  Google Scholar 

  52. Willaert K, Engelborghs Y (1991) The quenching of tryptophan fluorescence by protonated and unprotonated imidazole. Eur Biophys J 20:177–182

    CAS  Google Scholar 

  53. Willaert K, Loewenthal R, Sancho J et al (1992) Determination of the excited-state lifetimes of the tryptophan residues in barnase, via multifrequency phase fluorometry of tryptophan mutants. Biochemistry 31:711–716

    PubMed  CAS  Google Scholar 

  54. Eaton WA, Munoz V, Thompson PA et al (1998) Kinetics and dynamics of loops, alpha-helices, beta-hairpins, and fast-folding proteins. Acc Chem Res 31:745–753

    CAS  Google Scholar 

  55. Thompson PA, Munoz V, Jas GS et al (1999) Using tryptophan fluorescence to probe helix-coil kinetics. Biophys J 76:A175

    Google Scholar 

  56. Freddolino PL, Schulten K (2009) Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophys J 97:2338–2347

    PubMed  CAS  Google Scholar 

  57. Ensign DL, Kasson PM, Pande VS (2007) Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol 374:806–816

    PubMed  CAS  Google Scholar 

  58. Kubelka J, Chiu TK, Davies DR et al (2006) Sub-microsecond protein folding. J Mol Biol 359:546–553

    PubMed  CAS  Google Scholar 

  59. Cellmer T, Buscaglia M, Henry ER et al (2011) Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Proc Natl Acad Sci USA 108:6103–6108

    PubMed  CAS  Google Scholar 

  60. Reiner A, Henklein P, Kiefhaber T (2010) An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain. Proc Natl Acad Sci USA 107:4955–4960

    PubMed  CAS  Google Scholar 

  61. Beratan DN, Betts JN, Onuchic JN (1991) Protein electron transfer rates set by the bridging secondary and tertiary structure. Science 252:1285–1288

    PubMed  CAS  Google Scholar 

  62. Risser SM, Beratan DN, Meade TJ (1993) Electron-transfer in DNA—predictions of exponential-growth and decay of coupling with donor-acceptor distance. J Am Chem Soc 115:2508–2510

    CAS  Google Scholar 

  63. Kubelka J, Eaton WA, Hofrichter J (2003) Experimental tests of villin subdomain folding simulations. J Mol Biol 329:625–630

    PubMed  CAS  Google Scholar 

  64. Lindorff-Larsen K, Maragakis P, Piana S et al (2012) Systematic validation of protein force fields against experimental data. PLoS One 7:e32131

    PubMed  CAS  Google Scholar 

  65. Hennecke J, Sillen A, Huber WM et al (1997) Quenching of tryptophan fluorescence by the active-site disulfide bridge in the DsbA protein from Escherichia coli. Biochemistry 36:6391–6400

    PubMed  CAS  Google Scholar 

  66. Sillen A, Hennecke J, Roethlisberger D et al (1999) Fluorescence quenching in the DsbA protein from Escherichia coli: the complete picture of the excited-state energy pathway and evidence for the reshuffling dynamics of the microstates of tryptophan. Proteins 37:253–263

    PubMed  CAS  Google Scholar 

  67. Sillen A, Diaz JF, Engelborghs Y (2000) A step toward the prediction of the fluorescence lifetimes of tryptophan residues in proteins based on structural and spectral data. Protein Sci 9:158–169

    PubMed  CAS  Google Scholar 

  68. Toptygin D, Savtchenko RS, Meadow ND et al (2001) Homogeneous spectrally- and time-resolved fluorescence emission from single-tryptophan mutants of IIAGlc. J Phys Chem B 105:2043–2055

    CAS  Google Scholar 

  69. Toptygin D, Gronenborn AM, Brand L (2006) Nanosecond relaxation dynamics of protein GB1 identified by the time-dependent red shift in the fluorescence of tryptophan and 5-fluorotryptophan. J Phys Chem B 110:26292–26302

    PubMed  CAS  Google Scholar 

  70. Peon J, Pal SK, Zewail AH (2002) Hydration at the surface of the protein Monellin: dynamics with femtosecond resolution. Proc Natl Acad Sci USA 99:10964–10969

    PubMed  CAS  Google Scholar 

  71. Zhang LY, Yang Y, Kao YT et al (2009) Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations. J Am Chem Soc 131:10677–10691

    PubMed  CAS  Google Scholar 

  72. Abbyad P, Shi XH, Childs W et al (2007) Measurement of solvation responses at multiple sites in a globular protein. J Phys Chem B 111:8269–8276

    PubMed  CAS  Google Scholar 

  73. Knutson JR, Beechem JM, Brand L (1983) Simultaneous analysis of multiple fluorescence decay curves—a global approach. Chem Phys Lett 102:501–507

    CAS  Google Scholar 

  74. Beechem JM, Knutson JR, Ross JBA et al (1983) Global resolution of heterogeneous decay by phase modulation fluorometry—mixtures and proteins. Biochemistry 22:6054–6058

    CAS  Google Scholar 

  75. Knutson JR, Walbridge DG, Brand L (1983) Studies of ligand-binding to alcohol-dehydrogenase with decay-associated fluorescence spectroscopy. Biophys J 41:A268

    Google Scholar 

  76. Davenport L, Knutson JR, Brand L (1983) Fluorescence studies of the interaction of equilenin with liposomes. Biophys J 41:A373

    Google Scholar 

  77. Knutson JR, Walbridge DG, Brand L (1982) Decay-associated fluorescence-spectra and the heterogeneous emission of alcohol-dehydrogenase. Biochemistry 21:4671–4679

    PubMed  CAS  Google Scholar 

  78. De-Beuckeleer K, Volckaert G, Engelborghs Y (1999) Time resolved fluorescence and phosphorescence properties of the individual tryptophan residues of barnase: evidence for protein-protein interactions. Proteins 36:42–53

    PubMed  CAS  Google Scholar 

  79. Gastmans M, Volckaert G, Engelborghs Y (1999) Tryptophan microstate reshuffling upon the binding of cyclosporin A to human cyclophilin A. Proteins 35:464–474

    PubMed  CAS  Google Scholar 

  80. Hogue CWV, Doublie S, Xue H et al (1996) A concerted tryptophanyl-adenylate-dependent conformational change in Bacillus subtilis tryptophanyl-tRNA synthetase revealed by the fluorescence of Trp92. J Mol Biol 260:446–466

    PubMed  CAS  Google Scholar 

  81. Dahms TES, Willis KJ, Szabo AG (1995) Conformational heterogeneity of tryptophan in a protein crystal. J Am Chem Soc 117:2321–2326

    CAS  Google Scholar 

  82. Szabo AG, Rayner DM (1980) Fluorescence decay of tryptophan conformers in aqueous solution. J Am Chem Soc 102:554–563

    CAS  Google Scholar 

  83. Hudson BS, Huston JM, Soto-Campos G (1999) A reversible “dark state” mechanism for complexity of the fluorescence of tryptophan in proteins. J Phys Chem A 103:2227–2234

    CAS  Google Scholar 

  84. Merrill AR, Steer BA, Prentice GA et al (1997) Identification of a chameleon-like pH-sensitive segment within the colicin E1 channel domain that may serve as the pH-activated trigger for membrane bilayer association. Biochemistry 36:6874–6884

    PubMed  CAS  Google Scholar 

  85. Willis KJ, Szabo AG (1992) Conformation of parathyroid-hormone—time-resolved fluorescence studies. Biochemistry 31:8924–8931

    PubMed  CAS  Google Scholar 

  86. Alberti P, Bombarda E, Kintrup M et al (1997) Structural investigation of Tet repressor loop 154–167: a time-resolved fluorescence study of three single Trp mutants. Arch Biochem Biophys 346:230–240

    PubMed  CAS  Google Scholar 

  87. Neyroz P, Menna C, Polverini E et al (1996) Intrinsic fluorescence properties and structural analysis of p13(suc1) from Schizosaccharomyces pombe. J Biol Chem 271:27249–27258

    PubMed  CAS  Google Scholar 

  88. Kim SJ, Chowdhury FN, Stryjewski W et al (1993) Time-resolved fluorescence of the single tryptophan of Bacillus stearothermophilus phosphofructokinase. Biophys J 65:215–226

    PubMed  CAS  Google Scholar 

  89. Lakowicz J (2000) On spectral relaxation in proteins. Photochem Photobiol 72:421–437

    PubMed  CAS  Google Scholar 

  90. Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, New York

    Google Scholar 

  91. Pan CP, Barkley MD (2004) Conformational effects on tryptophan fluorescence in cyclic hexapeptides. Biophys J 86:3828–3835

    PubMed  CAS  Google Scholar 

  92. Adams PD, Chen Y, Ma K et al (2002) Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. J Am Chem Soc 124:9278–9286

    PubMed  CAS  Google Scholar 

  93. Pal SK, Peon J, Zewail AH (2002) Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution. Proc Natl Acad Sci USA 99:1763–1768

    PubMed  CAS  Google Scholar 

  94. Ridley J, Zerner M (1973) Intermediate neglect of differential overlap (INDO) technique for spectroscopy: pyrrole and the azines. Theor Chim Acta (Berl) 32:111–134

    CAS  Google Scholar 

  95. Thompson MA, Zerner MC (1991) A theoretical examination of the electronic structure and spectroscopy of the photosynthetic reaction center from Rhodopseudomonas viridis. J Am Chem Soc 113:8210–8215

    CAS  Google Scholar 

  96. Cory MG, Zerner MC, Xu XC et al (1998) Electronic excitations in aggregates of bacteriochlorophylls. J Phys Chem B 102:7640–7650

    CAS  Google Scholar 

  97. Theiste D, Callis PR, Woody RW (1991) Effects of the crystal field on transition moments in 9-ethylguanine. J Am Chem Soc 113:3260–3267

    CAS  Google Scholar 

  98. Sreerama N, Woody RW, Callis PR (1994) Theoretical study of the crystal field effects on the transition dipole moments in methylated adenines. J Phys Chem 98:10397–10407

    CAS  Google Scholar 

  99. Li J, Williams B, Cramer CJ et al (1999) A class IV charge model for molecular excited states. J Phys Chem 110:724–733

    CAS  Google Scholar 

  100. MacKerell AD Jr, Bashford D, Bellott M et al (1998) All atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616

    CAS  Google Scholar 

  101. Hess B, Kutzner C, van der Spoel D et al (2008) Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447

    CAS  Google Scholar 

  102. Qiu L, Pabit SA, Roitberg AE et al (2002) Smaller and faster: the 20-residue Trp-cage protein folds in 4μs. J Am Chem Soc 124:12952–12953

    PubMed  CAS  Google Scholar 

  103. Egan DA, Logan TM, Liang H et al (1993) Equilibrium denaturation of recombinant human FK binding protein in urea. Biochemistry 32:1920–1927

    PubMed  CAS  Google Scholar 

  104. Eftink MR (1991) Fluorescence techniques for studying protein structure. Methods Biochem Anal 35:127–205

    PubMed  CAS  Google Scholar 

  105. Harris DL, Hudson BS (1991) Fluorescence and molecular dynamics study of the internal motion of the buried tryptophan in bacteriophage T4 lysozyme: effects of temperature and alteration of nonbonded networks. Chem Phys 158:353–382

    CAS  Google Scholar 

  106. Kubelka J. Unpublished work. 2011.

    Google Scholar 

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Acknowledgements

We gratefully acknowledge support from NSF Grants MCB-0446542 and MCB-0847047, and crucial supercomputer resource TRAC grants MCB090176 from Teragrid/XSEDE for the years 2009–2012. We also acknowledge contributions to the work presented here by Drs. James Vivian, Tiqing Liu, Alexander Petrenko, Pedro Muino, and Chia-Pin Pan. We thank Drs. Ludwig Brand, Bruce Hudson, Mary Barkley, Jay Knutson, Dimitri Toptygin, Robert Woody, Andy Albrecht, Jonathan King, Linda Kurz, Jaap Broos, Dongping Zhong, Jan Kubelka, William Eaton, and J. Michael Schurr for collaboration, inspiration, and helpful conversations.

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  1. Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA

    Patrik R. Callis & Jose R. Tusell

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  1. Patrik R. Callis
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  1. KULeuven-Biomolecular Dynamics BioSCENTer, Leuven, Belgium

    Yves Engelborghs

  2. MicroSpectroscopy Centre, University of Wageningen Biochemistry, Wageningen, The Netherlands

    Antonie J.W.G. Visser

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Callis, P.R., Tusell, J.R. (2014). MD + QM Correlations with Tryptophan Fluorescence Spectral Shifts and Lifetimes. In: Engelborghs, Y., Visser, A. (eds) Fluorescence Spectroscopy and Microscopy. Methods in Molecular Biology, vol 1076. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-649-8_8

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