Techniques for higher-order structure determination

Biophysics for Therapeutic Protein Development

Volumn , Issue , 2013, Pages 33-82

  Kranz, James ^a   AlAzzam, Fatma ^b   Saluja, Atul ^c   Svitel, Juraj ^d   Al Azzam, Wasfi ^a  

^a GLAXOSMITHKLINE   (United States)

^b TechnoPharmaSphere LLC   (United States)

^c BRISTOL MYERS SQUIBB   (United States)

^d AMGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84877924130     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-4316-2_3     Document Type: Chapter

References (184)

1. Adams PD, Chen Y, Ma K, Zagorski MG, Sonnichsen FD, McLaughlin ML, Barkley MD (2002) Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. J Am Chem Soc 124:9278-9286.
2. Ahmad F, Salahuddin A (1976) Reversible unfolding of the major fraction of ovalbumin by guanidine hydrochloride. Biochemistry 15(23):5168-5175.
3. Al-Lazikani B, Lesk AM, Chothia C (1997) Standard conformations for the canonical structures of immunoglobulins. J Mol Biol 273:927-948.
4. Asher SA, Bormett RW, Chen XG, Lemmon DH, Cho N (1993) UV resonance Raman spectroscopy using a new cw laser source: convenience and experimental simplicity. Appl Spectrosc 47:628-633.
5. Bai Y, Sosnick TR, Mayne L, Englander SW (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269:192-197.
6. Baldwin AJ, Kay LE (2009) NMR spectroscopy brings invisible protein states into focus. Nat Chem Biol 5:808-814.
7. Bandekar J (1992) Amide modes and protein conformation. Biochim Biophys Acta 1120:123-143.
8. Barron LD (2006) Structure and behaviour of biomolecules from Raman optical activity. Curr Opin Struct Biol 16:638-643.
9. Barron LD, Hecht L, Bell AF, Wilson G (1996) Recent developments in Raman optical activity of biopolymers. Appl Spectrosc 50:619-629.
10. Barron LD, Hecht L, Blanch EW, Bell AF (2000) Solution structure and dynamics of biomolecules from Raman optical activity. Prog Biophys Mol Biol 73:1-49.
11. Bartlett AI, Radford SE (2009) An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 16:582-588.
12. Baumruk V, Keiderling TA (1993) Vibrational circular dichroism of proteins in H2O solution. J Am Chem Soc 115:6939-6942.
13. Benevides JM, Overman SA, Thomas GJ Jr (2004) Raman spectroscopy of proteins. Curr Protoc Protein Sci, Chapter 17, Unit 17.18.
14. Billeter M, Vendrell J, Wider G, Aviles FX, Coll M, Guasch A, Huber R, Wuthrich K (1992) Comparison of the NMR solution structure with the X-ray crystal structure of the activation domain from procarboxypeptidase B. J Biomol NMR 2:1-10.
15. Billeter M, Wagner G, Wuthrich K (2008) Solution NMR structure determination of proteins revisited. J Biomol NMR 42:155-158.
16. Boehr DD, Dyson HJ, Wright PE (2006) An NMR perspective on enzyme dynamics. Chem Rev 106:3055-3079.
17. Brandts JF, Lin LN (1990) Study of strong to ultratight protein interactions using differential scanning calorimetry. Biochemistry 29:6927-6940.
18. Brennan JF, Wang Y, Ramachandra RD, Feld MS (1997) Near-infrared Raman spectrometer systems for human studies. Appl Spectrosc 51:201-208.
19. Byler DM, Susi H (1986) Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25:469-487.
20. Cantor RC, Schimmel PR (1980) Biophysical Chemistry: techniques for the study of biological structure and function, vol 2. W. H. Freeman, San Francisco.
21. Cao XL, Dukor RK, Nafie LA (2008) Reduction of linear birefringence in vibrational circular dichroism measurement: use of a rotating half-wave plate. Theor Chem Acc 119:69-79.
22. Carpenter JF, Prestrelski SJ, Dong A (1998) Application of infrared spectroscopy to development of stable lyophilized protein formulations. Eur J Pharm Biopharm 45:231-238.
23. Chalmers J, Griffiths P (eds) (2002) Handbook of vibrational spectroscopy. Wiley, Chichester.
24. Chance B (1953) The carbon monoxide compounds of the cytochrome oxidases. I. Difference spectra. J Biol Chem 202:383-396.
25. Chance B, Pappenheimer AM Jr (1954) Kinetic and spectrophotometric studies of cytochrome b5 in midgut homogenates of cecropia. J Biol Chem 209:931-943.
26. Chill JH, Naider F (2011) A solution NMR view of protein dynamics in the biological membrane. Curr Opin Struct Biol 21:627-633.
27. Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR et al (1989) Conformations of immunoglobulin hypervariable regions. Nature 342:877-883.
28. Cimmperman P, Baranauskiene L, Jachimoviciute S, Jachno J, Torresan J, Michailoviene V, Matuliene J, Sereikaite J, Bumelis V, Matulis D (2008) A quantitative model of thermal stabilization and destabilization of proteins by ligands. Biophys J 95:3222-3231.
29. Daniel E, Weber G (1966) Cooperative effects in binding by bovine serum albumin. I. The binding of 1-anilino-8-naphthalenesulfonate. Fluorimetric titrations. Biochemistry 5:1893-1900.
30. D'Antonio J, Murphy BM, Manning MC, Al-Azzam WA (2012) Comparability of protein therapeutics:quantitative comparison of second-derivative amide I infrared spectra. J Pharm Sci 101:2025-2033.
31. Davies DR, Cohen GH (1996) Interactions of protein antigens with antibodies. Proc Natl Acad Sci USA 93:7-12.
32. Dong A, Huang P, Caughey WS (1990) Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29:3303-3308.
33. Dong J, Dinakarpandian D, Carey PR (1998) Extending the Raman analysis of biological samples to the 100 micromolar concentration range. Appl Spectrosc 52:1117-1122.
34. dos Remedios CG, Moens PD (1995) Fluorescence resonance energy transfer spectroscopy is a reliable "ruler" for measuring structural changes in proteins. Dispelling the problem of the unknown orientation factor. J Struct Biol 115:175-185.
35. Dousseau F, Pezolet M (1990) Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods. Biochemistry 29:8771-8779.
36. Dukor RK, Keiderling TA (1991) Reassessment of the random coil conformation: vibrational CD study of proline oligopeptides and related polypeptides. Biopolymers 31:1747-1761.
37. Eberstein W, Georgalis Y, Saenger W (1994) Molecular interactions in crystallizing lysozyme solutions studied by photon correlation spectroscopy. J Cryst Growth 143:71-78.
38. Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117-121.
39. Englander SW (2000) Protein folding intermediates and pathways studied by hydrogen exchange. Annu Rev Biophys Biomol Struct 29:213-238.
40. Englander SW (2006) Hydrogen exchange and mass spectrometry: a historical perspective. J Am Soc Mass Spectrom 17:1481-1489.
41. Englander SW, Mayne L, Bai Y, Sosnick TR (1997) Hydrogen exchange: the modern legacy of Linderstrom-Lang. Protein Sci 6:1101-1109.
42. Epstein HF, Schechter AN, Chen RF, Anfinsen CB (1971) Folding of staphylococcal nuclease:kinetic studies of two processes in acid renaturation. J Mol Biol 60:499-508.
43. Ferreon AC, Moran CR, Gambin Y, Deniz AA (2011) Single-molecule fluorescence studies of intrinsically disordered proteins. Methods Enzymol 472:179-204.
44. Flanagan JM, Kataoka M, Shortle D, Engelman DM (1992) Truncated staphylococcal nuclease is compact but disordered. Proc Natl Acad Sci USA 89:748-752.
45. Foldes-Papp Z, Demel U, Domej W, Tilz GP (2002) A new dimension for the development of fluorescence-based assays in solution: from physical principles of FCS detection to biological applications. Exp Biol Med (Maywood) 227:291-300.
46. Fu K, Griebenow K, Hsieh L, Klibanov AM, Langer R (1999) FTIR characterization of the secondary structure of proteins encapsulated within PLGA microspheres. J Control Release 58:357-366.
47. Goldberg DS, Bishop SM, Shah AU, Sathish HA (2010) Formulation development of therapeutic monoclonal antibodies using high-throughput fluorescence and static light scattering techniques:role of conformational and colloidal stability. J Pharm Sci.
48. Goldberg DS, Bishop SM, Shah AU, Sathish HA (2011) Formulation development of therapeutic monoclonal antibodies using high-throughput fluorescence and static light scattering techniques:role of conformational and colloidal stability. J Pharm Sci 100(4):1306-1315.
49. Goldstein SR, Kidder LH, Herne TM, Levin IW, Lewis EN (1996) The design and implementation of a high-fidelity Raman imaging microscope. J Microsc 184:35-45.
50. Grauw CJ, Otto C, Greve J (1997) Linescan Raman microspectrometry for biological applications. Appl Spectrosc 51:1607-1612.
51. Greenfield NJ (1996) Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. Anal Biochem 235:1-10.
52. Greenfield NJ (2006a) Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc 1(6):2876-2890.
53. Greenfield NJ (2006b) Determination of the folding of proteins as a function of denaturants, osmolytes or ligands using circular dichroism. Nat Protoc 1:2733-2741.
54. Greenfield NJ (2006c) Analysis of the kinetics of folding of proteins and peptides using circular dichroism. Nat Protoc 1:2891-2899.
55. Greenfield NJ (2007) Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions. Nat Protoc 1:2527-2535.
56. Greenfield N, Fasman GD (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8:4108-4116.
57. Griebenow K, Klibanov AM (1995) Lyophilization-induced reversible changes in the secondary structure of proteins. Proc Natl Acad Sci USA 92:10969-10976.
58. Griffiths PR, de Haseth JA (1986) Fourier transform infrared spectroscopy. Wiley Interscience, New York.
59. Hamuro Y, Weber PC, Griffin PR (2005) High-throughput analysis of protein structure by hydrogen/ deuterium exchange mass spectrometry. Methods Biochem Anal 45:131-157.
60. Harding SE (1980) The combination of the viscosity increment with the harmonic mean rotational relaxation time for determining the conformation of biological macromolecules in solution. Biochem J 189(2):359-361.
61. Harding SE (1981) A compound hydrodynamic shape function derived from viscosity and molecular covolume measurements. Int J Biol Macromol 3(5):340-341.
62. Harding SE (1997) The intrinsic viscosity of biological macromolecules. Progress in measurement, interpretation and application to structure in dilute solution. Prog Biophys Mol Biol 68(2-3):207-262.
63. Haris PI, Chapman D (1995) The conformational analysis of peptides using Fourier transform IR spectroscopy. Biopolymers 37:251-263.
64. Haris PI, Lee DC, Chapman D (1986) A Fourier transform infrared investigation of the structural differences between ribonuclease A and ribonuclease S. Biochim Biophys Acta 874:255-265.
65. Haris PI, Chapman D, Harrison RA, Smith KF, Perkins SJ (1990) Conformational transition between native and reactive center cleaved forms of alpha 1-antitrypsin by Fourier transform infrared spectroscopy and small-angle neutron scattering. Biochemistry 29:1377-1380.
66. Hashimoto S, Ikeda T, Takeuuchi H, Harada I (1993) Utilization of a prism monochromator as a sharp-cut bandpass filter in ultraviolet Raman spectroscopy. Appl Spectrosc 47:1283-1285.
67. Hawe A, Sutter M, Jiskoot W (2008) Extrinsic fluorescent dyes as tools for protein characterization. Pharm Res 25:1487-1499.
68. Hawe A, Rispens T, Herron JN, Jiskoot W (2011) Probing bis-ANS binding sites of different affinity on aggregated IgG by steady-state fluorescence, time-resolved fluorescence and isothermal titration calorimetry. J Pharm Sci 100:1294-1305.
69. He F, Hogan S, Latypov RF, Narhi LO, Razinkov VI (2009a) High throughput thermostability screening of monoclonal antibody formulations. J Pharm Sci 99:1707-1720.
70. He F, Phan DH, Hogan S, Bailey R, Becker GW, Narhi LO, Razinkov VI (2009b) Detection of IgG aggregation by a high throughput method based on extrinsic fluorescence. J Pharm Sci 99:2598-2608.
71. Hermansson AM (1972) Functional properties of proteins for foods. Lebensin-Wiss Technol 5:24.
72. Hermansson AM (1979) Aspects of protein structure, rheology and texturization. Food Texture Rheol [Proc Symp] 265-282.
73. Herr AB, Ballister ER, Bjorkman PJ (2003) Insights into IgA-mediated immune responses from the crystal structures of human FcalphaRI and its complex with IgA1-Fc. Nature 423:614-620.
74. van Holde KE, Johnson WC, Ho (2006) Methods for the Separation and Characterization of Macromolecules. In: van Holde KE, Johnson WC, Ho PS. Principles of Physical Biochemistry. 2nd ed. Upper Saddle River, NJ: Pearson Prentice Hall:213-275.
75. Hynes TR, Fox RO (1991) The crystal structure of staphylococcal nuclease refined at 1.7 A resolution. Proteins 10:92-105.
76. Jackson M, Mantsch HH (1995) The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit Rev Biochem Mol Biol 30:95-120.
77. Jares-Erijman EA, Jovin TM (2003) FRET imaging. Nat Biotechnol 21:1387-1395.
78. Jelesarov I, Bosshard HR (1999) Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. J Mol Recognit 12:3-18.
79. Kamerzell TJ, Esfandiary R, Joshi SB, Middaugh CR, Volkin DB (2011) Protein-excipient interactions:mechanisms and biophysical characterization applied to protein formulation development. Adv Drug Deliv Rev 63:1118-1159.
80. Kauzmann W (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14:1-63.
81. Keiderling TA, Silva RA, Yoder G, Dukor RK (1999) Vibrational circular dichroism spectroscopy of selected oligopeptide conformations. Bioorg Med Chem 7:133-141.
82. Keiderling TA, Kubelka J, Hilario J (eds) (2006) Vibrational circular dichroism of biopolymers:summary of methods and applications. CRC, Boca Raton.
83. Kielec JM, Valentine KG, Wand AJ (2009) A method for solution NMR structural studies of large integral membrane proteins: reverse micelle encapsulation. Biochim Biophys Acta 1798:150-160.
84. Kranz JK, Schalk-Hihi C (2011) Protein thermal shifts to identify low molecular weight fragments. Methods Enzymol 493:277-298.
85. Krimm S, Bandekar J (1986) Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv Protein Chem 38:181-364.
86. Krishinan KS, Brandts JF (1978) Scanning calorimetry. Methods Enzymol 49:3-14.
87. Kubelka J, Hofrichter J, Eaton WA (2004) The protein folding "speed limit". Curr Opin Struct Biol 14:76-88.
88. Kurouski D, Lombardi RA, Dukor RK, Lednev IK, Nafie LA (2010) Direct observation and pH control of reversed supramolecular chirality in insulin fibrils by vibrational circular dichroism. Chem Commun (Camb) 46:7154-7156.
89. Kurouski D, Dukor RK, Lu X, Nafie LA, Lednev IK (2012) Spontaneous inter-conversion of insulin fibril chirality. Chem Commun (Camb) 48:2837-2839.
90. Ladbury JE, Chowdhry BZ (1996) Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chem Biol 3:791-801.
91. Lakhani A, Malon P, Keiderling TA (2009) Comparison of vibrational circular dichroism instruments:development of a new dispersive VCD. Appl Spectrosc 63:775-785.
92. Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, New York.
93. LeTilly V, Royer CA (1993) Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding. Biochemistry 32:7753-7758.
94. Li CH, Li T (2009) Application of vibrational spectroscopy to the structural characterization of monoclonal antibody and its aggregate. Curr Pharm Biotechnol 10:391-399.
95. Li Y, Williams TD, Topp EM (2008) Effects of excipients on protein conformation in lyophilized solids by hydrogen/deuterium exchange mass spectrometry. Pharm Res 25:259-267.
96. Li Y, Mach H, Blue JT (2011) High throughput formulation screening for global aggregation behaviors of three monoclonal antibodies. J Pharm Sci 100:2120-2135.
97. Liu J, Andya JD, Shire SJ (2006) A critical review of analytical ultracentrifugation and field flow fractionation methods for measuring protein aggregation. AAPS J 8:E580-E589.
98. Loria JP, Berlow RB, Watt ED (2008) Characterization of enzyme motions by solution NMR relaxation dispersion. Acc Chem Res 41:214-221.
99. Lundqvist R (1999) Molecular weight studies on hydroxypropyl methyl cellulose. Part 2. Intrinsic viscosity. Int J Polym Anal Charact 5(1):61-84.
100. Ma S, Cao X, Mak M, Sadik A, Walkner C, Freedman TB, Lednev IK, Dukor RK, Nafie LA (2007) Vibrational circular dichroism shows unusual sensitivity to protein fibril formation and development in solution. J Am Chem Soc 129:12364-12365.
101. Machtle W, Borger L (2006) Sedimentation velocity. In: Machtle W, Borger L (eds) Analytical ultracentrifugation of polymers and nanoparticles. Heidelberg Springer:47-96.
102. Macosko CW (1994) In: Macosko CW (ed) Rheology: principles, measurements and applications. Wiley-VCH, New York, p 550.
103. Mandel M (1993) Applications of dynamic light scattering to polyelectrolytes in solution. In:Brown W (ed) Dynamic light scattering: the method and some applications. Oxford University Press, New York, pp 319-371.
104. Manley G, Loria JP (2012) NMR insights into protein allostery. Arch Biochem Biophys 519:223-231.
105. Mann CJ, Royer CA, Matthews CR (1993) Tryptophan replacements in the trp aporepressor from Escherichia coli: probing the equilibrium and kinetic folding models. Protein Sci 2:1853-1861.
106. Markley JL, Ulrich EL, Westler WM, Volkman BF (2003) Macromolecular structure determination by NMR spectroscopy. Methods Biochem Anal 44:89-113.
107. Matulis D, Kranz JK, Salemme FR, Todd MJ (2005) Thermodynamic stability of carbonic anhydrase:measurements of binding affinity and stoichiometry using ThermoFluor. Biochemistry 44:5258-5266.
108. Meyer JD, Bai SJ, Rani M, Suryanarayanan R, Nayar R, Carpenter JF, Manning MC (2004) Infrared spectroscopic studies of protein formulations containing glycine. J Pharm Sci 93:1359-1366.
109. Mezzasalma TM, Kranz JK, Chan W, Struble GT, Schalk-Hihi C, Deckman IC, Springer BA, Todd MJ (2007) Enhancing recombinant protein quality and yield by protein stability profiling. J Biomol Screen 12:418-428.
110. Mittermaier AK, Kay LE (2009) Observing biological dynamics at atomic resolution using NMR. Trends Biochem Sci 34:601-611.
111. Miura T, Takeuchi H, Harada I (1991) Raman spectroscopic characterization of tryptophan side chains in lysozyme bound to inhibitors: role of the hydrophobic box in the enzymatic function. Biochemistry 30:6074-6080.
112. Miyawaki A (2011) Proteins on the move: insights gained from fluorescent protein technologies. Nat Rev Mol Cell Biol 12:656-668.
113. Miyazawa T, Shimanouchi T, Mizushima S (1956) Characteristic infrared bands of monosubstituted amides. J Chem Phys 24:408.
114. Monkos K, Turczynski B (1991) Determination of the axial ratio of globular proteins in aqueous solution using viscometric measurements. Int J Biol Macromol 13(6):341-344.
115. Murphy KP, Freire E (1992) Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem 43:313-361.
116. Nafie LA (1996) Vibrational optical activity. Appl Spectrosc 50:14A-26A.
117. Nafie LA (2011) Vibrational optical activity: principles and applications. Wiley, Chichester.
118. Nafie LA, Dukor RK (eds) (2007) Applications of vibrational optical activity in the pharmaceutical industry. Wiley, Chichester.
119. Nashine VC, Hammes-Schiffer S, Benkovic SJ (2010) Coupled motions in enzyme catalysis. Curr Opin Chem Biol 14:644-651.
120. Norvaisas P, Petrauskas V, Matulis D (2012) Thermodynamics of cationic and anionic surfactant interaction. J Phys Chem B 116:2138-2144.
121. Otto MR, Lillo MP, Beechem JM (1994) Resolution of multiphasic reactions by the combination of fluorescence total-intensity and anisotropy stopped-flow kinetic experiments. Biophys J 67:2511-2521.
122. Perez C, Castellanos IJ, Costantino HR, Al-Azzam W, Griebenow K (2002) Recent trends in stabilizing protein structure upon encapsulation and release from bioerodible polymers. J Pharm Pharmacol 54:301-313.
123. Perrin F (1926) J Phys Radium 1:390-401.
124. Philo JS (2006) Is any measurement method optimal for all aggregate sizes and types? AAPS J 8:E564-E571.
125. Philo JS (2005) Analytical ultracentrifugation. In: Borchardt RT, Middaugh CR, series eds. Biotechnology: pharmaceutical aspects, Jiskoot W, Crommelin D, vol eds. Volume III: Methods for structural analysis of protein pharmaceuticals. AAPS Press, Arlington, pp 379-412.
126. Pollok BA, Heim R (1999) Using GFP in FRET-based applications. Trends Cell Biol 9:57-60.
127. Putnam WS, Prabhu S, Zheng Y, Subramanyam M, Wang YM (2010) Pharmacokinetic, pharmacodynamic and immunogenicity comparability assessment strategies for monoclonal antibodies. Trends Biotechnol 28:509-516.
128. Ramsey JD, Gill ML, Kamerzell TJ, Price ES, Joshi SB, Bishop SM, Oliver CN, Middaugh CR (2009) Using empirical phase diagrams to understand the role of intramolecular dynamics in immunoglobulin G stability. J Pharm Sci 98:2432-2447.
129. Raso SW, Clark PL, Haase-Pettingell C, King J, Thomas GJ Jr (2001) Distinct cysteine sulfhydryl environments detected by analysis of Raman S-hh markers of Cys->Ser mutant proteins. J Mol Biol 307:899-911.
130. Rossmann MG (2001) Molecular replacement-historical background. Acta Crystallogr D Biol Crystallogr 57:1360-1366.
131. Royer CA (1993) Understanding fluorescence decay in proteins. Biophys J 65:9-10.
132. Royer CA (1995) Fluorescence spectroscopy. Methods Mol Biol 40:65-89.
133. Royer CA (2006) Probing protein folding and conformational transitions with fluorescence. Chem Rev 106:1769-1784.
134. Royer CA, Scarlata SF (2008) Fluorescence approaches to quantifying biomolecular interactions. Methods Enzymol 450:79-106.
135. Sanchez-Ruiz JM (2011) Probing free-energy surfaces with differential scanning calorimetry. Annu Rev Phys Chem 62:231-255.
136. Sapienza PJ, Lee AL (2010) Using NMR to study fast dynamics in proteins: methods and applications. Curr Opin Pharmacol 10:723-730.
137. Schuck P, Perugini MA, Gonzales NR, Howlett GJ, Schubert D (2002) Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. Biophys J 82:1096-1111.
138. Schümmer P. Mechanics of Non-Newtonian Fluids. Von W. R. Schowalter. Pergamon Press, Oxford-Frankfurt 1978. 1. Aufl., IX, 300 S., zahlr. Abb. u. Tab., geb., $ 35.00. Chemie Ingenieur Technik. 1979;51(7):766-766.
139. Schweitzer-Stenner R, Eker F, Huang Q, Griebenow K, Mosz P, Kozlowski P (2002) Structure analysis of dipeptides in water by exploring and utilizing the structural sensitivity of amide III by polarized visible Raman, FTIR spectroscopy and DFT based normal coordinate analysis. J Phys Chem B 106:4294-4304.
140. Scott DJ, Schuck P (2005) A brief introduction to the analytical ultracentrifugation of proteins for beginners. In: Scott DJ, Harding SE, Rowe AJ (eds) Analytical ultracentrifugation techniques and methods. RSC Publishing, Cambridge, pp 1-25.
141. Sharp KA, Nicholls A, Friedman R, Honig B (1991) Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry 30:9686-9697.
142. Shaw DJ (1992) Rheology. Colloidal and surface chemistry, 4th edn. Butterworth-Heinemann, Boston.
143. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685-4690.
144. Shi Z, Chen K, Liu Z, Kallenbach NR (2006) Conformation of the backbone in unfolded proteins. Chem Rev 106:1877-1897.
145. Siamwiza MN, Lord RC, Chen MC, Takamatsu T, Harada I, Matsuura H, Shimanouchi T (1975) Interpretation of the doublet at 850 and 830 cm-1 in the Raman spectra of tyrosyl residues in proteins and certain model compounds. Biochemistry 14:4870-4876.
146. Skinner AL, Laurence JS (2008) High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands. J Pharm Sci 97:4670-4695.
147. Skinner AL, Laurence JS (2010) Probing residue-specific interactions in the stabilization of proteins using high-resolution NMR: a study of disulfide bond compensation. J Pharm Sci 99:2643-2654.
148. Skinner JJ, Lim WK, Bedard S, Black BE, Englander SW (2012) Protein dynamics viewed by hydrogen exchange. Protein Sci 21:996-1005.
149. Smith BC (1996) Fundamentals of fourier transform infrared spectroscopy. CRC, Boca Raton.
150. Socrates G (2004) Infrared and Raman characteristic group frequencies: tables and charts, 3rd edn.
151. Wiley, Chichester Sondermann P, Oosthuizen V (2002) X-ray crystallographic studies of IgG-Fc gamma receptor interactions. Biochem Soc Trans 30:481-486.
152. Spink CH (2008) Differential scanning calorimetry. Methods Cell Biol 84:115-141.
153. Stefani M, Dobson CM (2003) Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J Mol Med (Berl) 81:678-699.
154. Stern KG (1937) Spectroscopy of catalase. J Gen Physiol 20:631-648.
155. Stokes GG (1852) On the change of refrangibility of light. Philos Trans R Soc Lond 142:463-562.
156. Surewicz WK, Mantsch HH (1988) New insight into protein secondary structure from resolution-enhanced infrared spectra. Biochim Biophys Acta 952:115-130.
157. Suryaprakash P, Prakash V (2000) Unfolding of multimeric proteins in presence of denaturants. A case study of helianthinin from Helianthus annuus L. Nahrung 44(3):178-183.
158. Susi H, Byler DM (1986) Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol 130:290-311.
159. Susi H, Timasheff SN, Stevens L (1967) Infrared spectra and protein conformations in aqueous solutions. I. The amide I band in H2O and D2O solutions. J Biol Chem 242:5460-5466.
160. Tamm LK, Lai AL, Li Y (2007) Combined NMR and EPR spectroscopy to determine structures of viral fusion domains in membranes. Biochim Biophys Acta 1768:3052-3060.
161. Tanford C, Buzzell JG (1956) The viscosity of aqueous solutions of bovine serum albumin between pH 4.3 and 10.5. J Phys Chem 60:225-231.
162. Tsuboi M, Suzuki M, Overman SA, Thomas GJ Jr (2000) Intensity of the polarized Raman band at 1340-1345 cm-1 as an indicator of protein alpha-helix orientation: application to Pf1 filamentous virus. Biochemistry 39:2677-2684.
163. Tsutsui Y, Wintrode PL (2007) Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Curr Med Chem 14:2344-2358.
164. Tu RS, Breedveld V (2005) Microrheological detection of protein unfolding. Phys Rev E Stat Nonlin Soft Matter Phys 72(4 Pt 1):041914.
165. Van Holde KE, Johnson WC, Ho PS (2006) Principles of physical biochemistry. Pearson/Prentice Hall, Upper.
166. Saddle River Velazquez-Campoy A, Ohtaka H, Nezami A, Muzammil S, Freire E (2004) Isothermal titration calorimetry. Curr Protoc Cell Biol, Chapter 17, Unit 17.18.
167. Venyaminov S, Kalnin NN (1990a) Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands. Biopolymers 30:1243-1257.
168. Venyaminov S, Kalnin NN (1990b) Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in alpha-, beta-, and random coil conformations. Biopolymers 30:1259-1271.
169. Wand AJ (2001) Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat Struct Biol 8:926-931.
170. Wang Y, Purrello R, Jordan T, Spiro TG (1991) UVRR spectroscopy of the peptide bond. J Am Chem Soc 113:6359-6368.
171. Weber G (1952a) Polarization of the fluorescence of macromolecules. II. Fluorescent conjugates of ovalbumin and bovine serum albumin. Biochem J 51:155-167.
172. Weber G (1952b) Polarization of the fluorescence of macromolecules. I. Theory and experimental method. Biochem J 51:145-155.
173. Weber G, Daniel E (1966) Cooperative effects in binding by bovine serum albumin. II. The binding of 1-anilino-8-naphthalenesulfonate. Polarization of the ligand fluorescence and quenching of the protein fluorescence. Biochemistry 5:1900-1907.
174. Weber G, Laurence DJ (1954) Fluorescent indicators of adsorption in aqueous solution and on the solid phase. Biochem J 56:xxxi.
175. Weber PC, Salemme FR (2003) Applications of calorimetric methods to drug discovery and the study of protein interactions. Curr Opin Struct Biol 13:115-121.
176. Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RA (2002) Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. Chem Rev 102:371-386.
177. Wyatt PJ (1993) Light scattering and the absolute characterization of macromolecules. Anal Chim Acta 272(1):1-40.
178. Yang JT (1961) The viscosity of macromolecules in relation to molecular conformations. Adv Protein Chem 16:323-401.
179. Yoder G, Polese A, Silva RAGD, Formaggio F, Crisma M, Broxterman QB, Kamphuis J, Toniolo C, Keiderling TA (1997) Conformational characterization of terminally blocked L-(alpha Me) Val homopeptides using vibrational and electronic circular dichroism. 3(10)-helical stabilization by peptide-peptide interaction. J Am Chem Soc 119:10278-10285.
180. Zhang R, Monsma F (2010) Fluorescence-based thermal shift assays. Curr Opin Drug Discov Devel 13:389-402.
181. Zhu F, Tranter GE, Isaacs NW, Hecht L, Barron LD (2006) Delineation of protein structure classes from multivariate analysis of protein Raman optical activity data. J Mol Biol 363:19-26.
182. Ziarek JJ, Peterson FC, Lytle BL, Volkman BF (2011) Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol 493:241-275.
183. Zuber G, Prestrelski SJ, Benedek K (1992) Application of Fourier transform infrared spectroscopy to studies of aqueous protein solutions. Anal Biochem 207:150-156.
184. Zubriene A, Matuliene J, Baranauskiene L, Jachno J, Torresan J, Michailoviene V, Cimmperman P, Matulis D (2009) Measurement of nanomolar dissociation constants by titration calorimetry and thermal shift assay - radicicol binding to Hsp90 and ethoxzolamide binding to CAII. Int J Mol Sci 10:2662-2680.