Thesis final - after defense-7 - Jacobs University

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References 103. Lienqueo, M.E.; Mahn, A.; Asenjo, J.A. Mathematical correlations for predicting protein retention times in hydrophobic interaction chromatography. Journal of Chromatography A 2002, 978, 71-79. 104. Wilkins, M.R.; Gasteiger, E.; Sanchez, J.; Bairoch, A.; Hochstrasser, D.F. Twodimensional gel electrophoresis for proteome projects: The effects of protein hydrophobicity and copy number. Electrophoresis 1998, 19, 1501-1505. 105. Shevchenko, A.; Jensen, O.N.; Podtelejnikov, A.V.; Sagliocco, F.; Wilm, M.; Vorm, O.; Mortensen, P.; Shevchenko, A.; Boucherie, H.; Mann, M. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proceedings of the National Academy of Sciences 1996, 93, 14440. 106. Wilkins, M.R.; Pasquali, C.; Appel, R.D.; Ou, K.; Golaz, O.; Sanchez, J.C.; Yan, J.X.; Gooley, A.A.; Hughes, G.; Humphery-Smith, I. From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and arnino acid analysis. Nature Biotechnology 1996, 14, 61-65. 107. Herbert, B.; Righetti, P.; Citterio, A.; Boschetti, E. Sample preparation and prefractionation techniques for electrophoresis-based proteomics. Proteome Research 2007, 15-40. 108. Fountoulakis, M. and Juranville, J.F. Enrichment of low-abundance brain proteins by preparative electrophoresis. Analatyical Biochemistry 2003, 313, 267-282. 109. Fountoulakis, M.; Takács, M.; Berndt, P.; Langen, H.; Takács, B. Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography. Electrophoresis 1999, 20, 2181-2195. 110. Fountoulakis, M.; Juranville, J.F.; Tsangaris, G.; Suter, L. Fractionation of liver proteins by preparative electrophoresis. Amino Acids 2004, 26, 27-36. 111. Langen, H.; Takács, B.; Evers, S.; Berndt, P.; Lahm, H.W.; Wipf, B.; Gray, C.; Fountoulakis, M. Two‐dimensional map of the proteome of Haemophilus influenzae. Electrophoresis 2000, 21, 411-429. 127
References 112. Gu, Z. and Glatz, C.E. A method for three‐dimensional protein characterization and its application to a complex plant (corn) extract. Biotechnology and bioengineering 2007, 97, 1158-1169. 113. Fausnaugh, J.L. and Regnier, F.E. Solute and mobile phase contributions to retention in hydrophobic interaction chromatography of proteins. Journal of Chromatography A 1986, 359, 131-146. 114. Salgado, J.C.; Rapaport, I.; Asenjo, J.A. Prediction of retention times of proteins in hydrophobic interaction chromatography using only their amino acid composition. Journal of Chromatography A 2005, 1098, 44-54. 115. Fisher, H.F. A limiting law relating the size and shape of protein molecules to their composition. Proceedings of the National Academy of Sciences 1964, 51, 1285-1291. 116. Warshel, A. What about protein polarity? Nature 1987, 330, 15-16. 117. Capaldi, R.A. and V, Garret. The low polarity of many membrane proteins. Proceedings of the National Academy of Sciences 1972, 69, 930-932. 118. Lin, F.Y.; Chen, W.Y.; Hearn, M.T.W. Microcalorimetric studies on the interaction mechanism between proteins and hydrophobic solid surfaces in hydrophobic interaction chromatography: effects of salts, hydrophobicity of the sorbent, and structure of the protein. Analytical Chemistry 2001, 73, 3875-3883. 119. Gekko, K. and Hasegawa, Y. Compressibility-structure relationship of globular proteins. Biochemistry (N. Y. ) 1986, 25, 6563-6571. 120. Peter A., F. Review: Protein function at thermal extremes: balancing stability and flexibility. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology 2001, 129, 417-431. 121. Aasim, M.; Bibi, N.; Vennapusa, R.R.; Fernández, L. M. Extended DLVO calculations expose the role of the structural nature of the adsorbent beads during chromatography. Journal of Separation Science 2012, In Press. 128
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A proteome wide approach to underst
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I also want to mention the efforts
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Dedication To my father Haji Sher A
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Table of Contents 1. Introduction .
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3.3.2.2. Protein distributions on 2
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Chapter 1 1. Introduction 1.1. Intr
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Chapter 1 cell proteome to facilita
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Chapter 1 proteins. It is this diff
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Chapter 1 Salt conc. decreasing (Gr
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Chapter 1 The ions at the start of
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Chapter 1 exposure of hydrophobic r
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Chapter 1 based on the surface hydr
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Chapter 1 1.5. Analysis of the yeas
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Chapter 1 molecular weight impuriti
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Chapter 1 followed by its introduct
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Chapter 1 protein towards purificat
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Chapter 2 EXPERIMENTAL APPROACH
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Chapter 2 Yeast cell proteome and c
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Chapter 2 ligands (Toyopearl-Hexyl,
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Chapter 2 number of spots was count
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Chapter 2 (http://www.matrixscience
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Chapter 3 RESULTS AND DISCUSSION
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Chapter 3 to the retention behavior
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Chapter 3 investigate the hydrophob
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Chapter 3 the interior of the prote
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Chapter 3 A B C Figure 9: The cryst
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Chapter 3 of the comparative analys
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Chapter 3 Figure 11: Represent the
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Chapter 3 Ether, some 2-D gels were
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Chapter 3 Figure 13: Represent 2-D
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Chapter 3 Table 5. List of the iden
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Chapter 3 Table 7. List of the iden
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Chapter 3 amino acids by Cowan-Whit
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Chapter 3 Figure 15 C: Represents t
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Chapter 3 Figure 16 A: Represents t
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Chapter 3 The polarity value for th
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Chapter 3 Figure 17: Represents the
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Chapter 3 Figure 18: Represents the
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Chapter 3 published papers with mod
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Chapter 3 ligands revealed less dif
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Chapter 3 3.2. Influence of the dif
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Chapter 3 Table 10: The chemistry o
Page 85 and 86: Chapter 3 where approximately 50% o
Page 87 and 88: Chapter 3 3.2.3.2. The electrophore
Page 89 and 90: Chapter 3 Figure 22: Represent 2-D
Page 91 and 92: Chapter 3 Table 12. List of the ide
Page 93 and 94: Chapter 3 Table 14. List of the ide
Page 95 and 96: Chapter 3 r 2 values from the data
Page 97 and 98: Chapter 3 Figure 24 C: Represents t
Page 99 and 100: Chapter 3 approximately 47%. The me
Page 101 and 102: Chapter 3 Figure 25 B: Represents t
Page 103 and 104: Chapter 3 values have been reported
Page 105 and 106: Chapter 3 towards conformational ch
Page 107 and 108: Chapter 3 Figure 28: Represents the
Page 109 and 110: Chapter 3 among the adsorbents were
Page 111 and 112: Chapter 3 3.3. Protein distribution
Page 113 and 114: Chapter 3 3.3.2.2. Protein distribu
Page 115 and 116: Chapter 3 Figure 29 B: Represent th
Page 117 and 118: Chapter 3 When the number of smalle
Page 119 and 120: Chapter 3 and hydrophobic interacti
Page 121 and 122: Chapter 4 CONCLUSIONS
Page 123 and 124: Chapter 4 • The base supports rev
Page 125 and 126: Chapter 4 additional understanding
Page 127 and 128: References 13. Lienqueo, M.E.; Lese
Page 129 and 130: References 32. Salgado, J.C.; Rapap
Page 131 and 132: References 52. B.H.J., H. Accessibl
Page 133 and 134: References 71. Xindu, G. and Regnie
Page 135: References 91. Alonso-Orgaz, S.; Mo
Page 139: References 132. Reubsaet, J.L.E. an
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