Thesis final - after defense-7 - Jacobs University

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References 81. Shevchenko, A.; Loboda, A.; Ens, W.; Schraven, B.; Standing, K.G.; Shevchenko, A. Archived polyacrylamide gels as a resource for proteome characterization by mass spectrometry. Electrophoresis 2001, 22, 1194-1203. 82. YatesIII, J.R. Mass spectrometry: from genomics to proteomics. Trends in Genetics 2000, 16, 5-8. 83. Ekins, S.; Mestres, J.; Testa, B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. British journal of pharmacology 2007, 152, 9-20. 84. Swaan, P.W. and Ekins, S. Reengineering the pharmaceutical industry by crash-testing molecules. Drug discovery today 2005, 10, 1191-1200. 85. Wurm, F.M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nature Biotechnology 2004, 22, 1393-1398. 86. Nfor, B.K.; Verhaert, P.D.E.M.; van der Wielen, L.A.M.; Hubbuch, J.; Ottens, M. Rational and systematic protein purification process development: the next generation. Trends in biotechnology 2009, 27, 673-679. 87. Chen, J.; Yang, T.; Cramer, S.M. Prediction of protein retention times in gradient hydrophobic interaction chromatographic systems. Journal of Chromatography A 2008, 1177, 207-214. 88. Bak, H.; Kyhse-Andersen, J.; Thomas, O.R.T. High-throughput immunoturbidimetric assays for in-process determination of polyclonal antibody concentration and functionality in crude samples. Journal of Chromatography B 2007, 848, 142-150. 89. Neuhoff, V.; Arold, N.; Taube, D.; Ehrhardt, W. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9, 255- 262. 90. Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J.V.; Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature protocols 2007, 1, 2856- 2860. 125
References 91. Alonso-Orgaz, S.; Moreno, L.; Macaya, C.; Rico, L.; Mateos-Caiceres, P.J.; Sacristain, D.; Pacrez-Vizcaano, F.; Segura, A.; Tamargo, J.; Lapez-Farra, A. Proteomic Study of Plasma from Moderate Hypercholesterolemic Patients. Journal of Proteome Research 2006, 5, 2301- 2308. 92. Cowan, R., and Whittaker, R.G. Hydrophobicity indices for amino acid residues as determined by high-performance liquid chromatography. ScienceDirect 1990, 3, 75-80. 93. Frishman, D and Argos, P. Knowledge-based protein secondary structure assignment. Proteins: Structure, Function and Genetics 1995, 23, 566-579. 94. Ciorsac, A.; Craciun, D.; Ostafe, V.; Isvoran, A. Nonlinear correlations in the hydrophobicity and average flexibility along the glycolytic enzymes sequences. Chaos, Solitons & Fractals 2011, 44, 191-197. 95. Miyazawa, S., and Jernigan, R. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules ACS 1985, 18, 534-552. 96. Zimmerman, J.M; Eliezer, N; Simha, R. The characterization of amino acid sequences in proteins by statistical methods. Journal of Chemical Sciences 1968, 21, 170-201. 97. Grantham, R. Amino Acid difference formula to help explain protein evolution. Science 1974, 185, 862-864. 98. Bhaskaran , R. and Ponnuswamy, P.K. Positional flexibilities of amino acid residues in globular proteins. International journal of peptide and protein research 1988, 32, 241-255. 99. Tosoh Bioscience Hydrophobic interaction chromatography hand book B09P17A. 100. Regnier, F.E. The role of protein structure in chromatographic behavior. Science 1987, 238, 319-323. 101. Kato, Y.; Kitamura, T.; Hashimoto, T. New resin-based hydrophilic support for highperformance hydrophobic interaction chromatography. Journal of Chromatography A 1986, 360, 260-265. 102. Ochoa, J.L. Hydrophobic (interaction) chromatography. Biochimie 1978, 60, 1-15. 126
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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
Page 83 and 84: 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: References 71. Xindu, G. and Regnie
Page 137 and 138: References 112. Gu, Z. and Glatz, C
Page 139: References 132. Reubsaet, J.L.E. an
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