Thesis final - after defense-7 - Jacobs University

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Chapter 3 context of HIC based on the exposed amino acid residues of a three dimensional protein structure. The ASH of a protein has a direct proportionality to the exposed hydrophobic surface area on the protein surface. The three crystal structures identified in this work have been compared for their hydrophobic surface residues and elution position during chromatography (Figure 9). The crystal structures of the enzymes were obtained using chimera as a visualization tool (http://www.cgl.ucsf.edu/chimera). The protein such as Serine threonine protein kinase (A) has very less hydrophobic surface residues in comparison to the protein Ubiquitin carboxyl terminal hydrolase 4 (B). Due to this reason, the protein A was eluted earlier than protein B during chromatography. In the same way, the protein B has less hydrophobic surface residues as compared to the protein Phosphogycerate mutase 1 (C). Due to the less hydrophobic residues, the protein B was eluted earlier than protein C. There are several other important enzymes identified at different elution ranges and can be analyzed at the molecular level for their hydrophobic content and corresponding chromatographic behavior. These surface hydrophobic residues can be quantified in terms of ASH from the three dimensional structure of a protein utilizing MATLAB and STRIDE as computational tools. ASH has been widely exploited to predict the retention times of model proteins during HIC (103). However, all the above mentioned properties have been never studied in relation to the host derived proteins. Therefore, the above mentioned properties were investigated for their correlation with the chromatographic behavior and potential to differentiate among the ligands. This work was planned to provide the data from a real bioprocess for designing the purification model of the recombinant proteins utilizing an in silico approach. 41
Chapter 3 A B C Figure 9: The crystal structures of three proteins identified in this work. These proteins were eluted at different positions during chromatography depending on the surface hydrophobic residues. The red and blue colors represent the hydrophobic and hydrophilic surface residues, respectively. 42
Page 1 and 2: A proteome wide approach to underst
Page 3 and 4: I also want to mention the efforts
Page 5 and 6: Dedication To my father Haji Sher A
Page 7 and 8: Table of Contents 1. Introduction .
Page 9 and 10: 3.3.2.2. Protein distributions on 2
Page 11 and 12: Chapter 1 1. Introduction 1.1. Intr
Page 13 and 14: Chapter 1 cell proteome to facilita
Page 15 and 16: Chapter 1 proteins. It is this diff
Page 17 and 18: Chapter 1 Salt conc. decreasing (Gr
Page 19 and 20: Chapter 1 The ions at the start of
Page 21 and 22: Chapter 1 exposure of hydrophobic r
Page 23 and 24: Chapter 1 based on the surface hydr
Page 25 and 26: Chapter 1 1.5. Analysis of the yeas
Page 27 and 28: Chapter 1 molecular weight impuriti
Page 29 and 30: Chapter 1 followed by its introduct
Page 31 and 32: Chapter 1 protein towards purificat
Page 33 and 34: Chapter 2 EXPERIMENTAL APPROACH
Page 35 and 36: Chapter 2 Yeast cell proteome and c
Page 37 and 38: Chapter 2 ligands (Toyopearl-Hexyl,
Page 39 and 40: Chapter 2 number of spots was count
Page 41 and 42: Chapter 2 (http://www.matrixscience
Page 43 and 44: Chapter 3 RESULTS AND DISCUSSION
Page 45 and 46: Chapter 3 to the retention behavior
Page 47 and 48: Chapter 3 investigate the hydrophob
Page 49: Chapter 3 the interior of the prote
Page 53 and 54: Chapter 3 of the comparative analys
Page 55 and 56: Chapter 3 Figure 11: Represent the
Page 57 and 58: Chapter 3 Ether, some 2-D gels were
Page 59 and 60: Chapter 3 Figure 13: Represent 2-D
Page 61 and 62: Chapter 3 Table 5. List of the iden
Page 63 and 64: Chapter 3 Table 7. List of the iden
Page 65 and 66: Chapter 3 amino acids by Cowan-Whit
Page 67 and 68: Chapter 3 Figure 15 C: Represents t
Page 69 and 70: Chapter 3 Figure 16 A: Represents t
Page 71 and 72: Chapter 3 The polarity value for th
Page 73 and 74: Chapter 3 Figure 17: Represents the
Page 75 and 76: Chapter 3 Figure 18: Represents the
Page 77 and 78: Chapter 3 published papers with mod
Page 79 and 80: Chapter 3 ligands revealed less dif
Page 81 and 82: 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 and 134:
References 71. Xindu, G. and Regnie
Page 135 and 136:
References 91. Alonso-Orgaz, S.; Mo
Page 137 and 138:
References 112. Gu, Z. and Glatz, C
Page 139:
References 132. Reubsaet, J.L.E. an
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Thesis final - after defense-7 - Jacobs University

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