Thesis final - after defense-7 - Jacobs University

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Chapter 3 such as D3-SP, B4-PS and B4-SP were eluted earlier during chromatography than E1-SP, C1- PS and C1-SP, respectively although they have almost similar ASH. This could be due to the higher flexibilities of the proteins which allow them to retain longer during chromatography. The same behavior was also reported with model proteins where ribonuclease S has shown higher retention on Sepharose-Butyl than other proteins, although they had almost identical surface hydrophobicity. It was claimed that higher flexibility of ribonulcease S might be favoring longer retention (63). The highly flexible proteins have revealed more unfolding and most of the hydrophobic residues were exposed which has given tight binding and in result most of them eluted at the end of the chromatography. Less flexible proteins were not able to stay longer due to their compact nature and most of hydrophobic parts were in the inner core, which resulted in less hydrophobic interactions and elution occurred at the beginning of the chromatography. Although the flexibility has no decisive role in retention, however it can be considered as the contributing parameter during HIC. The flexibility has given a correlation with retention of proteins; however it has not exhibited any differences among the base supports for their hydrophobic characters. The average bulkiness was also calculated for the tabulated proteins using Zimmerman’s scale (Tables 12-14). The average bulkiness of the proteins has revealed no significant relationship (r 2 = 0.04, p = 0.38) with the chromatographic separation of proteins in HIC (Figure 28). The bulkiness has been never reported for its contribution in HIC. In the previous report, Zimmerman had investigated to correlate polarity and bulkiness of cytochrome c protein in different organisms (96). However, no significant trend was observed between polarity and bulkiness in his studies. This also confirmed that if bulkiness has no relation with the polarity of the proteins, then it is supposed to have no relation with protein hydrophobicity as evidenced here. The bulkiness has also exhibited no differences among the different base supports. 97
Chapter 3 Figure 28: Represents the average bulkiness calculated by Zimmerman’s scale. The protein average bulkiness values of the three base supports were correlated with the respective salt concentrations where the fractions were collected. The error bars represent the standard deviations of the average bulkiness values in each fraction. The statistical analysis revealed a non significant correlation (r 2 = 0.04; p = 0.38). 3.2.3.4. Comparative studies of the different base supports based on average protein properties The comparison of the base supports has been done for the first time in this work with the proteome wide approach. The protein properties such as average surface hydrophobicity, average hydrophobicity, average flexibility and average polarity have shown a correlation with the retention of proteins during chromatography. However, these properties have a limited ability to differentiate among the base supports for their hydrophobicity (Table 15). 98
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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
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: Chapter 3 towards conformational ch
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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