Thesis final - after defense-7 - Jacobs University

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Chapter 3 protein. It has been reported before that the retention of proteins in reverse phase chromatography (RPC) was dependent on the total hydrophobicity of a protein (70). This can give an additional advantage to average hydrophobicity and this parameter should also be explored in RPC. The trend lines of the three ligands were statistically non significant which revealed that average hydrophobicity have no ability to differentiate among the hydrophobic characters of the three ligands (Figure 15 A-C). The reason could be that average hydrophobicity was representing the total residues of a protein instead of only surface hydrophobic residues. 3.1.3.3.2. Average polarity (AP) The average polarity of the proteins has been reported in the previous studies for its contribution in the three dimensional structure of a protein; however average polarity has been rarely explored in HIC (64, 115-117). The average polarity was calculated for the tabulated proteins utilizing the scales proposed by Grantham and Zimmerman (Tables 5-7) (96, 97). The polarity values for early and late eluted proteins were more than 0.49 (49%) and less than 0.41 (41%), respectively on Grantham’s scale. The same trend was also observed on Zimmerman’s scale where early eluted proteins had a higher polarity 0.35 (> 35%) than the late eluted ones 0.24 (< 24%). The membrane proteins were reported to have less polarity (< 40%) while soluble proteins have higher polarity, approximately 47%. The membrane proteins with the less polarity need detergents to be separated from respective membranes due to hydrophobic interactions. (117). It was also reported before with model proteins that a decrease in the polar surface area of the protein will increase the binding affinity on the adsorbents (62). However, the effect of polarity was examined for the first time in this work with the process proteomics approach. The average polarity of the proteins has revealed a statistically significant (r 2 = 0.82, p < 0.0001) inverse correlation with the protein retention during HIC (Figure 16 A-B). 59
Chapter 3 Figure 16 A: Represents the average polarity calculated by Grantham’s scale. The protein average polarity values of the three ligands were correlated with the respective salt concentrations where the fractions were collected. The error bars represent the standard deviations of the average polarity values in each fraction. The statistical analysis revealed a significant correlation (r 2 = 0.89; p < 0.0001). 60
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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
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 and 50: Chapter 3 the interior of the prote
Page 51 and 52: Chapter 3 A B C Figure 9: The cryst
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: Chapter 3 Figure 15 C: Represents t
Page 71 and 72: Chapter 3 The polarity value for th
Page 73 and 74: Chapter 3 Figure 17: 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 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
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Chapter 3 and hydrophobic interacti
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Chapter 4 CONCLUSIONS
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Chapter 4 • The base supports rev
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Chapter 4 additional understanding
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References 13. Lienqueo, M.E.; Lese
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References 32. Salgado, J.C.; Rapap
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References 52. B.H.J., H. Accessibl
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References 71. Xindu, G. and Regnie
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References 91. Alonso-Orgaz, S.; Mo
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References 112. Gu, Z. and Glatz, C
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References 132. Reubsaet, J.L.E. an
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Thesis final - after defense-7 - Jacobs University

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