Thesis final - after defense-7 - Jacobs University

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3.1.3. Results and Discussion ............................................................................................... 45 3.1.3.1. Chromatographic profiles of different ligands .................................................... 45 3.1.3.2. Two dimensional gel electrophoresis and proteins identification ....................... 47 3.1.3.3. Influence of the ligands chemistries and average protein properties .................. 55 3.1.3.3.1. Average hydrophobicity (AH) ............................................................................. 55 3.1.3.3.2. Average polarity (AP) .......................................................................................... 59 3.1.3.3.3. Average flexibility (AF)....................................................................................... 62 3.1.3.3.4. Average Bulkiness (AB) ...................................................................................... 65 3.1.3.3.5. Average surface hydrophobicity (ASH)............................................................... 66 3.1.3.4. Comparative studies of the hydrophobic ligands based on average protein properties .......................................................................................................................... 68 3.1.3.5. Application note .................................................................................................. 70 3.1.4. Partial conclusions ...................................................................................................... 71 3.2. Influence of the different base support chemistries during hydrophobic interaction chromatography ........................................................................................................................ 72 3.2.1. Summary .................................................................................................................... 72 3.2.2. Chemistry of the base supports .................................................................................. 73 3.2.3. Results and Discussion ............................................................................................... 75 3.2.3.1. Chromatographic fractionation ........................................................................... 75 3.2.3.2. The electrophoretic separation and proteins identification ................................. 78 3.2.3.3. Influence of the base support chemistries and average protein properties .......... 85 3.2.3.3.1. Average hydrophobicity (AH) ............................................................................. 85 3.2.3.3.2. Average polarity (AP) .......................................................................................... 89 3.2.3.3.3. Average surface hydrophobicity (ASH)............................................................... 93 3.2.3.3.4. Other protein properties affecting the chromatographic behavior ....................... 95 3.2.3.4. Comparative studies of the different base supports based on average protein properties .......................................................................................................................... 98 3.2.3.5. Application note ................................................................................................ 100 3.2.3. Partial conclusions .................................................................................................... 101 3.3. Protein distributions on 2-D gels: the influence of molecular weight and isoelectric point coordinates ............................................................................................................................. 102 3.3.1. Summary .................................................................................................................. 102 3.3.2. Results and Discussion ............................................................................................. 103 3.3.2.1. Unfolding of proteins during HIC ..................................................................... 103 3
3.3.2.2. Protein distributions on 2-D gels ....................................................................... 104 3.3.2.3. The effect of protein molecular mass on the chromatographic behavior .......... 106 3.3.2.3. The influence of protein isoelectric point on the chromatographic behavior ... 108 3.3.3. Partial conclusions .................................................................................................... 111 4. Conclusions and Remarks .................................................................................................. 113 4.1. General conclusions and remarks ................................................................................ 113 4.2. Influence of different ligands ...................................................................................... 113 4.3. Influence of different base supports ............................................................................ 113 4.4. Effect of protein properties on separation behavior during chromatography ............. 114 4.5. 2-D gels analysis ......................................................................................................... 115 4.5. Additional conclusions ................................................................................................ 115 4.6. Recommendations for future work .............................................................................. 116 5. References .......................................................................................................................... 117 4
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: Table of Contents 1. Introduction .
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 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
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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
Page 75 and 76:
Page 77 and 78:
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
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Chapter 3 where approximately 50% o
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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
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Chapter 3 r 2 values from the data
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Chapter 3 Figure 24 C: Represents t
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Chapter 3 approximately 47%. The me
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Chapter 3 Figure 25 B: Represents t
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Chapter 3 values have been reported
Page 105 and 106:
Chapter 3 towards conformational ch
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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
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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
Page 127 and 128:
References 13. Lienqueo, M.E.; Lese
Page 129 and 130:
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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