Thesis final - after defense-7 - Jacobs University

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Chapter 3 3.1.2.2. Protein properties in the context of HIC The physicochemical properties of the proteins such as average hydrophobicity, average polarity, average flexibility and average bulkiness can be determined by different scales proposed by several researchers (Table 4). These average properties were based on the exposed and buried amino acid residues of a protein. The average hydrophobicity is the average of the hydrophobicities of the exposed and buried amino acids of a protein. The average hydrophobicity of the proteins can be measured by the scales proposed by different researchers (25, 92, 95). Several experimental and theoretical approaches were used to determine the hydrophobicity indices for the individual amino acids. These methods have assigned different hydrophobicity values for each amino acid and can be used as different amino acid hydrophobicity scales. The scale of Cowan-Whittaker was derived from the amino acid retention times during chromatographic experiments by RP-HPLC (92). The scale of Miyazawa-Jernigan was based on the contact energies estimated from the protein tertiary structures. A direct relationship was observed between the contact energies of adjacent residues in the crystal structure and their corresponding hydrophobicities reported by Tanford (25, 95). The theoretical contact energies between amino acid residues in the crystal structures were used to assign the hydrophobicity value to each amino acid. The amino acid hydrophobicity scale proposed by Tanford was based on the amino acids solubility in water as well as in spontaneously increasing concentration of organic solvent (ethanol). The amino acids were classified as hydrophobic, intermediate and hydrophilic based on the free energy change by the transfer of amino acids from ethanol to water. Based on the data, a hydrophobicity scale was proposed for amino acid residues, where their free energy transfer values become more and more positive as the hydrophobic character of the protein increases (102). This revealed that hydrophobic amino acids will tend towards organic phase while hydrophilic amino acids will prefer to stay in the water. In other words, charged residues of the protein will tend towards the surface and in contrast, the hydrophobic residues will stay in 39
Chapter 3 the interior of the protein (25). The average hydrophobicity parameter was reported in literature for its relation to protein structure (66). However, this parameter was rarely investigated in context of the HIC. Average flexibility is another property which can be calculated by using Bhaskaran and Ponnuswamy’s scale. Average flexibility represents the average fluctuations of the all residues in a given protein. It was reported that proteins with high flexibility will have more chances to unfold and expose hydrophobic residues on the protein surface. This will increase hydrophobic interactions between proteins and adsorbents and result in longer retention of proteins during chromatographic experiments (33). Table 4: The physicochemical properties of the proteins investigated in this study Protein properties Scales Bioinformatic tools Source Average hydrophobicity Cowan-Whittaker’s scale, Expasy ProtScale tool Primary structure Miyazawa-Jernigan’s scale Tanford’s scale Average flexibility Bhaskaran and Ponnuswamy’s scale Expasy ProtScale tool Primary structure Average polarity Grantham’s scale, Zimmerman’s scale. Expasy ProtScale tool Primary structure Average bulkiness Zimmerman’s scale Expasy ProtScale tool Primary structure Average surface hydrophobicity Cowan-Whittaker’s scale Expasy ProtScale tool, MATLAB and STRIDE softwares Three dimensional structure The polarity scales proposed by Grantham and Zimmerman were used to quantify the polarity based on the protein sequence (96, 97). All the above mentioned properties were based on the primary structure of a protein. However, ASH was the most remarkable property in the 40
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: Chapter 3 investigate the hydrophob
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 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
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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
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Chapter 3 towards conformational ch
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Chapter 3 Figure 28: Represents the
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Chapter 3 among the adsorbents were
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Chapter 3 3.3. Protein distribution
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Chapter 3 3.3.2.2. Protein distribu
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Chapter 3 Figure 29 B: Represent th
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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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