changes in protein profiles in bortezomib applied multiple myeloma ...

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2.1.4.1. Gel Electrophoresis Electrophoresis is a bio-analytical method utilized for the isolation of biomolecules depending on the mobility of charged molecules under the influence of an electric field. When an electric field is applied, any charged molecule in solution will migrate. (Twyman, 2004). Mobility of a molecule is based upon the magnitude of its charge, molecular weight, and structure. Many biopolymers, such as proteins are charged either by coating with the anionic detergent sodium dodecylsulfate (SDS) or by acid-base association-dissociation reactions of amine and carboxylic acid parts of them, so they can also be separated by electrophoretic methods (Mikkelsen and Corton 2004). Electrophoresis, which is the central component of the proteomic research, is commonly carried out in a gel that is formed by the polymerization of acrylamide, so it is called polyacrylamide gel electrophoresis. The reaction mechanism that results in a gel with a characteristic porosity which depends on the polymerization conditions and monomer concentrations can be seen in Figure 2.3 (Kinter and Sherman 2000). Figure 2.3. Reaction of polyacrylamide gel formation (Source: Gallagher, 2008) In the presence of an initiator generally ammonium persulfate and a catalyst commonly tetramethylethylenediamine [TEMED, (CH3)2N(CH2)2N(CH3)2], polyacrylamide gels are prepared by the copolymerization of acrylamide monomer with 31
is-acrylamide (N,N'-methylene-bisacrylamide). Polymerization is initiated by ammonium persulfate and TEMED. The degree of cross-linking is very important in the formation of polyacrylamide gel. Because, the lower degrees of cross-linking gel allows to pass larger protein transition. 2.1.4.1.1. One-Dimensional Gel Electrophoresis (1D PAGE) One-dimensional gel electrophoresis (1D-GE or SDS-PAGE) is the most commonly used protein seperation technique in proteomic studies. This method basically depends on separating proteins according to their molecular weight (size) difference. Most commonly, the strong anionic detergent SDS is used in combination with a reducing agent (mercaptoethanol or DTT) to surround the proteins homogeneously to dissociate them. The denatured polypeptides (simple rod-like shape of the proteins) gain a negative charge in constant proportion to molecular weight by binding SDS. By this way, the newly formed complex starts to migrate through the pores of the polyacrylamide gel towards the positive electrode, when the gel expose to high voltage. As compared to larger ones, smaller proteins migrate further through the gel, depending on their molecular weight (Liebler, 2002). 2.1.4.1.2. Two-Dimensional Gel Electrophoresis (2D PAGE) SDS-PAGE has been utilized for several decades for the protein separation. The method is delicate to separate only 80-100 different protein components where cell proteomes are intensely complex holding several thousand of proteins. So, it is not sufficient for some comprehensive protein studies. Two-dimensional gel electrophoresis (2D-GE or 2D PAGE) firstly introduced by O’Farrell in 1975 (O’Farrell 1975). 2D PAGE can separate thousands of proteins simultaneously. Additionally, it can be also used to determine the protein alterations given a stress condition. Because of these reasons, it is is still the most accepted protein separation method in proteomics studies. Every single spot formed in 2D PAGE analysis demonstrates an individual protein species and its specific coordinates. The intensity of a spot in the gel implies the amount of that actual protein produced (Bendixen 2005). 32
Page 1 and 2: CHANGES IN PROTEIN PROFILES IN BORT
Page 3 and 4: ACKNOWLEDGEMENTS First of all, with
Page 5 and 6: ÖZET BORTEZOMĠB UYGULANAN MULTĠP
Page 7 and 8: 2.1.4.1.2. Two-Dimensional Gel Elec
Page 9 and 10: LIST OF FIGURES Figure Page Figure
Page 11 and 12: LIST OF TABLES Table Page Table 1.1
Page 13 and 14: When normal cells in the body begin
Page 15 and 16: Figure 1.2. Development of Cancer S
Page 17 and 18: the myeloma cells does not help fig
Page 19 and 20: A rare form of MM called Nonsecreto
Page 21 and 22: 1.2.3. Risk Factors for MM A risk f
Page 23 and 24: of the mineralizations by adjusting
Page 25 and 26: To measure the levels of red cells,
Page 27 and 28: The levels of blood urea nitrogen (
Page 29 and 30: By using the system introduced by D
Page 31 and 32: 1.2.7.2. Biology of The Proteasome
Page 33 and 34: Figure 1.10. Ubiquitin-Proteasome P
Page 35 and 36: Figure 1.12. Effect of Bortezomib o
Page 37 and 38: encompasses the investigation of pr
Page 39 and 40: of modification. Ubiquitin is a sma
Page 41: the given cells. On the other hand,
Page 45 and 46: 2.1.4.2. Detection of Protein Spots
Page 47 and 48: ange of 600-2500 Da. This is the id
Page 49 and 50: ions resolved by the mass analyzer
Page 51 and 52: 2.1.4.5.2. Mass Analyzers Figure 2.
Page 53 and 54: There is no doubt that different ma
Page 55 and 56: mask low-quantity proteins that may
Page 57 and 58: 3.1. Materials 3.1.1. Medias CHAPTE
Page 59 and 60: 3.2.5. Cell Proliferation Assay Ant
Page 61 and 62: After 72 hour incubation period at
Page 63 and 64: eceptors of the Tumor Necrosis Fact
Page 65 and 66: The preparation of stock BSA Standa
Page 67 and 68: 3.2.6.3. Detection of the Loss of M
Page 69 and 70: centrifugation, the supernatant was
Page 71 and 72: selected symmetrically to load the
Page 73 and 74: approximately 35 ml, the volume of
Page 75 and 76: After electrophoresis was finished,
Page 77 and 78: 7 Day Two: Reduction, Alkylation, a
Page 79 and 80: CHAPTER 4 RESULTS AND DISCUSSION 4.
Page 81 and 82: % Changes in Cytoplasmic/Mitochondr
Page 83 and 84: Table 4.1. Magnified Segments of Di
Page 85 and 86: Table 4.1. Magnified Segments of Di
Page 87 and 88: After labeling, black and red color
Page 89 and 90: 78 7 8 Y2S Y3S Table 4.2. Results o
Page 91 and 92: 80 12 S4Ca Table 4.2. Results of Di
Page 93 and 94:
82 27 Y5S Table 4.2. Results of Dif
Page 95 and 96:
Spot 4, Ubiquitin-conjugating enzym
Page 97 and 98:
is a transcriptional repressor, but
Page 99 and 100:
activity and loss of mitochondrial
Page 101 and 102:
distributed, but correlate with nat
Page 103 and 104:
DeMartino, G. N. and Slaughter, C.
Page 105 and 106:
proteomic analyses of a systematica
Page 107 and 108:
Mahindraa, A., Hideshimab, T. and A
Page 109 and 110:
Richardson, P. G., Hideshima, T. an
Page 111 and 112:
Terpos, E. 2008. Bortezomib Directl
Page 113 and 114:
A.1. RPMI-1640 Growth Medium APPEND
Page 115 and 116:
Table B.1. Chemicals and Reagents U
Page 117 and 118:
B.4.3. Standard Curve for BSA Table
Page 119 and 120:
Urea (8M) 4.8 g CHAPS (%2) 0.2 g DT
Page 121 and 122:
E. F. G. STOCK REAGENT PREPARATION
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