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34. Witherick J, Wilkins A, Scolding N (2011) Mechanisms of oxidative damage in multiple sclerosis and a cell therapy approach to treatment. Autoimmune Dis 2011: 164608. 35. Frischer JM, Bramow S, Dal-Bianco A, Lucchinetti CF, Rauschka H, et al. (2009) The relation between inflammation and neurodegeneration in multiple sclerosis brains. Brain 132: 1175-89. 36. Negre-Salvayre A, Coatrieux C, Ingueneau C, Salvayre R (2008) Advanced lipid peroxidation end products in oxidative damage to proteins. Potential role in diseases and therapeutic prospects for the inhibitors. British J Pharmacol 153: 6-20. 37. Gonsette R (2008) Oxidative stress and excitotoxicity: a therapeutic issue in multiple sclerosis? Mult Scler 14: 22-34. 38. Dietrich-Muszalska A, Olas B, Głowacki R, Bald E (2009) Oxidative/nitrative modifications of plasma proteins and thiols from patients with schizophrenia. Neuropsychobiology 59: 1-7. 39. 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Berlett BS, Friguet B, Yim MB, Chock PB, Stadtman ER (1996) Peroxynitrite-mediated nitration of tyrosine residues in Escherichia coli glutamine synthetase mimics adenylylation: relevance to signal transduction. Proc Natl Acad Sci U.S.A 93: 1776-1780. 51. Kong SK, Yim MB, Stadtman ER, Chock PB (1996) Peroxynitrite disables the tyrosine phosphorylation regulatory mechanism: lymphocytespecific tyrosine kinase fails to phosphorylate nitrated cdc2(6-20)NH2 peptide. Proc Natl Acad Sci U.S.A 93: 3377-3382. 52. Kamisaki Y, Wada K, Bian K, Balabanli B, Davis K, et al. (1998) An activity in rat tissues that modifies nitrotyrosine-containing proteins. Proc Natl Acad Sci U.S.A 95: 11584-11589. 53. MacMillan-Crow LA, Thompson JA (1999) Tyrosine modifications and inactivation of active site manganese superoxide dismutase mutant (Y34F) by peroxynitrite. Arch Biochem Biophys 366: 82-88. 54. 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Oligoclonality of the antibody response and recognition of a determinant composed of histones H2A, H2B and DNA. J Immunol 48: 1561-1569. 67. Crow JP (1999) Measurement and significance of free and protein-bound 3-nitrotyrosine, 3-chlorotyrosine, and free 3-nitro-4- hydroxyphenylacetic acid in biologic samples: A high performance liquid chromatography method using electrochemical detection. Methods Enzymol 301: 151-160. 68. Duncan MW (2003) A review of approaches to the analysis of 3-nitrotyrosine. Amino Acids 25: 351-361. 69. Yang B, Rizzo V (2007) TNF-α potentiates protein tyrosine nitration through activation of NADPH oxidase and eNOS localized in membrane rafts and caveolae of bovine aortic endothelial cells. Am J Physiol Heart Circ Physiol 292: 954-962. 70. Calabrese V, Scapagnini G, Ravagna A, Bella R, Foresti R, et al. (2002) Nitric oxide synthetase is present in the cerebrospinal fluid of patients with active multiple sclerosis and is associated with increases in cerebrospinal fluid protein nitrotyrosine and S-nitrosothiols and changes in glutathione levels. J Neurosci Res 70: 580-587. 71. Shishehbor Mviles RJ, Brennan ML, Fu X, Goormastic M, Pearce GL, et al. (2003) Association of nitrotyrosine levels with cardiovascular disease and modulation by statin therapy. JAMA 289: 1675-1680. 72. Souza JM, Peluffo G, Radi R (2008) Protein tyrosine nitration-Functional alteration or just a biomarker? Free Radic Biol Med 45: 357-366. 73. Tsikas D (2012) Analytical methods for 3-nitrotyrosine quantification in biological samples: the unique role of tandem mass spectrometry. Amino Acids 42: 45-63. 74. Lee JR, Kim JK, Lee SJ, Kim KP (2009) Role of tyrosine nitration in neurodegenerative diseases and atherosclerosis. Arch Pharm Res 32: 1109-1118. 75. Ohshima H, Friesen M, Brouet I, Bartsch H (1999) Nitrotyrosine as new marker for endogenous nitrosation and nitration of proteins. Food Chem Toxicol 28: 647-52. 76. Dixit K, Khan MA, Sharma YD, Moinuddin, Alam K (2011) Peroxynitrite-induced modification of H2A histone presents epitopes which are strongly bound by human anti-DNA autoantibodies: role of peroxynitrite-modified-H2A in SLE induction and progression. Hum Immunol 72: 219-225. 77. Ohmori H, Oka M, Nishikawa Y, Shigemitsu H, Takeuchi M, et al. (2005) Immunogenicity of autologous IgG bearing the inflammationassociated marker 3-nitrotyrosine. Immunol Lett 96: 47-54. 78. Khan F, Siddiqui AA (2006) Prevalence of anti-3-nitrotyrosine antibodies in the joint synovial fluid of patients with rheumatoid arthritis, osteoarthritis and systemic lupus erythematosus. Clin Chim Acta 370: 100-107. 79. Anderton SM (2004) Post-translational modifications of self antigens: implications for autoimmunity. Curr Opin Immunol 16: 753- 758. 80. Oates JC, Christensen EF, Reilly CM, Self SE, Gilkeson GS (1999) Prospective measure of serum 3-nitrotyrosine levels in systemic lupus erythematosus: correlation with disease activity. Proc Assoc Am Physicians 111: 611-621. 81. Ohmori H, Kanayama N (2005) Immunogenicity of an inflammation associated product, tyrosine nitrated self-proteins. Autoimmun Rev 4: 224-229. 82. Birnboim HC, Lemay AM, Lam DK, Goldstein R, Webb JR (2003) Cutting edge: MHC class II-restricted peptides containing the inflammation-associated marker 3-nitrotyrosine evade central tolerance and elicit a robust cell-mediated immune response. J Immunol 171: 528-532. 83. Khan F, Ali R (2006) Antibodies against nitric oxide damaged poly L-tyrosine and 3-nitrotyrosine levels in systemic lupus erythematosus. J Biochem Mol Biol 39: 189-196. 84. Thomson L, Christie J, Vadseth C, Lanken PN, Fu X, et al. (2007) Identification of immunoglobulins that recognize 3-nitrotyrosine in patients with acute lung injury after major trauma. Am J Respir Cell Mol Biol 36: 152-157. 85. Ahmad R, Ahsan H (2012) Role of peroxynitrite modified biomolecules in the etiopathogenesis of systemic lupus erythematosus. Clin Exp Med (Epub ahead of print). 86. Radi R, Peluffo G, Alvarez MN, Naviliat M, Cayota A (2001) Unraveling peroxynitrite formation in biological systems. Free Radic Biol Med 30: 463-488. 87. Guilgen G, Werneck ML, de Noronha L, Martins AP, Varela AM, et al. (2011) Increased calcification and protein nitration in arteries of chronic kidney disease patients. Blood Purif 32: 296-302. OMICS Group eBooks 009
Page 1 and 2: www.esciencecentral.org/ebooks Adva
Page 3 and 4: Tyrosine Nitrated Proteins: Biochem
Page 5 and 6: [58-61]. Protein sulfhydryls [62] a
Page 7: 2. Souza JM, Daikhin E, Yudkoff M,
Page 11 and 12: The Recent Methodologies of Protein
Page 13 and 14: are due to altering protein activit
Page 15 and 16: Figure 6: At Domain Level, Protein
Page 17 and 18: Brownian Dynamics (BD) method Prote
Page 19 and 20: protein demonstrate the lowest ener
Page 21 and 22: Figure 12: Steps in Protein Prepara
Page 23 and 24: FlexServ The flexibility of protein
Page 25 and 26: 21. van der Kamp MW, Shaw KE, Woods
Page 27 and 28: Advances in Protein Thermodynamics
Page 29 and 30: 3. Fluorescence correlation spectro
Page 31 and 32: Figure 3: Molecular Chaperone (Top
Page 33 and 34: Figure 7: A Potherse is Consists of
Page 35 and 36: Figure 12: Residue Clusters with Mu
Page 37 and 38: Figure 16: Various Features at the
Page 39 and 40: Figure 21: Stability of protein str
Page 41 and 42: Advances in Protein Chemistry Chapt
Page 43 and 44: MMPs are believed to remodel the EC
Page 45 and 46: MMPs7 (Matrilysin, PUMP 1) A big ro
Page 47 and 48: MMP27 (MMP-22, C-MMP) mRNAs for MMP
Page 49 and 50: Signal transduction MMP production
Page 51 and 52: a | Active MMPs are generated throu
Page 53 and 54: Future Perspective Research into ne
Page 55 and 56: 56. Yonemura Y, Endo Y, Fujita H, K
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Proteins and Peptides- Reemergence
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Figure 3: Schematic representation
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Figure 6: Different mechanisms of c
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[30,33]. Clinical trials with autoi
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Therapeutic Proteins Figure 9: Mole
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Coming years will witness increasin
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Advances in Protein Chemistry Chapt
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purification methodology and laid t
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An overview of various purification
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Affinity chromatography (AC): The p
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molecules such as proteins. Further
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However, for proteins with poor sol
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The schematic of an HPLC instrument
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» Denaturation of all proteins giv
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the biological society access to th
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identifier, since a single macromol
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Furthermore, the initial models for
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evaluation [78], Whatcheck [79] and
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corresponding to gaps in the FR ali
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programming (IP) problem based on t
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or almost the entire target. - Temp
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3.2.1.10 Geno3D http://geno3d-pbil.
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80. Laskowski RA, MacArthur MW, Mos
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165. Zhang Y, Kolinski A, Skolnick
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Figure 1: Biochemical and biophysic
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equilibrium an equilibrium concentr
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for virtually all macromolecules to
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egion) for estimating fraction or p
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etween proteins in living cells. It
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pre-requisite in understanding how
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82. Rodger A, Marrington R, Roper D
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New Peptide Based Therapeutic Appro
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ability to selectively target cells
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24 amino acid extracellular domain
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separation efficiency. However, use
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the peptides through acetylation an
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63. Mesiano AJ, Beckman EJ, Russell
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Antimicrob Agents Chemother 49: 330
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Protein Detection Techniques Dennis
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technique has been applied to the i
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involves placing our protein of int
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