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6. Shea JE, Onuchic JN, Brooks CL 3rd (1999) Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci U S A 96: 12512-12517. 7. Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450: 964-972. 8. Dill KA (1999) Polymer principles and protein folding. Protein Sci 8: 1166-1180. 9. La-Rosa C, Milardi D, Grasso D, Guzzi R, Sportelli L (1995) Thermodynamics of the Thermal Unfolding of Azurin. The Journal of Physical Chemistry 99: 14864-14870. 10. Zhao Q (2001) Irreversible thermodynamics theory of protein folding and protein thermodynamics structure. Prog Biochem Biophys 28: 429-435. 11. Benkovic SJ, Hammes-Schiffer S (2003) A perspective on enzyme catalysis. Science 301: 1196-1202. 12. Jiang Y, Lee A, Chen J, Ruta V, Cadene M, et al. (2003) X-ray structure of a voltage-dependent K+ channel. Nature 423: 33-41. 13. Sagermann M, Gay L, Matthews BW (2003) Long-distance conformational changes in a protein engineered by modulated sequence duplication. Proc Natl Acad Sci U S A 100: 9191-9195. 14. Klymkowsky MW (2010) Thinking about the conceptual foundations of the biological sciences. CBE Life Sci Educ 9: 405-407. 15. Pace CN, Hebert EJ, Shaw KL, Schell D, Both V, et al. (1998) Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3. J Mol Biol 279: 271-286. 16. George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, et al. (2005) Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci U S A 102: 12299-12304. 17. Keskin O, Ma B, Nussinov R (2005) Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol 345: 1281-1294. 18. Li X, Keskin O, Ma B, Nussinov R, Liang J (2004) Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol 344: 781-795. 19. Stormo GD, Fields DS (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 23: 109-113. 20. Wang X, Gao H, Shen Y, Weinstock GM, Zhou J, et al. (2008) A high-throughput percentage-of-binding strategy to measure binding energies in DNAprotein interactions: application to genome-scale site discovery. Nucleic Acids Res 36: 4863-4871. 21. Bulyk ML (2003) Computational prediction of transcription-factor binding site locations. Genome Biol 5: 201. 22. Brenner SE, Levitt M (2000) Expectations from structural genomics. Protein Sci 9: 197-200. 23. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, et al. (2002) Structural genomics of the Thermotoga maritima proteome implemented in a highthroughput structure determination pipeline. Proc Natl Acad Sci U S A 99: 11664-11669. 24. Chen YC, Lim C (2008) Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Res 36: 7078-7087. 25. Chandler D (2005) Interfaces and the driving force of hydrophobic assembly. Nature 437: 640-647. 26. Gromiha MM, Sarai A (2010) Thermodynamic database for proteins: features and applications. Methods Mol Biol 609: 97-112. 27. Fulton KF, Devlin GL, Jodun RA, Silvestri L, Bottomley SP, et al. (2005) PFD: a database for the investigation of protein folding kinetics and stability. Nucleic Acids Res 33: 279-283. 28. Worth CL, Preissner R, Blundell TL (2011) SDM--a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res 39: 215-222. 29. Magyar C, Gromiha MM, Pujadas G, Tusnády GE, Simon I (2005) SRide: a server for identifying stabilizing residues in proteins. Nucleic Acids Res 33: 303-305. 30. Champ PC, Camacho CJ (2007) FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Res 35: 556-560. 31. Cao ZW, Xue Y, Han LY, Xie B, Zhou H, et al. (2004) MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Res 32: 679-685. OMICS Group eBooks 017
Advances in Protein Chemistry Chapter: Role of Matrix Metalloproteinases in Cancer Edited by: Ghulam Md Ashraf and Ishfaq Ahmed Sheikh Published by OMICS Group eBooks 731 Gull Ave, Foster City. CA 94404, USA Copyright © 2013 OMICS Group All book chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. However, users who aim to disseminate and distribute copies of this book as a whole must not seek monetary compensation for such service (excluded OMICS Group representatives and agreed collaborations). After this work has been published by OMICS Group, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Notice: Statements and opinions expressed in the book are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Cover OMICS Group Design team First published September, 2013 A free online edition of this book is available at www.esciencecentral.org/ebooks Additional hard copies can be obtained from orders @ www.esciencecentral.org/ebooks
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 and 8: 2. Souza JM, Daikhin E, Yudkoff M,
Page 9 and 10: Oligoclonality of the antibody resp
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: Figure 21: Stability of protein str
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
Page 57 and 58: 126. López-Boado YS, Wilson CL, Ho
Page 59 and 60: Proteins and Peptides- Reemergence
Page 61 and 62: Figure 3: Schematic representation
Page 63 and 64: Figure 6: Different mechanisms of c
Page 65 and 66: [30,33]. Clinical trials with autoi
Page 67 and 68: Therapeutic Proteins Figure 9: Mole
Page 69 and 70: Coming years will witness increasin
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Page 73 and 74: purification methodology and laid t
Page 75 and 76: An overview of various purification
Page 77 and 78: Affinity chromatography (AC): The p
Page 79 and 80: molecules such as proteins. Further
Page 81 and 82: However, for proteins with poor sol
Page 83 and 84: The schematic of an HPLC instrument
Page 85 and 86: » Denaturation of all proteins giv
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Page 89 and 90: 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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Advances in Protein Chemistry Chapt
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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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