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esearch literature. UniProt provides four core databases: UniProtKB (with sub-parts Swiss-Prot and TrEMBL), UniParc, UniRef, and UniMes [51]. RasMol RasMol is used for molecular graphics visualization intended and primarily for the depiction and exploration of biological macromolecule structures. RasMol has an important educational tool as well as ongoing to be an important tool for research in structural biology. BLAST (Basic Local Alignment Search Tool) It is an algorithm for comparing primary biological sequence information, such as the nucleotides or amino-acid sequences. BLAST search enables a researcher to compare a query sequence with database of sequences, and recognize sequences that are similar to the query sequence [52]. BLAST can be used for several purposes. Purpose Identifying Species Locating Domains Establishing Phylogeny DNA Mapping Comparison Particulars For the identification of species and homologous sequence While working with sequences, identification of domains Create a phylogenetic tree Looking for gene sequence at unknown place in known species Locating common sequences in species while working on genes Table 3: Applications of Blast. T-Coffee (Evaluation of alignment) Multiple sequence alignment is studied by T-Coffee. Sequences could be merged into each other and library of pair wise alignments could be generated. Structural data could be obtained from protein data bank regarding sequence alignment [53]. Various modes of T-coffee are listed below: Mode M-Coffee Expresso and 3D-Coffee R-Coffee PSI-Coffee TM-Coffee Pro-Coffee Particulars It combines the results of different multiple sequence analyzing programs It combines sequences and structures in particular alignment RNA sequences could be aligned Proteins are aligned by homology extension Transmembrane proteins are aligned Promoter regions are aligned Table 4: Various Modes of T-Coffee. References 1. Richards FM (1977) Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 6: 151-176. 2. Montell C, Devreotes P (2004) From protein dynamics to animal behavior: new insights into complex cell regulatory mechanisms. Curr Opin Cell Biol 16: 115-118. 3. Weiss M, Hashimoto H, Nilsson T (2003) Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy. Biophys J 84: 4043-4052. 4. Bacia K, Scherfeld D, Kahya N, Schwille P (2004) Fluorescence correlation spectroscopy relates rafts in model and native membranes. Biophys J 87: 1034-1043. 5. Douglass AD, Vale RD (2005) Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell 121: 937-950. 6. Kusumi A, Nakada C, Ritchie K, Murase K, Suzuki K, et al. (2005) Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules. Annu Rev Biophys Biomol Struct 34: 351-378. 7. Pike LJ (2006) Rafts defined: a report on the Keystone Symposium on Lipid Rafts and Cell Function. J Lipid Res 47: 1597-1598. 8. Singer SJ, Nicolson GL (1972) The fluid mosaic model of the structure of cell membranes. Science 175: 720-731. 9. Gohlke H, Kuhn LA, Case DA (2004) Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 56: 322-337. 10. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, et al. (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305: 386-389. 11. Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357: 423-424. 12. Cui Q, Li G, Ma J, Karplus M (2004) A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol 340: 345-372. 13. Vitagliano L, Merlino A, Zagari A, Mazzarella L (2002) Reversible substrate-induced domain motions in ribonuclease A. Proteins 46: 97-104. 14. Fayer MD (2001) Fast protein dynamics probed with infrared vibrational echo experiments. Annu Rev Phys Chem 52: 315-356. 15. Schlessinger J (1988) Signal transduction by allosteric receptor oligomerization. Trends Biochem Sci 13: 443-447. 16. Yap AS, Brieher WM, Gumbiner BM (1997) Molecular and functional analysis of cadherin-based adherens junctions. Annu Rev Cell Dev Biol 13: 119-146. 17. Perez-Moreno M, Jamora C, Fuchs E (2003) Sticky business: orchestrating cellular signals at adherens junctions. Cell 112: 535-548. 18. Pujuguet P, Del Maestro L, Gautreau A, Louvard D, Arpin M (2003) Ezrin regulates E-cadherin-dependent adherens junction assembly through Rac1 activation. Mol Biol Cell 14: 2181-2191. 19. Boehr DD, Dyson HJ, Wright PE (2006) An NMR perspective on enzyme dynamics. Chem Rev 106: 3055-3079. 20. Benkovic SJ, Hammes-Schiffer S (2003) A perspective on enzyme catalysis. Science 301: 1196-1202. OMICS Group eBooks 017
21. van der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ (2008) Biomolecular simulation and modelling: status, progress and prospects. J R Soc Interface 5 Suppl 3: S173-190. 22. Beck DA, Daggett V (2004) Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods 34: 112-120. 23. Cui M, Shen J, Briggs JM, Fu W, Wu J, et al. (2002) Brownian dynamics simulations of the recognition of the scorpion toxin P05 with the smallconductance calcium-activated potassium channels. J Mol Biol 318: 417-428. 24. Yu L, Sun C, Song D, Shen J, Xu N, et al. (2005) Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex. Biochemistry 44: 15834-15841. 25. Meng XY, Xu Y, Zhang HX, Mezei M, Cui M (2012) Predicting protein interactions by Brownian dynamics simulations. J Biomed Biotechnol 2012: 121034. 26. Angarica VE, Sancho J (2012) Protein dynamics governed by interfaces of high polarity and low packing density. PLoS One 7: e48212. 27. Kong J, Yu S (2007) Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Biochim Biophys Sin (Shanghai) 39: 549-559. 28. Dimitrova M, D Ivanova, I Karamancheva, A Milev, I Dobrev (2009) Application of FTIR-Spectroscopy for Diagnosis of Breast Cancer Tumors. Journal of the University of Chemical Technology and Metallurgy 44: 297-300. 29. Karim K, JD Taylor, DC Cullen, MJ Swann, NJ Freeman (2007) Measurement of conformational changes in the structure of transglutaminase on binding calcium ions using optical evanescent dual polarisation interferometry. Analytical Chemistry 79: 3023-3031. 30. Berney H, Oliver K (2005) Dual polarization interferometry size and density characterisation of DNA immobilisation and hybridisation. Biosens Bioelectron 21: 618-626. 31. Lillis B, Manning M, Berney H, Hurley E, Mathewson A, et al. (2006) Dual polarisation interferometry characterisation of DNA immobilisation and hybridisation detection on a silanised support. Biosens Bioelectron 21: 1459-1467. 32. Ringler P, Heymann BJ, Engel A (2000) Two-dimensional crystallization of membrane proteins. Edited by Baldwin SA: Oxford University Press, Oxford. 33. Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, et al. (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213: 899-929. 34. Mitsuoka K, Hirai T, Murata K, Miyazawa A, Kidera A, et al. (1999) The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution. J Mol Biol 286: 861-882. 35. Kühlbrandt W, Wang DN, Fujiyoshi Y (1994) Atomic model of plant light-harvesting complex by electron crystallography. Nature 367: 614-621. 36. Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, et al. (2000) Structural determinants of water permeation through aquaporin-1. Nature 407: 599-605. 37. Ren G, Cheng A, Reddy V, Melnyk P, Mitra AK (2000) Three-dimensional fold of the human AQP1 water channel determined at 4 A resolution by electron crystallography of two-dimensional crystals embedded in ice. J Mol Biol 301: 369-387. 38. Nogales E, Wolf SG, Downing KH (1998) Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391: 199-203. 39. Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, et al. (2003) ModView, visualization of multiple protein sequences and structures. Bioinformatics 19: 165-166. 40. Li F, Li P, Xu W, Peng Y, Bo X, et al. (2010) Perturbation Analyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. Bioinformatics 26: 275-277. 41. Saqi MA, Wild DL, Hartshorn MJ (1999) Protein analyst--a distributed object environment for protein sequence and structure analysis. Bioinformatics 15: 521-522. 42. Salama JJ, Feldman HJ, Hogue CW (2001) VISTRAJ: exploring protein conformational space. Bioinformatics 17: 851-852. 43. Pietal MJ, Tuszynska I, Bujnicki JM (2007) PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. Bioinformatics 23: 1429-1430. 44. Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, et al. (2009) FlexServ: an integrated tool for the analysis of protein flexibility. Bioinformatics 25: 1709-1710. 45. Sharma S, Ding F, Nie H, Watson D, Unnithan A, et al. (2006) iFold: a platform for interactive folding simulations of proteins. Bioinformatics 22: 2693- 2694. 46. Grant BJ, Rodrigues AP, ElSawy KM, McCammon JA, Caves LS (2006) Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22: 2695-2696. 47. Ho HK, Kuiper MJ, Kotagiri R (2008) PConPy--a Python module for generating 2D protein maps. Bioinformatics 24: 2934-2935. 48. Vertrees J, Phillip Barritt, Steve Whitten, Vincent J Hilser (2005) COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures. Bio-Informatics 21: 3318–3319. 49. Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, et al. (2012) CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol 8: e1002708. 50. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, et al. (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31: 3784-3788. 51. UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214-219. 52. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410. 53. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217. OMICS Group eBooks 018
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
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Page 19 and 20: protein demonstrate the lowest ener
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Page 23: FlexServ The flexibility of protein
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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
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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
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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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Advances in Protein Chemistry Chapt
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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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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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