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advantages in characterizing the vibrational spectra and secondary structural affinity of native unfolded proteins. Raman spectra can be achieved in dilute aqueous solution, a good feature that is of enhanced significance in characterizing natively unfolded proteins because of their inclination to aggregate at higher concentrations. Moreover, Raman spectra permit the environment of several amino acid side chains to be characterized, including the acidic residues, sulfur-containing residues and aromatic amino acids in different physical states. Dual Polarization Interferometry (DPI) Dual polarization interferometery is greatly sensitive analytical methodology employed for the determination of structure, function as well as orientation of biological and other layers at solid-liquid interface, providing the measures of multiple parameters of molecules at a surface showing information associating with packing and thickness related to layer refractive index (RI), stoichiomety (mass), surface loading and density. DPI has been employed to investigate multiple types of phospholipids. Moreover, peptides relating to plasma membrane like duramycin and V4 (antimicrobial peptide) and Melitti (component of bee venom) have been scrutinized (interaction between meittin-lipid) by DPI. Mass and structural changes, in various proteins due to the function of metal ion concentration, including Ca 2+ in calmodulin, prion containing Fe 2+ , β-amyloid associated with Cu 2+ etc have been studied by DPI [29]. DPI methodology has also been employed for evaluating immobilization approach for DNA sensing surface and is challenging because of high charge on DNA backbone rendering reachable orientation of molecule hard to accomplish [30,31]. Crystallographic analysis As mentioned in the section of “Introduction”, x-ray crystallography is a type of high resolution microscopy which facilitates the researchers to scrutinize the protein structures at the protein level and enhances the insight into protein functionality. As far function is concerned, interaction of protein with other molecules, process of catalysis in case of enzymes and changes in conformational alteration and studied during x-ray crystallographic analysis. Figure 11: Use of Crystallography in Protein Structure and Function Determination. In all types of microscopy, the detail and/or resolution depends upon the wavelength (λ) of the electromagnetic radiation used. Light microscopy (λ= ~300nm) shows individual cells and its components (sub-cellular organelles). On contrary, electron microscopy (λ=
Figure 12: Steps in Protein Preparation and Analysis. X-Ray data collection: In x-ray crystallographic analysis, several aspects are studied for a given crystal of sample (protein). The resolution limit, the unit cell parameter, crystal symmetry and crystal orientation are studied usually. With the help of these parameters’ information, a data collection approach is formed. During collection of data set of typical medium resolution, may take up to three days by employing x-ray source. While for high resolution data, a synchrotron radiation is utilized, where the intensity of x-rays is greater and time is shorter in case of data collection. Figure 13: Use of X-Ray Data in Determination of Various Aspects of a Crystal. Electron crystallography: Results have shown that electron crystallography of two dimensional crystals has progressed to atomic resolution. Verities of proteins have been crystallized in two dimensional format and conformation [32]. The structure obtained by electron crystallography like tubulin, the light harvesting complex -2 (LH2), aquaporin-1 (AQP1) and bacteriorhodopsin (BR) have allowed significant atomic models to be built [33-38]. Many membranous proteins have been examined by electron crystallography and their structures studied to a resolution that produced the secondary structure to be clearly illustrated. This technique has advantage over the others because it provides fast data collection and processing. Figure 14: Significance of Electron Crystallography in the Formation of Atomic Models of Biological Molecules. Atomic Force Microscopy (AFM): Atomic force microscopy (AFM) allows the investigation of two-dimensional (2D) membrane OMICS Group eBooks 014
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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
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Page 15 and 16: Figure 6: At Domain Level, Protein
Page 17 and 18: Brownian Dynamics (BD) method Prote
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Page 23 and 24: FlexServ The flexibility of protein
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Page 47 and 48: MMP27 (MMP-22, C-MMP) mRNAs for MMP
Page 49 and 50: Signal transduction MMP production
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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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identifier, since a single macromol
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New Peptide Based Therapeutic Appro
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ability to selectively target cells
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separation efficiency. However, use
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Antimicrob Agents Chemother 49: 330
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Protein Detection Techniques Dennis
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