Circular Dichroism and Secondary Structure of Proteins Essay Example for Free

Circular Dichroism and Secondary Structure of Proteins Essay Proteins are vital to an organism life; they are involved in nearly all cellular functions. It is an essential part of enzymes, the cellular membrane, active transport, protein synthesis and wound healing. Because one relies so heavily upon proteins and its function the structure of proteins is also very important. â€Å"The way a protein will fold over its self-determines how it interacts with other chemicals in its proximity, primarily because of different attractive forces being subjected at specific angles from certain amino acids on the protein’s primary structure and the final shape in the tertiary and quandary structure (Circular dichroism ). † The structure of proteins can range from simple to complex molecules. Proteins may consist of a primary, secondary, tertiary, and quaternary structure. The secondary structure consists of hydrogen bonds which join amide and carboxyl groups. These bonds aren’t far from the backbone of proteins. This structure is capable of structures such as alpha helicies, beta sheets, and beta turns (Jim, 2007). The physical, secondary structure is important because it helps in determining the activity of a protein. Circular Dichrosim spectroscopy has been identified as prevalent application used in structural biology in determining whether a protein is folded, characterizing its secondary structure, tertiary structure, and the structural family along with other uses as well (Circular dichroism ). Circular dichroism, CD spectroscopy has defined a form of light absorption spectroscopy. It measures the difference in the absorption of circular polarized light by a substance on the right and left. The secondary structure of a protein can be analyzed between the spectrum of approximately 260 and 180 nm. Estimates of secondary proteins can be compared to X-ray crystallography or NMR (Kelly, Jess, C., 2005).The structures identified in this spectrum are the alpha helix, parallel and antiparallel beta sheet, and turns (Berndt, 1996). The only drawback with CD is that even with the implied spectrum, it has been found that there is no exact standard reference spectrum for a pure secondary structure. Synthetic homopolypeptides used to obtain reference spectra are in general, poor models for the secondary structures found in proteins (Berndt, 1996). The CD signal reflect the entire molecular population; it can determines how much of a certain structure and protein contains. It cannot determine the specific residues involved in the alpha-helical portion. In Circular Dichroism a linear polarized light passes through a optically active sample of a protein. This protein has a different absorbance for components. The amplitude of the stronger absorbed component will smaller than that of the less absorbed component. A projection is created of the resulting amplitude. The result is no longer a linear line but and ellipse (PARTHASARATHY, 1985). Different analyses have been developed to help with various contributions that arise from the different types of secondary structures present in a single molecule. The use of reference spectra have been created from known protein structures to help find the overall and secondary structure of unknown proteins (Whitmore A., 2007). â€Å"Recently a new reference dataset of SRCD spectra of proteins of known structure, designed to cover secondary structure and fold space (Berndt, 1996).† Works Cited Berndt, K. D. (1996, May 31). 4.2.1 Circular dichroism spectroscopy. Retrieved October 02, 2012, from 4.2.1 Circular dichroism spectroscopy Circular dichroism . (n.d.). Retrieved October 02, 2012, from APlab: http://www.ap-lab.com/circular_dichroism.htm Jim, C. (2007, August). The Structure of Proteins. Retrieved October 02, 2012, from Chemguide: http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html Kelly, S. M., Jess, T. J., C., P. N. (2005). How to study proteins by circular dichroism. Biochimica et Biophysica Acta 1751, 119 – 139. PARTHASARATHY, M. (1985). Protein secondary structure from circular dichroism spectra. Proc. Int. Symp. Biomol. Struct. Interactions, 141-149. Whitmore, L., A., W. B. (2007). Protein Secondary Structure Analyses from Circular Dichroism. Biopolymers, 392-400. `