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Characterization of Protein Secondary Structure using Latent Semantic Analysis

Ganapathiraju, Madhavi K and Klein-Seetharaman, Judith and Balakrishnan, N and Reddy, Raj (2004) Characterization of Protein Secondary Structure using Latent Semantic Analysis. In: IEEE Signal Processing Magazine, 21 (3). pp. 78-87.


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A small organic molecule, 11-cis retinal, a Vitamin A derivative, readjusts its shape by changing a single bond on seeing light to form all-trans retinal. While this small change may not seem very significant, it makes a big difference for perception of light in human vision: This is the way by which the brain knows that a photon has landed on the eye. How? The retinal is embedded inside another molecule, called rhodopsin, which belongs to a family of molecules called proteins. Rhodopsin provides multiple molecular interactions to the retinal (Figure 1), and many of these interactions are perturbed by the small change in the retinal induced by light. These perturbations in the immediate neighborhood of the retinal induce other perturbations in more distant parts of rhodopsin, and these changes are recognized by other proteins that interact with rhodopsin, inducing a complex cascade of molecular changes. These molecular changes are ultimately converted into an electrical signal that is recognized by the neurons in the brain. Thus the initial information of light isomerization is the signal that is processed by the proteins so that the human body can understand and react to it. "Signal transduction", as the transport of information is called, is only one of the many functions performed by proteins. Other examples for functions in which proteins are involved are the immune system, cell replication and utilization of nutrients. Besides function, proteins also play structural roles, such as formation of muscular fibers and tissues. Proteins are undoubtedly the most important functional units in living organisms and there are more than 30,000 different types of proteins in the human body. Understanding how these proteins work is crucial to the understanding of the complex biological functions and malfunctions that occur in diseases. How do proteins look like? Proteins are composed of fundamental building blocks of chemical molecules called amino acids. When a protein is synthesized by the cells, initially, it is just a string of amino acids. This string arranges itself in a process called protein folding into a complex three-dimensional structure capable of exerting the function of the specific protein.

Item Type: Journal Article
Publication: IEEE Signal Processing Magazine
Publisher: IEEE
Additional Information: ©2004 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
Keywords: Latent semantic analysis;Secondary structure prediction
Department/Centre: Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited: 25 Aug 2008
Last Modified: 19 Sep 2010 04:14
URI: http://eprints.iisc.ac.in/id/eprint/1183

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