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Advances in Protein Chemistry Chapter: Advances in Protein Thermodynamics 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
Advances in Protein Thermodynamics Introduction Arif Malik 1 , Mahmood Rasool 2 *, Abdul Manan 1 , Aamer Qazi 3 and Mahmood Husain Qazi 4 1 Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Pakistan 2 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia 3 Ontario Institute for Cancer Research, Toronto, Canada 4 Center for Research in Molecular Medicine (CRiMM), The University of Lahore-Pakistan *Corresponding author: Dr. Mahmood Rasool, PhD Assistant Professor, Center of Excellence in Genomic Medicine Research, Post Box No. 80216, King Abdulaziz University, Jeddah 21589, Saudi Arabia, Tel: +966-582-254267; E-mail: mahmoodrasool@yahoo.com Proteins are synthesized in the cytoplasm or in vitro as amorphous polypeptide chains that, usually, assemble into their functionally active three-dimensional (3D) shapes, a process; known as protein folding. In physico-chemical perspective, it is achievable in characterizing the folding mechanism of a given protein at molecular as well as atomic level and to restructure its free-energy landscape. Biological systems abide by the natural laws of chemistry and physics. The gradual progress in the field of biological sciences involve the information on various mechanisms/action that have affected the living systems at the molecular level during the investigations of the biological mechanisms in turn the structure of several molecules like proteins and nucleic acids have been determined. The physical sciences, including thermodynamics, can make a crucial contribution to the biological sciences for understanding of various biological mechanisms. Thermodynamics is distinct by the energy level distribution; the dilemma lies in the production of a pragmatic/practical proteinlike model that would suitably take hold of most of thermodynamic properties of proteins like the denaturation temperature, Entropy, enthalpy, heat capacity. Thermodynamics plays an important part in driving the dynamics of protein folding. It is well recognized that the greater part of proteins can achieve their native states and they can also refold to their native states after been denatured. To account for these astonishing properties the familiarity of the energy level distribution is not satisfactory, in other words the distribution of energy in forming the new bonds between the residues of protein need to be explored at molecular as well as atomic levels. It turns out that the dynamics of protein folding is much more complicated to understand regarding protein thermodynamics. Simple systems quickly develop towards equilibrium, because an isolated system is distinguished by utmost Entropy (Disorder). On the contrary, the living system does not reach at the state of stability or equilibrium easily. The biological development shows the increasing trend of growth of multi-cellular organism from the unit cell. The thermodynamic studies of such a complicated system in various organisms are really a big challenge to biologists. Equilibrium thermodynamics helps for the study of biological processes in vitro environment. Equilibrium characteristics of biological macromolecules are one of the basic requirements and essential for the researchers to know about them. Moreover, the combination of statistical and molecular models with equilibrium thermodynamics provides microscopic understanding of various mechanisms operating the living systems. In receipt of above mentioned mechanisms there are some processes regarding binding between biological macromolecules in cells or between a macromolecule and a ligand outside the cell. Various complex events take place in the biological system; they comprise active diffusion, translocation of proteins, conformational changes, membrane fusion, virus assembly, vesicle budding and DNA unwinding. Moreover, posttranslational modification (PTM), a crucial process, is everywhere in the cell and control the function of proteins frequently by modulating their biophysical properties. These modifications are methylation, glycosylation, acetylation, ubiquitination, S-nitrosylation, lipidation and phosphorylation which can regulate the structural features of proteins thermodynamic and kinetic. The current chapter has main two parts one based on practical/experimental approach and the other on computational approach in which tools of bioinformatics and various databases have been mentioned which are used to study various aspects of proteins including their thermodynamic aspects. Thermodynamics deals with the association between heat and work. Proteins, polymer of amino acids, exhibit several crucial physiological behaviors and have unique structural characters like stability. Environmental conditions are also crucial factors in the folding of proteins, since a change in conditions can annihilate the native (Folded) structure. The folding and unfolding mechanisms are described in terms of thermodynamics. S r.no Various Applications of Thermodynamics in Proteins 1 Stability of proteins 2 Improvement of bioprocess 3 Biomass and metabolite production 4 Cell transport 5 Equilibrium studies in downstream process 6 Properties of biomolecules Study of thermodynamics depends upon the basic physical laws of thermodynamics. The first law (law of energy conservation) deals OMICS Group eBooks 004
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