advances-in-protein-chemistry

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
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