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The finishing stage of folding depends on the precise and specific sequence of amino acids, while previously folding stages are supposed to be mostly insensitive to information of sequence [3]. Thermodynamics of Protein Conformational Changes The folded conformation seems to be at narrow free energy (ΔG) state but any change in the folded conformation depends upon the significant increment in free energy. The change in heat capacity when protein unfolding occurs is the temperature at which the stability is high in its value. As far as free energy is concerned, the highest stability occurs when S=0, on the other hand calculation by the equilibrium constant appears when enthalpy change is zero. The maximum stabilities could be occurred at different temperature ranges, but both are considered in different cases. The stabilities of native form decrease at both lower and higher temperatures. The other factors such as binding interactions among the amino acids seem to be playing an elaborative role in the stability of the protein conformation but these are not responsible for the significant stability and similar situation happens in the unfolded state, while the bonding between native protein and solvent is expected to be strong enough as compared to the bonding between unfolded coil and the surrounding environment. Moreover, the hydrophobic effect is considered to be the major stabilizing player. Energy Landscape Theory and Thermodynamics of Protein Stability Protein folding is one of the complex processes. Frauenfelder et al. and Bryngelson et al. describe the complexity of protein folding by restoring to a statistical approach to the energetic of protein conformation in the form of energy landscape [4-5]. Bryngelson et al. refers it mathematical procedure that assist in understanding of microscopic behavior of molecular system. It gives quantitative explanations of folded protein state, ensembles of conformational sub-states, ensembles of folding intermediates and denatured or unfolded states and considered as the realistic model of protein [6-7]. Bryngelson et al. describes an energy landscape, in mathematical form, of a system with “n” degrees of freedom is an energy function [5]: F(x) = F(x 1 , x 2 , x 3 ,..., x n ) Here, x 1 , x 2 , x 3 ,…, x n are variables for the microscopic state of the system [8] and F(x) is defined as the free energy. As far as protein is concerned, these variables (x 1 , x 2 , x 3 ,…, x n ) are all the dihedral angles of the chain and showing a single conformation of protein. The stability of the protein can be determined by examining the set of values x 1 , x 2 , x 3 ,…, x n that gives minimum value of free energy function, F(x). Moreover, the thermodynamics of protein stability is modeled reasonably well by the Energy Landscape Theory. Stability of medium depends upon the ground and excited states of atoms and nuclear particles which are the simplest as well as basic models while the understanding of complicated system like protein molecules contains far more complex idea and insight into ground and excited states. The ground state of native structure is well illustrated by using energy landscape model where energy represents a function of the topological alignment of atoms. Energy values generated by mountains and ridges are representation of spatial surface with the large number of different co-ordinates. Figure 2: Uses of Energy Landscape Models. Protein Folding and Unfolding Free and attached ribosomes are involved in the production of proteins within the biological system in the form of linear polypeptide chain. The primary or linear structure is converted into stable three dimensional structures with the help of folding process. The whole process of folding is controlled thermodynamically or kinetically by other proteins and/or enzymes, like molecular chaperones. The process of folding represents that the information required for the precise folding is available in the polypeptide chain. On the other hand, the three dimensional structure of proteins are damaged or affected by various reasons including miscoding due to errors in protein synthesis and/or misfolding due to errors in protein folding. Molecular Chaperones The chaperones have significant impact on the process of protein folding. As far as their function is concerned, it belongs to the class of proteins that assist in precise folding of proteins. The molecular chaperones are divided into following classes; Class I chaperones exhibit the affinity to bind with the hydrophobic regions, subsequently preventing aggregation and unfolding polymer is transported to various organelles. Class II chaperones present inside the organelles assist in misfolding with the help of multiple bonds. It has been observed that when cells are under stress proteins folding become improper. OMICS Group eBooks 007
Figure 3: Molecular Chaperone (Top View, Taken From Pdb). Intramolecular chaperones Specific sequence of amino acids is essential in the primary structure for proper folding, this sequence is called intramolecular chaperones and this part is cleaved by cellular proteases and precise folding is accomplished. The stability of a folded protein against denaturation or aggregation is frequently a few times the typical strength of a hydrogen bond in water (About 5~kcal/mol). This stability results from large competing effects that arise from hydration effects and the intra-molecular interactions in the protein. Biological systems also include ions and osmolytes (small organic solutes) in the solvent matrix that can change this delicate balance of interactions for stabilizing a protein. The adaptability in response to various stresses is seen in all living systems. The phenomena underlying such alteration are of fundamental importance in understanding how the solvent controls structure of biomolecules, function, and organization. Figure 4: Role of Molecular Chaperones in Protein Stability. Steric repulsion among the atoms in the covalent bonds exhibit limited elasticity/flexibility in the local region. Unfolded protein has the hydrodynamic characteristics in the presence of denaturants like urea or guanidinium chloride. Experimental investigations support that unfolded proteins are not random coils in a true sense under other physical conditions like pH and temperature extremes in the absence of denaturants. The equilibrium behavior of protein structure is represented by following ways; N↔U “N” represents the native (folded) state “U” represents the unfolded state The compact intermediate state represents a subset of unfolded state that is altering constantly among the different energetically unfavorable states [2]. Thermodynamics of Unfolding of Azurin Researchers have investigated the thermodynamics of unfolding of azurin (small blue copper protein) which is responsible for electron OMICS Group eBooks 008
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