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A qualitative understanding is sufficient for achieving the idea of thermodynamic system. Cells are non-equilibrium systems in which information plays an essential role. Folding of Proteins and Metalloproteins Metalloproteins design necessitates an accurately folded protein scaffold containing the suitable number and type of ligands with the accurate geometry to encapsulate and activate the metal for chemical catalysis. Thermodynamics of Folding of Ribonucleases Ribonucleases contain three small, extracellular enzymes (Sa, Sa2, and Sa3) produced by different strains of Streptomyces aureofaciens with amino acid sequences that are 50% of homology. The unfolding of these enzymes by heat and urea has been studied to determine the conformational stability and its dependence on temperature, pH, NaCl, and the disulfide bond. Urea and guanidinium chloride are responsible for denaturing the protein structure. Both compounds show their interaction in the medium but are weak in their interaction. Molar amount is required for denaturation process. Many ideas have proposed that denaturants show their interaction by direct binding to the protein molecules or by altering the properties of the solvent. On the other hand, disulfide bonds increase the conformational stability of a protein mainly by constraining the unfolded structures or conformations of the protein and by this means decreasing their conformational Entropy. Accordingly, the hydrophobic effect and hydrogen bonding make large but equal contributions to the conformational stability of the proteins [15]. Figure 10: 3D Structure of Ribonuclease A. (Rendered by Chimera, ver. 1.8) Protein-DNA Interactions and Thermodynamic In protein-protein interactions, evolutionary conserved amino acids have been studied by many researchers and have been found to be correlated with hotspot residues. A hotspot is a residue whose mutation or change could to be a drop of more than 2kcal/mol in binding free energy [16]. The regions where the hotspot are tightly packed, called Hotspot Regions. Hence, they exhibit rigid packing, they are considered as important role player in stabilization of the structure. Moreover, the contribution of hotspot residues is independent between hotspot regions [17,18]. Various transcription factor proteins recognize and bind with DNA sequences with various affinities [19,20]. The binding ability makes the cells capable of scheming thousands of genes with reasonably few regulatory proteins [21]. Conservation of Amino Acids Structural Hotspots Protein Function Figure 11: The Relationship between Protein and Other Types of Molecules. Amino acid residues participate as important components in protein function and are often conserved. Thermodynamic and structural data of protein-DNA interactions is investigated and found a relationship between sequence conservation, free energy and structural sequence. Nearly all stabilizing residues or recognized hotspots are those which occur as clusters of conserved molecules/residues. The compact packing density of the clusters and accessible experimental thermodynamic data of mutations suggest cooperativity between conserved residues in the clusters. Conserved single residue contributes to the strength of protein-DNA complexes to a lesser extent. In protein-protein interactions, conserved residues are highly associated with experimental residue hotspots, giving dominantly and often cooperatively to the stability of protein-protein complexes. On the whole, the conservation models of the stabilizing residues in DNAbinding proteins also emphasize the implication of clustering as compared to single residue conservation. OMICS Group eBooks 011
Figure 12: Residue Clusters with Multiple Interfaces. Binding Sites between Proteins and Other Macromolecules Interactions between proteins and other biological macromolecules are basic requirement for the variety of mechanisms in a biological system. Studies have revealed that macromolecules contains special site in their structure for the binding with other and/or similar macromolecules. The binding sites for DNA, RNA, obligate protein and non-obligate protein binding and interaction have been studied. Fundamental principles for binding with respect to thermodynamic which govern the interaction of different macromolecules responsible for the chemical reactions at the binding site. Moreover amino acids involved in the binding attribute make a net constructive enthalpy and entropic role to the free binding energy [22,23]. Figure 13: Interactions among protein and other biological macromolecules leads to various cellular mechanisms at molecular level. Regarding DNA-binding, proteins achieve binding through: (i) Affinity between the protein and DNA could be observed by the positively charged residues (Arg and Lys) of proteins and negatively charged phosphate backbone of the DNA double helix. (ii) Specificity could be analyzed by observing side by side van der Waals (VDW) interactions and hydrogen bonding among the positively and negatively charged binding sites [24]. Figure 14: Electrostatic potentials of DNA-binding Site deals with various parameters. OMICS Group eBooks 012
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for virtually all macromolecules to
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New Peptide Based Therapeutic Appro
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ability to selectively target cells
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separation efficiency. However, use
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Protein Detection Techniques Dennis
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