Sharif Digital Repository

Folded protein experience several conformational substates. Each substate reperesents a minimum in the free energy surface of the system. Since Myoglobin is the smallest protein that can reversibly bind to gas molecules and, it can be used as prototype for more complex systems.IR pecrtum of CO inside of myolgobin shows that distinct conformational substates can occur. It was shown that Histidine residue inside heme pocket plays an essential rolle in structural properties of substates. In this study, we used molecular dynamice simulation together with umbrella sampling method to obtain free energy profile of MbCO system. The configuration of distal Histidine (His64), CO and Heme is studied... 

This thesis is divided into three parts: In part I, interactions of neutral and anionic forms of histidine with coinage metal nano clusters M3 (M = Au, Ag and Cu) are investigated. Results demonstrate that nonconventional M…H-O hydrogen bonds and M-X bonds (X = N, O) play stabilization roles in interactions of histidine and metal nano clusters. Presence of negative charge in ligand leads to increase of binding energy of complexes. In the next step, the effects of coinage metal nano clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine is compared with the acidity of its Au3–, Ag3– and Cu3–complexed species. Moreover, pKa... 

Due to the importance of using pure proteins in the industry and basic research in order to study them in the structural contexts and interactions of proteins in recent years, purification methods have been extensively developed. The purification steps usually depend on the size of the protein, its physical and chemical properties, the binding affinity and the biological activity of the protein in question, In the purification process, the protein portion is separated from the non-protein portion. The biggest challenge is when we want to separate different proteins. Different chromatographic methods are used, depending on the properties of the impure proteins. One of these chromatographic... 

In the first part of this research, a single-component colorimetric sensor array based on the aggregation of AuNPs has been designed for the quantification and classification of antidepressant drugs (fluvoxamine (Flu), nortriptyline (Nor), citalopram (Cit), alprazolam (Alp), diazpam (Dia), sertraline (Ser), zolpidem (Zol), and imipramine (Imi)). Tuning the pH and ionic strength enabled the single-component probe to interact with the target analytes through different binding modes, providing the required cross-reactivity. To generate the array, a single AuNP was embedded into six experimental conditions: three different buffers (acidic, neutral and basic) each at two concentration levels (1mM...