Energetics of ion-protein interactions
نویسنده
چکیده
In keeping with the goals of our laboratory, efforts in this thesis are directed towards improving our understanding, and therefore our ability to calculate, the energetics of protein-ligand interactions. Electrostatic contributions to protein-ligand binding events are poorly understood, and underrepresented in data sets used to parameterize the energetics of protein unfolding and binding. Therefore, the focus in this thesis is placed on ion-protein interactions as model systems that can give insight into the contribution of charge-charge interactions to the enthalpy, entropy, and heat capacity changes associated with binding. In order to measure the energetics of charge-charge interactions, both differential scanning calorimetry and isothermal titration calorimetry
منابع مشابه
Biological Applications of Isothermal Titration Calorimetry
Most of the biological phenomena are influenced by intermolecular recognition and interaction. Thus, understanding the thermodynamics of biomacromolecule ligand interaction is a very interesting area in biochemistry and biotechnology. One of the most powerful techniques to obtain precise information about the energetics of (bio) molecules binding to other biological macromolecules is isoth...
متن کاملExperimental Approaches to Determine the Thermodynamics of Protein-Ligand Interactions
Used appropriately and judiciously, thermodynamic parameters can offer insight into the energetics of protein-ligand interactions that is not readily attainable by other means. The utility or application of thermodynamic analysis has traditionally been considered more the domain of (bio)chemistry than biology. However, the modern recognition of an interface in the case of protein-ligand interac...
متن کاملEnergetics of Zn2+ adsorption in silicate MEL-type nanoporous material
Density-functional-based and ab initio calculations were implemented at different computational levels to estimate the binding energy of Zn2+ ion adsorbed on the available sites of a silicate MEL-type adsorbent. B3LYP and MP2 were used in combination with the 6-31G*, 6-31+G*, LanL2DZ, 6-311+G*, and Def2-TZVP basis sets. The zinc cation was found to preferentially occupy the 6MR sites followed b...
متن کاملMechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations.
Ion channel-toxin complexes are ideal systems for computational studies of protein-ligand interactions, because, in most cases, the channel axis provides a natural reaction coordinate for unbinding of a ligand and a wealth of physiological data is available to check the computational results. We use a recently determined structure of a potassium channel-charybdotoxin complex in molecular dynami...
متن کاملThe role of bulk protein in local models of ion-binding to proteins: comparative study of KcsA, its semisynthetic analog with a locked-in binding site, and valinomycin.
In studying ion-selectivity in biomaterials, it is common to study ion-protein interactions within a local neighborhood around the ion. This local system analysis for the S(2) site of KcsA, its semisynthetic analog, and valinomycin yields the free energy change in exchanging K(+) with Na(+) in quantitative agreement with the value obtained by considering ion-interactions with the entire system....
متن کامل