Free energy calculation of ion and ligand binding to membrane proteins

Thesis Type: Doctorate

Institution Of The Thesis: Gazi University, Fen Bilimleri Enstitüsü, Turkey

Approval Date: 2013

Thesis Language: Turkish


Consultant: Akif Özbay


Membrane proteins, such as ion channels, transporters and receptors are biologically among the most important proteins because they allow the cells to communicate with their environments; they are the targets of most, and perhaps all, pharmaceuticals. Recent developments emerging in experimental and computational sciences in recent years increased the interest in membrane proteins significantly. Milestone of the development of this area, of course, has been to obtain the crystal structure of membrane proteins. Firstly crystal structure of a bacterial KcsA potassium channel was obtained and then the crystal structures of mammalian potassium channels were found. Nearly a decade later, the crystal structure of glutamate transporter (GltPhT) was obtained. The latest developments in the experimental study are obtaining of the crystal structure of Na channel (NavAb). Similar to experimental progress or even more rapid advances are seen in computer technologies. Developments of parallel computing algorithms in molecular modeling and simulation methods, following the hardware technologies, intensified the computational studies of membrane proteins. In this study, molecular dynamics simulations of NavAb ion channel and leucine (Leu) transporter, which are examples of membrane proteins, were performed. Ion binding mechanism in the leucine transporters was studied by using free energy methods. In the experimental study it was shown that Na2 binding site is found the deepest potential energy, and secondly deep potential energy is found in the Na1 binding site and the shallowest potential energy is found for the amino acid of Leu. Na ions entering into an open Leu transporter is going to occupy firstly the Na2 binding site and secondly the Na1 binding site and finally Leu is going to bind. Since closed structure exists, in experimental studies only ion/ligand binding process was investigated. The second part of the study is molecular dynamics modeling of the NavAb ion channel. The crystal structure of the voltage-gated bacterial Nav channel was obtained in 2011 by Payandeh et al. Voltage-gated sodium channels is very important due to the onset of action potentials. Molecular dynamics modeling has been conducted to understand the structure-function relationship for this channel. Using free energy methods, energetics of ion binding is studied and the binding energies and positions were obtained for Na+ ions in the filter. It has been known from the experimental data that Nav and Cav channels are similar and Ca++ ions are permiating in the Nav channels. A potential of mean force calculation is performed for Ca++ ion through the channel axis of the Nav. As a result of this study we observed Ca++ ions have a higher binding affinity than that Na+. Based on these findings, we studied the transport of Na+ ion through the filter of the channel when there is Ca++ ion in it was studied with potential of mean force and it was observed that Ca++ ion blocks the channel.