Date of Award

7-8-2008

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biology

First Advisor

Robert W. Harrison - Committee Chair

Second Advisor

Chun Jiang - Committee Member

Third Advisor

Irene T. Weber - Committee Member

Fourth Advisor

Phang C. Tai - Committee Member

Abstract

ATP Binding Cassette (ABC) transporters are trans-membrane proteins that exist in all phyla. Mutations in this family of proteins can cause inherited diseases like Cystic Fibrosis. ABC transporters consist of dimers of nucleotide binding domains (NBDs) and transmembrane domains (TMDs). NBDs regulate ABC transporters by binding to and hydrolyzing ATP. Although NBD-ATP interactions, NBD-TMD interactions and NBD-water interactions are known to be crucial to the function of these proteins, it is still not clear what structural and energetic factors are involved in the NBD-NTP interactions, how NBD and TMD interact with each other, how water is involved in the functions of ABC transporters and what are the structures and energetics of protein bound water. Molecular modeling and molecular dynamics (MD) simulations were conducted to interpret and predict the structural and energetic factors in control and action of two ABC transporters, CvaB and SUR2B. Water is essential for ABC transporters to carry out their functions, to increase the accuracy of simulations. Therefore, water potentials in molecular modeling and dynamics simulations were improved based on the calculation of water structures from protein surface. Previous study showed the NBDs of ABC transporter CvaB bind tighter to GTP than to ATP at lower temperature but not at high temperature. The MD simulations in this study suggested the velocity of water molecules initiates the temperature dependent functional change of proteins. Previous study found that Ser1387 in the NBD of SUR2B, an ABC transporter in vascular smooth muscles, is critical to Kir6.1/SUR2B channel. The molecular modeling and dynamics simulation conducted on SUR2B showed that Ser1387 is located at a region that contacts a TMD. Upon the phosphorylation, the interaction between the NBD and TMD was enhanced which led to an inter domain movement. Water is essential for ABC transporters to carry out their functions, to increase the accuracy of simulations, and, therefore, the structures and energetics of protein bound water were studied. The water radial distribution function for protein bound water was calculated from 105 atomic resolution protein crystal structures and was found to be sharper than that observed for bulk water.

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Biology Commons

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