Research • Research Areas

Structural Analysis and Classification of Protein Conformational Motions by Perturbation Response Scanning and Molecular Dynamics

Upon binding ligands, many proteins undergo structural changes compared to the unbound form. We have recently introduced a methodology that we term perturbation-response scanning (PRS) to monitor these changes and to study which mechanisms arrange conformational shifts between the liganded and free forms. Our method is simple, yet it efficiently characterizes the response of proteins to a given perturbation on systematically selected residues. In this project, we shall generalize PRS to different types of perturbations and to establish it as an accessible, yet precise method in the study of protein dynamics. For this purpose, we will compare the findings of PRS with those from other perturbational methods developed for all-atom protein representations such as scanning by molecular mechanics and steered MD. We will also generalize the PRS method to incorporate perturbations introduced at multiple sites simultaneously so as to mimic the effect of larger or multiple ligands.

Related web sites:

http://midst.sabanciuniv.edu

http://people.sabanciuniv.edu/atilgan

http://people.sabanciuniv.edu/canan

Related references:

Atilgan, C., Atilgan, A.R., Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein. PloS Computational Biology, 5(10), 14, (2009). [http://dx.doi.org/10.1371/journal.pcbi.1000544]

Atilgan, C., Gerek, Z.N., Ozkan, S.B., Atilgan, A.R., Manipulation of Conformational Change in Proteins by Single-Residue Perturbations. Biophysical Journal, 99(3), 933-943, (2010). [http://dx.doi.org/10.1016/j.bpj.2010.05.020]

Funding:

This project is funded by the Scientific and Technical Research Council of Turkey. Three graduate student scholarships are available in this project beginning Fall 2011.

Student enrollment in the Materials Science and Engineering program is not a must to do research in our group. You may enroll in any programs of the Faculty of Engineering and Natural Science suitable to your background. Deadline for grad applications is 27 May 2011.