Flexible Receptor Docking Method Development and Molecular Dynamics Studies Towards Targeting Dynamic Protein Surfaces.

flexible receptor docking development;CHARMM simulation package;computational biophysics;protein-ligand interactions;KIX domain of CREB binding protein;coarse-grained go-like models;Chemistry;Science;Chemistry

Gagnon, Jessica K.Mapp, Anna K ;

University of Michigan

关键词: flexible receptor docking development;    CHARMM simulation package;    computational biophysics;    protein-ligand interactions;    KIX domain of CREB binding protein;    coarse-grained go-like models;    Chemistry;    Science;    Chemistry;   

Others  :  https://deepblue.lib.umich.edu/bitstream/handle/2027.42/116710/gagnonj_1.pdf?sequence=1&isAllowed=y

瑞士|英语

来源: The Illinois Digital Environment for Access to Learning and Scholarship

【 摘 要 】

Protein-protein interactions are integral for cellular function, playing a huge rolein processes such as cell signaling and transcription regulation. Targeting these essential interactions with small molecule inhibitors is important from a biochemical and pharmaceutical perspective. This dissertation contains chapters on multidisciplinary, collaborative approaches to investigate transcription regulation as well as MHC Class I assembly, which is involved in the immune response. During these projects I applied a variety of computational tools and developed a new docking methodology in CHARMM (CDOCKER). This new version of CDOCKER incorporates receptor flexibility through maintaining selected side-chains in an all-atom representation, while the rest of the receptor is represented as a grid. This version of CDOCKER includes a newly implemented sampling protocol that leads to docking accuracy that is competitive with and even exceeds that of other commonly used docking software in redocking trials.This docking methodology was applied to identify a putative ATP binding on calreticulin (CRT), a chaperone key to MHC Class I assembly and the immune response. This work was a collaborative effort with the Raghavan research group at the University of Michigan and was the first demonstration that CRT both binds and catalyzes ATP. We added further automated functionality to the CDOCKER method to investigate small- molecules covalently bound to receptors in collaboration with the Mapp research group at the University of Michigan. The tethering method was able to stabilize the dynamic surface of GACKIX for crystallization and modeled small-molecules that were identified experimentally but were unable to be crystalized. Finally, we employed Gō-like modelsto investigate the allosteric signaling between the two binding sites on GACKIX. These studies demonstrated the positive allostery arises from the first peptide paying the entropic cost of binding for the second peptide.The developments in docking methodology within CHARMM allow for targeting of fluid receptors such as GACKIX. A multidisciplinary approach to investigate complex cellular processes such as transcription regulation or the immune response takes advantage of the strengths of the different approaches and leads to advancements in understanding of the process at different size scales, atomistic to in vitro and even in vivo.