This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We are requesting node hours on the Anton supercomputer in order to determine the tertiary structure of the tetratricopeptide repeat unit in the cargo binding domain of a kinesin motor protein. Preliminary data obtained using the Desmond molecular dynamics software with standard force fields and explicit solvent models suggests that this ~200 residue domain is a """"""""fast-folder"""""""" and likely follows the nucleation-condensation folding mechanism. In addition to determining the 3D structure of an important and biologically functional domain, the ensemble of structures obtained from a multi-microsecond simulation will enable a fundamental analysis of the applicability of various protein folding models and provide structural insight into misfolded and semi-folded states that are not accessible to experimental methods. These results will also be utilized to exhaustively validate the suitability of lattice-based mathematical models for describing folding behavior of repeat proteins.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
3P41RR006009-20S1
Application #
8364207
Study Section
Special Emphasis Panel (ZRG1-BCMB-Q (40))
Project Start
2011-09-15
Project End
2013-07-31
Budget Start
2011-09-15
Budget End
2013-07-31
Support Year
20
Fiscal Year
2011
Total Cost
$1,094
Indirect Cost
Name
Carnegie-Mellon University
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
052184116
City
Pittsburgh
State
PA
Country
United States
Zip Code
15213
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