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Tumor suppressor INK4: Refinement of p16INK4A structure and determination of p15INK4B structure by comparative modeling and NMR data

Published online by Cambridge University Press:  01 June 2000

CHUNHUA YUAN
Affiliation:
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
THOMAS L. SELBY
Affiliation:
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
JUNAN LI
Affiliation:
Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210
IN-JA L. BYEON
Affiliation:
Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210
MING-DAW TSAI
Affiliation:
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210 Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210 Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210 Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
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Abstract

Within the tumor suppressor protein INK4 (inhibitor of cyclin-dependent kinase 4) family, p15INK4B is the smallest and the only one whose structure has not been determined previously, probably due to the protein's conformational flexibility and instability. In this work, multidimensional NMR studies were performed on this protein. The first tertiary structure was built by comparative modeling with p16INK4A as the template, followed by restrained energy minimization with NMR constraints (NOE and H-bonds). For this purpose, the solution structure of p16INK4A, whose quality was also limited by similar problems, was refined with additional NMR experiments conducted on an 800 MHz spectrometer and by structure-based iterative NOE assignments. The nonhelical regions showed major improvement with root-mean-square deviation (RMSD) improved from 1.23 to 0.68 Å for backbone heavy atoms. The completion of p15INK4B coupled with refinement of p16INK4A made it possible to compare the structures of the four INK4 members in depth, and to compare the structures of p16INK4A in the free form and in the p16INK4A-CDK6 complex. This is an important step toward a comprehensive understanding of the precise functional roles of each INK4 member.

Type
Research Article
Copyright
2000 The Protein Society

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