Protein Engineering, Vol. 12, No. 8, 673-680,
August 1999
© 1999 Oxford University Press
A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation
1,8
1 Division of Biological Science, Graduate School of Science, NaGya University, Furo-cho, Chikusa, NaGya 464-8602,
3 Department of Bioapplied Chemistry, Faculty of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585,
5 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 and
6 Japan Advanced Institute of Science and Technology, Hokuriku, 15 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
A globular domain can be decomposed into compact modules consisting of contiguous 10–30 amino acid residues. The correlation between modules and exons observed in different proteins suggests that each module was encoded by an ancestral exon and that modules were combined into globular domains by exon fusion. Barnase is a single domain RNase consisting of 110 amino acid residues and was decomposed into six modules. We designed a mini-protein by removing the second module, M2, from barnase in order to gain an insight into the structural and functional roles of the module. In the molecular modeling of the mini-protein, we evaluated thermodynamic stability and aqueous solubility together with mechanical stability of the model. We chemically synthesized a mini-barnase with 15N-labeling at 10 residues, whose corresponding residues in barnase are all found in the region around the hydrophobic core. Circular dichroism and NMR measurements revealed that mini-barnase takes a non-random specific conformation that has a similar hydrophobic core structure to that of barnase. This result, that a module could be deleted without altering the structure of core region of barnase, supports the view that modules act as the building blocks of protein design.
Keywords: barnase/mini-protein/molecular modeling/NMR
2 Present address: Department of Industrial Chemistry, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
4 Present address: Department of Industrial Chemistry, Tokai University, 1117 Kitakaname, Hiratsuka 259-1292, Japan
7 Present address: Faculty of Pharmaceutical Science, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
8 To whom correspondence should be addressed
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. Tsuji, T. Nagata, and H. Yanagawa N- and C-terminal Fragments of a Globular Protein Constructed by Elongation of Modules as a Units Associated for Functional Complementation J. Biochem., October 1, 2008; 144(4): 513 - 521. [Abstract] [Full Text] [PDF]
|
|