1B7M

VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES

Summary for 1B7M

• Entry DOI: 10.2210/pdb1b7m/pdb
• Descriptor: PROTEIN (LYSOZYME), SODIUM ION (3 entities in total)
• Functional Keywords: mutant stability, human lysozyme, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Secreted: P61626
• Total number of polymer chains: 1
• Total formula weight: 14803.80

Authors

Takano, K.,Ota, M.,Ogasahara, K.,Yamagata, Y.,Nishikawa, K.,Yutani, K. (deposition date: 1999-01-24, release date: 1999-01-27, Last modification date: 2024-04-03)

Primary citation

Takano, K.,Ota, M.,Ogasahara, K.,Yamagata, Y.,Nishikawa, K.,Yutani, K.
Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.
Protein Eng., 12:663-672, 1999

PubMed Abstract: The stability profile of mutant protein (SPMP) (Ota,M., Kanaya,S. and Nishikawa,K., 1995, J. Mol. Biol., 248, 733-738) estimates the changes in conformational stability due to single amino acid substitutions using a pseudo-energy potential developed for evaluating structure-sequence compatibility in the structure prediction method, the 3D-1D compatibility evaluation. Nine mutant human lysozymes expected to significantly increase in stability from SPMP were constructed, in order to experimentally verify the reliability of SPMP. The thermodynamic parameters for denaturation and crystal structures of these mutant proteins were determined. One mutant protein was stabilized as expected, compared with the wild-type protein. However, the others were not stabilized even though the structural changes were subtle, indicating that SPMP overestimates the increase in stability or underestimates negative effects due to substitution. The stability changes in the other mutant human lysozymes previously reported were also analyzed by SPMP. The correlation of the stability changes between the experiment and prediction depended on the types of substitution: there were some correlations for proline mutants and cavity-creating mutants, but no correlation for mutants related to side-chain hydrogen bonds. The present results may indicate some additional factors that should be considered in the calculation of SPMP, suggesting that SPMP can be refined further.

PubMed: 10469827
DOI: 10.1093/protein/12.8.663

Experimental method

X-RAY DIFFRACTION (2.2 Å)