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Chin. Phys. B, 2011, Vol. 20(5): 058701    DOI: 10.1088/1674-1056/20/5/058701
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev  

The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

Qi Jian-Xun(齐建勋)a)b) and Jiang Fan(江凡) a)†
a Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; b Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
Abstract  The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.
Keywords:  crystallographic temperature factor      denaturation      conformational flexibility      active site prediction  
Received:  03 December 2010      Revised:  08 January 2011      Accepted manuscript online: 
PACS:  87.15.hp (Conformational changes)  
  61.05.C- (X-ray diffraction and scattering)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 10674172 and 10874229).

Cite this article: 

Qi Jian-Xun(齐建勋) and Jiang Fan(江凡) The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme 2011 Chin. Phys. B 20 058701

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