Specific radiation damage to acidic residues and its relation to their chemical and structural environment

• Published in: Journal of synchrotron radiation 2007-01, Vol.14 (1), p.84-91
• Main Authors: Fioravanti, Emanuela, Vellieux, Frédéric M. D., Amara, Patricia, Madern, Dominique, Weik, Martin
• Format: Article
• Language: English
• Subjects: acidic residues; Amino Acids - chemistry; Amino Acids - radiation effects; Computer Simulation; Crystallography, X-Ray - methods; Dose-Response Relationship, Radiation; Haloarcula marismortui - chemistry; halophilic malate dehydrogenase; Hydrogen-Ion Concentration; Malate Dehydrogenase - chemistry; Malate Dehydrogenase - radiation effects; Malate Dehydrogenase - ultrastructure; Models, Chemical; Models, Molecular; Protein Conformation - radiation effects; Protein Denaturation - radiation effects; radiation damage; Radiation Dosage; Solutions; Solvents - chemistry; Structure-Activity Relationship; X-Rays
• ISSN: 1600-5775; 0909-0495; 1600-5775
• DOI: 10.1107/S0909049506038623

Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X‐ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side‐chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side‐chains. This suggests that residues with higher pKa values are more vulnerable to damage than those with a lower pKa. However, such a correlation was not found when calculated pKa values were inspected. (ii) Acidic side‐chains located in the enzymatic active site are the most radiation‐sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.