Open AccessSpecific radiation damage to acidic residues and its relation to their chemical and structural environment
Author(s) -
Fioravanti Emanuela,
Vellieux Frédéric M. D.,
Amara Patricia,
Madern Dominique,
Weik Martin
Publication year - 2007
Publication title -
journal of synchrotron radiation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.172
H-Index - 99
ISSN - 1600-5775
DOI - 10.1107/s0909049506038623
Subject(s) - chemistry , side chain , tyrosine , radiation damage , lysine , enzyme , serine , monomer , threonine , amino acid , crystallography , stereochemistry , biochemistry , irradiation , organic chemistry , physics , nuclear physics , polymer
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 p K a values are more vulnerable to damage than those with a lower p K a . However, such a correlation was not found when calculated p K a 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.