Handling of Selenomethionines in Macromolecular Refinement

Abstract

In the Protein Data Bank, we can find X-ray structures which were determined from selenium-derivatized proteins, but the deposited coordinates, to our surprise, contain native methionines. The problem is likely due to not complete substitution of native methionines with selenomethionines during chemical reaction. When the crystal grows from such sample, and later is subjected for X-ray analysis, it may show partial presence of native sulfur. This paper is a voice in discussion how to handle the refinement of selenomethionines. The purpose of this work is to explain why selenomethionines can't be refined purely as native methionines, particularly in macromolecular structures determined at high resolution. It is important because selenium and sulfur are different chemical elements. To explain the importance of refinement of correct atom type, author provides evidence, collected mainly from his previously reported small organic structures containing sulfur or selenium. Author emphasizes that the Xray structures, which contain selenium, are never identical with their sulfur-containing analogs. They differ at least in the respective bond lengths. Two available publicly X-ray structures have been re-refined, one small molecule and one macromolecule, in which the atom type was intentionally changed. Refinement of chemically incorrect atom type yielded non-natural behavior of atomic displacement parameters. Author concludes that the structures which contain incorrect atom types can't represent the experimental data but can serve only as models. There are examples, in the PDB, which show that selenomethionines in not fully Se-Met derivatized proteins can be refined with arbitrarily assumed fractional, less than 100%, occupancies. This inspired the author to perform various re-refinements, of the above mentioned Se-Met structure that contained S atoms in coordinates. In these re-refinements, selenomethionines are handled in different manners, and the results are compared. Author suggests refinement of chemical identities, selenium and sulfur, with fractional occupancies, as a method.

BANΔIT: B’‐Factor Analysis for Drug Design and Structural Biology

“…9). For ordinary residues the difference might be small (C=12 u–S=32 u), but for selenomethionines (Se=79 u) and high‐resolution X‐ray structures which enable the positioning of hydrogen atoms (H=1 u) significant deviations are known [22,23] …”