Journal Article

Charge-density analysis of an iron–sulfur protein at an ultra-high resolution of 0.48 Å

Hirano, Yu, Takeda, Kazuki, Miki, Kunio

2016

Overview

The ultra-high-resolution structure of the high-potential iron–sulfur protein at 0.48 Å, the highest-resolution X-ray crystal structure of a protein reported so far. A metalloprotein structure at 0.48 Å resolution High-resolution X-ray crystal structures of proteins feature prominently in the scientific literature, but the resolutions of these structures are rarely better than 3.0–1.5 Å. This study reports the structure of the high-potential iron–sulfur protein (HiPIP) electron carrier protein from the thermophilic purple photosynthetic bacterium Thermochromatium tepidum bacterium at 0.48 Å. This is one of the highest resolution X-ray crystal structures of a protein reported to date. The ultra-high resolution structure of this metalloprotein has enabled the authors to perform a charge-density analysis of the iron–sulfur cluster at its centre, and to visualize the distributions of valence electrons around the iron and sulphur atoms in the Fe 4 S 4 cluster. The result contributes to the understanding of the relationship between structure and function of metalloproteins at the subatomic level. The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0–1.5 Å resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints 1 , 2 . Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with pre-existing common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins 3 . Here we report a charge-density analysis of the high-potential iron–sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 Å. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3 d and sulfur 3 p electron densities of the Fe 4 S 4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron–sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/45/49/1141 / 631/535/1266 / Amino acids / Bacterial Proteins - chemistry / Charge density waves / Chemical bonds / Chemical properties / Chromatiaceae - chemistry / Crystallography, X-Ray / Electron Transport / Electrons / Humanities and Social Sciences / Hydrogen - chemistry / Iron / Iron-Sulfur Proteins - chemistry / letter / Ligands / Models, Molecular / Molecular structure / multidisciplinary / Peptides / Photosynthetic Reaction Center Complex Proteins - chemistry / Photosynthetic reaction centers / Protein Conformation / Protein research / Proteins / Quantum Theory / Science / Static Electricity / Sulfur / Valence electrons