Determination of chemical identity and occupancy from experimental density maps

Abstract

Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73-Å resolution, and to an experimental CD map at 2.2-Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II-light harvesting complex II supercomplex at 3.2-Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α-helices.

Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups

“…The axis is chosen for the 1D plot using the shortest eigenvector of anisotropy B‐factor tensors present in the co‐ordinates, which happens to be in the direction with no overlapping of ED from chemically bonded neighboring atoms. When the B factor component is larger than 9.5 Å 2 , the ED distribution can be approximated using a single Gaussian function . Logarithm of any Gaussian function, as a function of distance squared ( x 2 ), is a straight line.…”

“…When the B factor component is larger than 9.5 Å 2 , the ED distribution can be approximated using a single Gaussian function. [5][6][7] Logarithm of any Gaussian function, as a function of distance squared (x 2 ), is a straight line. The slope of this line is inversely proportional to its variance, which is defined the B-factor component along this axis:…”

“…In this study, the electron density (ED) reported for HPP/5EQA is re-examined using electron quantification methods recently developed for chemical identification. [5][6][7] Results show that the bridge formed between side chains Cys-245 and Lys-158 is O, as an oxidation product of the sulfhydryl group, instead of a CH 2 group as reduction of CO 2 .…”

Local and global analysis of macromolecular atomic displacement parameters

“…Therefore, to analyse the differences between B values of atoms, the resolution, as well as the ADPs, needs to be accounted for. Wang (2018) uses a similar idea to analyse the occupancies of atoms of different elements in crystals. Here, this idea is used to calculate the differences between ADPs as well as the potential adjustment of occupancies to make the ADPs of neighbouring atoms similar.…”

Local and global analysis of macromolecular Atomic Displacement Parameters

“…Therefore, to analyse differences between B values of atoms the resolution as well as the ADPs need to be accounted for. Wang (2018) uses a similar idea to analyse the occupancies of atoms for different elements in crystals. Here this idea is used to calculate differences between ADPs as well as potential adjustment of occupancies to make ADPs of neighbouring atoms similar.…”