title: Do we see what we should see? Describing non-covalent interactions in protein structures including precision.
abstract: The power of X-ray crystal structure analysis as a technique is to 'see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this 'seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.
authors: Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India.
authors: Manickam
authors: M
authors: Gurusaran
authors: Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India.
authors: Mani
authors: M
authors: Shankar
authors: Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India.
authors: Raju
authors: R
authors: Nagarajan
authors: School of Chemistry, University of Manchester , Brunswick Street, Manchester M13 9PL, England.
authors: John R
authors: JR
authors: Helliwell
authors: Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India.
authors: Kanagaraj
authors: K
authors: Sekar
keywords: DPI; crystal structure analysis; diffraction-component precision index; full-matrix least-squares method; measurement uncertainty; neutron diffraction; protein crystal structure precision; salt bridges