Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

Abstract:

:Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (RF) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

journal_name

J Chem Inf Model

authors

Zhang Q,Xu Z,Shi J,Zhu W

doi

10.1021/acs.jcim.7b00235

subject

Has Abstract

pub_date

2017-07-24 00:00:00

pages

1529-1534

issue

7

eissn

1549-9596

issn

1549-960X

journal_volume

57

pub_type

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