A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs [article]

Thu Nguyen, Kim L Phan, Dale E Kreitler, Lawrence C Andrews, Sandra B Gabelli, Dima Kozakov, Jean Jakoncic, Robert M Sweet, Alexei S Soares, Herbert J Bernstein
2020 bioRxiv   pre-print
AbstractOne often observes small but measurable differences in diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and potentially reflect the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step to extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can
more » ... e obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). State changes may be expressed as changes in morphology, so that a subset of the polystates may be observed as polymorphs. After mixed-state data are deliberately or inadvertently measured, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here we address this problem using a simple multi-factor clustering approach that classifies each data set using independent observables in order to assign each data set to the correct location in conformation space. We illustrate this method using two independent observables (unit cell constants and intensities) to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. We observe that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.
doi:10.1101/2020.12.14.422680 fatcat:u3r63xiap5ccvmcj67acljs3ei