*4.4. Cluster Analysis*

The conformational diversity of the structures generated during the MD simulations was characterized using the Gromos [43] clustering algorithm. In this method, an RMSD cutoff criterion is used to assign a structure in a cluster based on the root-mean-square differences of selected atoms among the conformations obtained from the simulations. An RMSD cutoff of 0.13 nm was used to determine neighboring backbone atom conformations of YqhD monomers to discriminate among the less varying conformations. For the cluster analysis, a total of 52,815 structures were evaluated for each monomer within the dimer over the 2 µs aggregated trajectory, using time intervals of 100 ps. [33]

**Author Contributions:** R.V. and K.R.M.-K. designed the project and wrote the manuscript. R.V. and J.M.E. performed the simulations. R.V. analyzed the data. All authors have read and agreed to the published version of the manuscript.

**Funding:** This material is based upon work supported by the National Science Foundation under Award No. EPS-0903806 and matching support from the State of Kansas through the Kansas Board of Regents. This project was supported by grants from the National Institute of General Medical Sciences (P20 GM103418) from the National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.

**Data Availability Statement:** The data presented in this study are available on request from the corresponding author.

**Acknowledgments:** This research is supported by Wichita State University (WSU), Department of Chemistry and Fairmount College of Liberal Arts and Sciences. This work was performed using the High Performance Computing Center at WSU, which was supported by the National Science Foundation under Grant No. EIA-0216178, and Grant No. EPS-0236913, with matching support from the State of Kansas and WSU.

**Conflicts of Interest:** The authors declare that they have no conflicts of interest with the contents of this article.

**Sample Availability:** Not applicable.
