Category Archives: Publication

DNA controls the dimerization of the human FoxP1 forkhead domain

Kolimi N, Ballard J, Peulen T, Goutam R, Duffy FX, 3rd, Ramirez-Sarmiento CA, Babul J, Medina E, Sanabria H. DNA controls the dimerization of the human FoxP1 forkhead domain. Cell Rep Phys Sci. 2024;5(3):101854. Epub 2024/04/08. doi: 10.1016/j.xcrp.2024.101854. PMID: 38585429.

DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility.

Coñuecar R., Asela I., Rivera M., Galaz-Davison P., González-Higueras J., Hamilton G. L., Engelberger F., Ramírez-Sarmiento C. A., Babul J., Sanabria H., & Medina E. (2023) DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 26(7):107228.

Domain tethering impacts dimerization and DNA-mediated allostery in the human transcription factor FoxP1

Cruz P., Paredes N., Asela I., Kolimi N., Molina J. A., Ramirez-Sarmiento C. A., Goutam R., Huang G., Medina E., & Sanabria H. (2023) Domain tethering impacts dimerization and DNA-mediated allostery in the human transcription factor FoxP1. J Chem Phys 158(19).

Coevolution and smFRET Enhances Conformation Sampling and FRET Experimental Design in Tandem PDZ1-2 Proteins

Krishnamohan A., Hamilton G. L., Goutam R., Sanabria H., & Morcos F. (2023) Coevolution and smFRET Enhances Conformation Sampling and FRET Experimental Design in Tandem PDZ1-2 Proteins. J Phys Chem B 127(4):884-898.

A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories

Gotz M., Barth A., Bohr S. S., Borner R., Chen J., Cordes T., Erie D. A., Gebhardt C., Hadzic M., Hamilton G. L., Hatzakis N. S., Hugel T., Kisley L., Lamb D. C., de Lannoy C., Mahn C., Dunukara D., de Ridder D., Sanabria H., Schimpf J., Seidel C. A. M., Sigel R. K. O.,…

Fuzzy supertertiary interactions within PSD-95 enable ligand binding

Hamilton G. L., Saikia N., Basak S., Welcome F. S., Wu F., Kubiak J., Zhang C., Hao Y., Seidel C. A. M., Ding F., Sanabria H., & Bowen M. E. (2022) Fuzzy supertertiary interactions within PSD-95 enable ligand binding. Elife 11:e77242.

Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks

Opanasyuk O., Barth A., Peulen T-O., Felekyan S., Kalinin S., Sanabria H., Seidel C.A.M., Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks. The Journal of Chemical Physics. 2022;157(3):031501. 

Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines

Barth A., Opanasyuk O., Peulen T-O., Felekyan S., Kalinin S., Sanabria H., Seidel C.A.M., Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines. The Journal of Chemical Physics. 2022;156(14):141501

Unraveling protein’s structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies

Medina E., Latham D.R., Sanabria H., Unraveling protein’s structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies. Curr Opin Struct Biol. 2021;66:129-38. Epub 2020/11/28. doi: 10.1016/j.sbi.2020.10.016. PMID: 33246199.

Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch

Ma J., Saikia N., Godar S., Hamilton G.L., Ding F., Alper J., Sanabria H., Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch. RNA. 2021;27(7):771-90. Epub 2021/04/18. doi: 10.1261/rna.075937.120. PMID: 33863818.