Publications

2023

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.

2022

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

2021

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.

The Case for Multidimensional, Integrated Single-Molecule Approaches

Kolimi N., Pabbathi A., Saikia N., Ding F., Sanabria H., Alper J.. Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches. J Phys Chem B. 2021;125(37):10404-18. Epub 2021/09/11. doi: 10.1021/acs.jpcb.1c02424. PMID: 34506140.

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25, Cell Reports Physical Science

Saikia N., Yanez-Orozco I.S., Qiu R., Hao P., Milikisiyants S., Ou E., Hamilton G.L., Weninger K.R., Smirnova T.I., Sanabria H., Ding F., Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. Cell Rep Phys Sci. 2021;2(11):100616. Epub 2021/12/11. doi: 10.1016/j.xcrp.2021.100616. PMID: 34888535.

2020

Structural Dynamics of Glutamate Signaling Systems by smFRET

Durham R.J., Latham D.R., Sanabria H., Jayaraman V., Structural Dynamics of Glutamate Signaling Systems by smFRET. Biophys J. 2020;119(10):1929-36. Epub 2020/10/24. doi: 10.1016/j.bpj.2020.10.009. PMID: 33096078.

Automated and optimally FRET-assisted structural modeling

Dimura M., Peulen T.O., Sanabria H., Rodnin D., Hemmen K., Hanke C.A., Seidel C.A.M., Gohlke H., Automated and optimally FRET-assisted structural modeling. Nat Commun. 2020;11(1):5394. Epub 2020/10/28. doi: 10.1038/s41467-020-19023-1. PMID: 33106483.

Intrinsically disordered regions of the DNA-binding domain of human FoxP1 facilitate domain swapping

Medina E., Villalobos P., Hamilton G.L., Komives E.A., Sanabria H., Ramirez-Sarmiento C.A., Babul J., Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping. J Mol Biol. 2020;432(19):5411-29. Epub 2020/08/01. doi: 10.1016/j.jmb.2020.07.017. PMID: 32735805.

The correlation between phase transition and photoluminescence properties of CsPbX3

Yi J., Ge X., Liu E., Cai T., Zhao C., Wen S., Sanabria H., Chen O., Rao A.M., Gao J., The correlation between phase transition and photoluminescence properties of CsPbX 3 (X= Cl, Br, I) perovskite nanocrystals. Nanoscale Advances. 2020;2(10):4390-4

Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A

Tsytlonok M., Hemmen K., Hamilton G., Kolimi N., Felekyan S., Seidel C.A.M., Tompa P., Sanabria H., Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A. J Mol Biol. 2020;432(9):2998-3017. Epub 2020/02/24. doi: 10.1016/j.jmb.2020.02.010. PMID: 32088186.

Resolving dynamics and function of transient states in single enzyme molecules

Sanabria H., Rodnin D., Hemmen K., Peulen T.O., Felekyan S., Fleissner M.R., Dimura M., Koberling F., Kuhnemuth R., Hubbell W., Gohlke H., Seidel C.A.M., Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun. 2020;11(1):1231. Epub 2020/03/08. doi: 10.1038/s41467-020-14886-w. PMID: 32144241.

Reporting on the Future of Integrative Structural Biology ORAOU workshop

Hamilton G.L., Alper J., Sanabria H., Reporting on the future of integrative structural biology ORAU workshop. Front Biosci (Landmark Ed). 2020;25(1):43-68. Epub 2019/10/06. doi: 10.2741/4794. PMID: 31585877.

2019

Manipulating charge transfer from core to shell in CdSe/CdS/Au heterojunction quantum dots

Liu E., Zhu H., Yi J., Kobbekaduwa K., Adhikari P., Liu J., Shi Y., Zhang J., Li H., Oprisan A., Rao A.M., Sanabria H., Chen O., Gao J., Manipulating Charge Transfer from Core to Shell in CdSe/CdS/Au Heterojunction Quantum Dots. ACS Appl Mater Interfaces. 2019;11(51):48551-5. Epub 2019/11/30. doi: 10.1021/acsami.9b17339. PMID: 31782302.

Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins. Biomolecules

Tsytlonok M., Sanabria H., Wang Y., Felekyan S., Hemmen K., Phillips A.H., Yun M.K., Waddell M.B., Park C.G., Vaithiyalingam S., Iconaru L., White S.W., Tompa P., Seidel C.A.M., Kriwacki R., Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation. Nat Commun. 2019;10(1):1676. Epub 2019/04/13. doi: 10.1038/s41467-019-09446-w. PMID: 30976006.

Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins. Biomolecules

Choi U.B., Sanabria H., Smirnova T., Bowen M.E., Weninger K.R., Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins. Biomolecules. 2019;9(3). Epub 2019/03/27. doi: 10.3390/biom9030114. PMID: 30909517.

Prior to 2019

Yanez-Orozco I. S, Levesque B, Ma J., Wang B., Spencer M., Rezaei Adariani S., Hamilton G.L., Ding F., Bowen M.E., Sanabria H.*, Identifying Weak Interdomain Interactions that Stabilize the Supertertiary Structure of the N-Terminal Tandem PDZ Domains of PSD-95, Nature Communications, 9, 3724, (2018).

Hamilton G.L., Disharoon Z., Sanabria H.*, Revisiting viscosity from macroscopic to nanoscale regimes, arXiv:1804.04028v1, Revista Mexicana de Física E, 64, 222-231, (2018).

Hellenkamp B., Schmid S., Doroshenko O., Opanasyuk O., Kühnemuth R., Rezaei Adariani S., Barth A., Birkedal V., Bowen M.E., Chen H., Cordes T., Eilert T., Fijen C., Götz M., Gouridis G., Gratton E., Ha T., Hanke C.A., Hartmann A., Hendrix J., Hildebrandt L. L., Hohlbein J., Hübner C. G., Kallis E., Kapanidis A. N., Kim J.Y., Krainer G., Lamb D.C., Lee N.K., Lemke E. A., Levesque B., Levitus M., McCann J. J., Naredi-Rainer N., Nettels D., Ngo T., Qiu R., Röcker C., Sanabria H., Schlierf M., Schuler B., Seidel H., Streit L., Tinnefeld P., Tyagi S., Vandenberk N., Weninger K. R., Wünsch B., Yanez-Orozco I. S., Michaelis J., Seidel C.A.M., Craggs T. D., Hugel T., Precision and accuracy of single-molecule FRET measurements 1 – a multi-laboratory benchmark study, arXiv:1710.03807, Nature Methods, 15, 669, (2018).

Hoffman, L., Li, l., Alexov, E., Sanabria, H.*, Waxham, M.N., “Cytoskeletal-like filaments of CaMKII are formed in a regulated and Zn²⁺-dependent manner”, Biochemistry, 56, 2149-2160, (2017).

Ma, J., Yanez-Orozco I.S., Rezaei-Adariani, S., Dolino D., Jayaraman, V., Sanabria, H.*, High Precision FRET at Single-molecule Level for Biomolecule Structure Determination, Journal of Visualized Experiments, e55623. (2017).

Dolino, D., Rezaei-Adariani, S., Jayaraman, V., Sanabria, H.*, Conformational selection and submillisecond dynamics of the ligand-binding domain of the N-methyl-D-Aspartate receptor, Journal of Biological Chemistry, 291, 16175-16185. (2016).

Hoffman L., Wang X., Sanabria H., Cheung M.S., Putkey J., Waxham M.N., Relative Cosolute Size Influences the Kinetics of Protein-Protein Interactions, Biophysical Journal, 109, 510-520, (2015).

Felekyan, S., Sanabria, H., Kalinin, S., Kuhnemuth, R. and Seidel, C. A., “Analyzing Forster resonance energy transfer with fluctuation algorithms”, Methods in Enzymology, 519, 39-85 (2013).

Felekyan, S., Kalinin, S., Sanabria, H., Valeri, A. and Seidel, C. A., “Filtered FCS: species auto- and cross-correlation functions highlight binding and dynamics in biomolecules”, ChemPhysChem, 13, 1036-1053 (2012).

Sanabria, H. and Waxham, M. N., “Transient anomalous subdiffusion: effects of specific and nonspecific probe binding with actin gels”, Journal of Physical Chemistry B, 114, 959-972 (2010).

Kim, S. A., Sanabria, H., Digman, M. A., Gratton, E., Schwille, P., Zipfel, W. R. and Waxham, M. N., “Quantifying translational mobility in neurons: comparison between current optical techniques”, Journal of Neuroscience, 30, 16409-16416 (2010).

Sanabria, H., Swulius, M. T., Kolodziej, S. J., Liu, J. and Waxham, M. N., “βCaMKII regulates actin assembly and structure”, Journal of Biological Chemistry, 284, 9770-9780 (2009).

Homouz, D., Sanabria, H., Waxham, M. N. and Cheung, M. S., “Modulation of calmodulin plasticity by the effect of macromolecular crowding”, Journal of Molecular Biology, 391, 933-943 (2009).

Vajrala, V., Claycomb, J. R., Sanabria, H. and Miller, J. H., Jr., “Effects of oscillatory electric fields on internal membranes: an analytical model”, Biophysical Journal, 94, 2043-2052 (2008).

Sanabria, H., Digman, M. A., Gratton, E. and Waxham, M. N., “Spatial diffusivity and availability of intracellular calmodulin”, Biophysical Journal, 95, 6002-6015 (2008).

Goins, A. B., Sanabria, H. and Waxham, M. N., “Macromolecular crowding and size effects on probe microviscosity”, Biophysical Journal, 95, 5362-5373 (2008).

Sanabria, H., Kubota, Y. and Waxham, M. N., “Multiple diffusion mechanisms due to nanostructuring in crowded environments”, Biophysical Journal, 92, 313-322 (2007).

Sanabria, H. and Rodríguez-Lara, B. M., “An introduction to quantum interferometry: Young’s experiment with fock and coherent states”, Revista Mexicana de Física E, 53, 97-105 (2007).

Sanabria, H., Miller, J. H., Jr., Mershin, A., Luduena, R. F., Kolomenski, A. A., Schuessler, H. A. and Nanopoulos, D. V., “Impedance spectroscopy of alpha-beta tubulin heterodimer suspensions”, Biophysical Journal, 90, 4644-4650 (2006).

Sanabria, H. and Miller, J. H., Jr., “Relaxation processes due to the electrode-electrolyte interface in ionic solutions”, Physical Review E Stat Nonlin Soft Matter Phys, 74, 051505 (2006).