Publications

SpringSaLaD and rule-based modeling

• Michalski PJ, Loew LM. SpringSaLaD: a spatial, particle-based biochemical simulation platform with excluded volume. Biophysical journal. 2016 Feb 2;110(3):523-9. PMID:26840718

• Masison J, Michalski PJ, Loew LM, Schuyler AD. mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling. Bioinformatics. 2018 Nov 15;34(22):3948-50. PMID:29931043

• Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. Rules for modeling signal-transduction systems. Science’s STKE. 2006 Jul 18;2006(344):re6-. PMID:16849649

Biological studies where SpringSaLaD and described post-processing were used

• Chattaraj A, Baltaci Z, Chung S, Mayer BJ, Loew LM, Ditlev JA. Measurement of solubility product reveals the interplay of oligomerization and self-association for defining condensate formation. Molecular Biology of the Cell. 2024 Sep 1;35(9):ar122. PMID:39046778

• Chattaraj, A. and L.M. Loew, The maximum solubility product marks the threshold for condensation of multivalent biomolecules. Biophysical Journal, 2023. 122(9): p. 1678-1690. PMID:36987392

• Chattaraj, A., M.L. Blinov, and L.M. Loew, The solubility product extends the buffering concept to heterotypic biomolecular condensates. eLife, 2021. 10: p. e67176. PMID:34236318

• Chattaraj A, Youngstrom M, Loew LM. The interplay of structural and cellular biophysics controls clustering of multivalent molecules. Biophysical Journal. 2019 Feb 5;116(3):560-72. PMID:30661665

Clustering of multivalent proteins

• Mayer, B. J., Blinov, M. L., & Loew, L. M. (2009). Molecular machines or pleiomorphic ensembles: signaling complexes revisited. Journal of biology, 8(9), 1-8.

• Suderman, R. and E.J. Deeds, Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes. PLoS Comput Biol, 2013. 9(10): p. e1003278.

• Falkenberg, C.V., M.L. Blinov, and L.M. Loew, Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. Biophysical journal, 2013. 105(11): p. 2451-2460.

• Falkenberg, C.V., J.H. Carson, and M.L. Blinov, Multivalent Molecules as Modulators of RNA Granule Size and Composition. Biophys J, 2017. 113(2): p. 235-245.

• Goldman, J., S. Andrews, and D. Bray, Size and composition of membrane protein clusters predicted by Monte Carlo analysis. Eur Biophys J, 2004. 33(6): p. 506-12.

• Nag, A., et al., Modeling and Simulation of Aggregation of Membrane Protein LAT with Molecular Variability in the Number of Binding Sites for Cytosolic Grb2-SOS1-Grb2. PLOS ONE, 2012. 7(3): p. e28758

• Hsieh, M.Y., et al., Spatio-temporal modeling of signaling protein recruitment to EGFR. BMC Syst Biol, 2010. 4: p. 57.

• Nag, A., et al., Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys J, 2009. 96(7): p. 2604-23.

• Nag, A., et al., A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells. J Immunol, 2010. 185(6): p. 3268-76.

• Marquez-Lago, T.T. and S. Steinberg, Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity. Sci Rep, 2022. 12(1): p. 11791.

• Wollman, A.J.M., et al., Critical roles for EGFR and EGFR-HER2 clusters in EGF binding of SW620 human carcinoma cells. J R Soc Interface, 2022. 19(190): p. 20220088.