Yuhua Song Research Group

Position Open for Graduate Student, Postdoc or Researcher, updated on 08/25/2023

Group in the News: Alzheimer’s: An M.D./Ph.D. graduate student’s request for Yuhua Song as mentor leads to two NIH R01 awards totaling $5 million

An Integrated Multiscale Computational Modeling and Experimental Research Program

Selected Publications

  1. Biophysical mapping of TREM2-ligand interactions reveals shared surfaces for engagement of multiple Alzheimer’s disease ligands. 2025;20(1):3. Molecular Neurodegeneration, Greven et al. https://doi.org/10.1186/s13024-024-00795-9
  2. Multimerization of TREM2 is impaired by Alzheimer’s disease–associated variants. Alzheimer’s & Dementia. 2024;20(9):6332-50. First published: 20 July 2024, Dean and Greer et al., https://doi.org/10.1002/alz.14124.
  3. Melatonin and its metabolites can serve as agonists on the AhR and PPARγ. International Journal of Molecular Sciences, 2023, 24(20), 15496, Slominski et al. ; https://doi.org/10.3390/ijms242015496.
  4. Electronegative clusters modulate folding status and RNA binding of unstructured RNA-binding proteins. Protein Science. Zaharias et al. 2023 Apr 15;e4643. Zaharias et al. https://doi.org/10.1002/pro.4643.
  5. Metabolic activation of tachysterol3 to biologically active hydroxyderivatives in the human system that act on VDR, AhR, LXRs and PPARγ receptors. The FASEB Journal. Slominski et al. 2022; 36(8): e22451. doi: https://doi.org/10.1096/fj.202200578R.
  6. Molecular and structural basis of interactions of vitamin D3 hydroxyderivatives with aryl hydrocarbon receptor (AhR): an integrated experimental and computational study. International Journal of Biological Macromolecules, Song et al. 2022; 209:1111-23. doi: https://doi.org/10.1016/j.ijbiomac.2022.04.048
  7. Chemical synthesis, biological activities and action on nuclear receptors of 20S(OH)D3, 20S,25(OH)2D3, 20S,23S(OH)2D3 and 20S,23R(OH)2D3. Bioorganic Chemistry. Brzeminski, et al. 2022;121:105660. doi: https://doi.org/10.1016/j.bioorg.2022.105660.
  8. Vitamin D3 and its Hydroxyderivatives as Promising Drugs to Disrupt SARS-CoV-2 Entry against COVID-19:  A Computational Study. Journal of Biomolecular Structure and Dynamics, Song et al. 2021:1-17. Epub 2021/08/21. doi: 10.1080/07391102.2021.1964601.
  9. Sam68 promotes hepatic gluconeogenesis. Nature Communications. Qiao et al. 2021;12(1):3340. doi: 10.1038/s41467-021-23624-9.
  10. Biologically Active Vitamin D and Lumisterol Derivatives Act on Liver X Receptors (LXRs). Scientific Reports. Slominski et al. 2021; 11: 8002, doi:10.1038/s41598-021-87061-w.
  11. In silico identification of available drugs targeting cell surface BiP to disrupt SARS-CoV-2 binding and replication: Drug repurposing approach. European Journal of Pharmaceutical Sciences. Zhang et al. 2021:105771. Online ahead of print, doi: https://doi.org/10.1016/j.ejps.2021.105771
  12. Functional insights from biophysical study of TREM2 interactions with ApoE and Ab1-42. Featured Article, Alzheimer’s and Dementia,Kober et al. 2020, Online ahead of print, Oct 8, 2020, https://doi.org/10.1002/alz.12194
  13. Photoprotective properties of vitamin D and lumisterol hydroxyderivatives. Cell Biochemistry and Biophysics,  Slominski etc. 2020. 78(2): p. 165-180, https://doi.org/10.1007/s12013-020-00913-6 
  14. Molecular Insight for the Role of Key Residues of Calreticulin in its Binding Activities: A Computational Study. Computational Biology and Chemistry, Yang et al. [In press, published online ahead of print, February 3, 2020] https://doi.org/10.1016/j.compbiolchem.2020.107228.
  15. Molecular insights into the effect of an apoptotic raft-like bilayer on the conformation and dynamics of calreticulin. Biochimica et Biophysica Acta (BBA) – Biomembranes. Wang et al. 2020,1862(2): p. 183146. [In press, published online ahead of print, December 6, 2019]. https://doi.org/10.1016/j.bbamem.2019.183146
  16. Neurodegenerative Disease–Associated Variants in TREM2 Destabilize the Apical Ligand-Binding Region of the Immunoglobulin Domain. Frontiers in Neurology, Dean et al. 2019, 10(1252). Published on November 26, 2019. doi: 10.3389/fneur.2019.01252
  17. Multiscale Simulation of the Interaction of Calreticulin-Thrombospondin-1 Complex with a Model Membrane Microdomain.  J Biomol Struct Dyn., Wang et al. 2019, 37(3):811-822. doi: 10.1080/07391102.2018.1433065.  
  18. Calmodulin antagonist enhances DR5-mediated apoptotic signaling in TRA-8 resistant triple negative breast cancer cells. J Cell Biochem. Fancy et al. published:16 April 2018, https://doi.org/10.1002/jcb.26848 
  19. Activation Mechanisms of αVβ3 Integrin by Binding to Fibronectin: A Computational Study. Protein Science, Wang et al. 2017, June; 26(6):1124-1137.  DOI:10.1002/pro.3163 
  20. Calmodulin Binding to Death Receptor 5-mediated Death-inducing Signaling Complex in Breast Cancer Cells.  J Cell Biochem. Fancy et al. 2017 Aug;118(8):2285-2294. doi: 10.1002/jcb.25882. Epub 2017 Apr 12.
  21. Characterization of the Interactions between Calmodulin and Death Receptor 5 in Triple-Negative and Estrogen Receptor Positive Breast Cancer Cells: An Integrated Experimental and Computational Study. J Biol Chem. Fancy et al,  2016, 291:12862-12870
  22. Structural insight for roles of DR5 death domain mutations on oligomerization of DR5 death domain – FADD complex in the death-inducing signaling complex formation: a computational study.  Journal of Molecular Modeling, Yang et al. 2016, 22 (4):89.
  23. Molecular insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry, Liu et al., 2014, 53(40):6309-22; 
  24. Characterization  of calmodulin and Fas death domain interaction: an integrated experimental and  computational study. Biochemistry, Fancy et al., 2014, 53 (16), 2680–2688; 
  25. Structural Insight for the Roles of Fas Death Domain Binding to FADD and  Oligomerization Degree of the Fas – FADD complex in the Death Inducing  Signaling Complex Formation: A Computational Study.Proteins: Structure, Function, and Bioinformatic, Yan et al., 2013, 81(3):377-85;
  26. Effects of altered  restraints in β1 integrin on the force-regulated interaction between the  glycosylated I-like domain of β1 integrin and fibronectin III9-10: a steered  molecular dynamic study.Molecular & Cellular Biomechanics, Pan et al., 2011, 8(3): 233-52;
  27. Trifluoperazine Regulation of Calmodulin Binding to Fas: A  Computational Study. Proteins: Structure, Function, and Bioinformatic, Pan et al., 2011, 79(8):2543-56;
  28. Cell Surface Engineering with Polyelectrolyte Multilayer Thin Films. J Am Chem Soc., Wilson et al., 2011,133(18):7054-64;
  29. Molecular and Structural Insight  for the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1-  Calreticulin Binding. Biochemistry, Yan et al., 2011, 50(4): 566-573;
  30. Role of Altered Sialylation of the  I-like Domain of β1 Integrin in the Binding of Fibronectin to β1 Integrin: Thermodynamics  and Conformational Analyses. Biophys J, Pan et al., 2010, 99 (1): 208-217;
  31. Structural Insight for the Role of  Thrombospondin-1 Binding to Calreticulin in Calreticulin-Induced Focal Adhesion  Disassembly. Biochemistry, Yan et al., 2010, 49(17): 3685-3694;
  32. Amiloride Docking to Acid-sensing Ion Channel-1. Journal of Biological Chemistry, Qadri et al., 2010, 285(13): 9627-9635.
  33. Psalmotoxin-1 docking to  human acid sensing ion channel-1. Journal of Biological Chemistry, Qadri et al., 2009, 284(26): 17625-17633;
  34. Conformation  and Free Energy Analyses of the Complex of Ca2+-Bound Calmodulin and the Fas  Death Domain. Biophys J, Suever et al., 2008, 95(12): 5913-5921;
  35. Effect  of Altered Glycosylation on the Structure of the I-like Domain of beta1  Integrin: A Molecular Dynamics Study. Proteins: Structure, Function, and Bioinformatic, Liu et al., 2008, 73(4): 989-1000;
  36. Breaking an Extracellular α−β Clasp Activates β3 Integrins.Biochemistry, Vomund et al. , 2008, 47 (44): 11616-11624;
  37. Molecular  dynamics simulations of asymmetric NaCl and KCl solutions separated by  phosphatidylcholine bilayers: potential drops and structural changes induced by  strong Na+-lipid interactions and finite size effects. Biophys J, Lee et al.,2008, 94(9): 3565-3576;
  38. D-Periodic Collagen-Mimetic Microfibers. J Am Chem Soc., Rele et al., 2007, 129(47): 14780-14787;
  39. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, Cheng et al., 2007, 92(10): 3397-406;
  40. Molecular dynamics simulation of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer.Biochemistry, Song et al., 2005, 44(41), 13425-13438;
  41. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state smoluchowski equation using finite element methods.Biophys. J, Zhang et al., 2005, 88(3):1659-1665;
  42. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis.Biophys. J, Song et al., 2004, 87(3):1558-1566;
  43. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys. J, Song et al., 2004, 86(4):2017-2029;
  44. Three Dimensional Finite Element Model of the Human Anterior Cruciate Ligament – A Computational Analysis with Experimental Validation. J Biomech., Song et al., 2004, 37(3):383-390

    Department of Biomedical Engineering           The University of Alabama at Birmingham