Yuhua Song Research Group

(Position Open for Graduate Student, Postdoc or Researcher, updated on Oct 2, 2021)

An Integrated Multiscale Computational Modeling and Experimental Research Program

Selected Publications

  1. 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.
  2. 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
  3. 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.
  4. 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.
  5. Sam68 promotes hepatic gluconeogenesis. Nature Communications. Qiao et al. 2021;12(1):3340. doi: 10.1038/s41467-021-23624-9.
  6. 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.
  7. 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
  8. Functional insights from biophysical study of TREM2 interactions with ApoE and Ab1-42Featured Article, Alzheimer’s and Dementia,Kober et al. 2020, Online ahead of print, Oct 8, 2020, https://doi.org/10.1002/alz.12194
  9. 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 
  10. 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.
  11. 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
  12. 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
  13. 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.  
  14. 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 
  15. 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 
  16. 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.
  17. 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
  18. 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.
  19. Molecular insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry, Liu et al., 2014, 53(40):6309-22; 
  20. Characterization  of calmodulin and Fas death domain interaction: an integrated experimental and  computational studyBiochemistry, Fancy et al., 2014, 53 (16), 2680–2688; 
  21. 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;
  22. 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;
  23. Trifluoperazine Regulation of Calmodulin Binding to Fas: A  Computational Study. Proteins: Structure, Function, and Bioinformatic, Pan et al., 2011, 79(8):2543-56;
  24. Cell Surface Engineering with Polyelectrolyte Multilayer Thin FilmsJ Am Chem Soc., Wilson et al., 2011,133(18):7054-64;
  25. 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;
  26. Role of Altered Sialylation of the  I-like Domain of β1 Integrin in the Binding of Fibronectin to β1 Integrin: Thermodynamics  and Conformational AnalysesBiophys J, Pan et al., 2010, 99 (1): 208-217;
  27. 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;
  28. Amiloride Docking to Acid-sensing Ion Channel-1. Journal of Biological Chemistry, Qadri et al., 2010, 285(13): 9627-9635.
  29. Psalmotoxin-1 docking to  human acid sensing ion channel-1. Journal of Biological Chemistry, Qadri et al., 2009, 284(26): 17625-17633;
  30. Conformation  and Free Energy Analyses of the Complex of Ca2+-Bound Calmodulin and the Fas  Death DomainBiophys J, Suever et al., 2008, 95(12): 5913-5921;
  31. 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;
  32. Breaking an Extracellular α−β Clasp Activates β3 Integrins.Biochemistry, Vomund et al. , 2008, 47 (44): 11616-11624;
  33. 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;
  34. D-Periodic Collagen-Mimetic Microfibers. J Am Chem Soc., Rele et al., 2007, 129(47): 14780-14787;
  35. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, Cheng et al., 2007, 92(10): 3397-406;
  36. 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;
  37. 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;
  38. 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;
  39. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys. J, Song et al., 2004, 86(4):2017-2029;
  40. 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