Topics:<\/p>\n
a) Protein folding thermodynamics and kinetics<\/p>\n
b) Protein folding transition states<\/p>\n
c) Protein folding pathways<\/p>\n
d) Protein conformational dynamics<\/p>\n
<\/span> 26. S. Parris, J. Lovell, F. Ding, Z. Zhang, J. Olvey, J. Olvey II, J. Schmutz, J. Grimwood, A. Sreedasyam,S. Kumar, Z. Li, P. Joshi, J. Jenkins, C. Plott, A. Stewart, J. Webber, W. Stiller, D. Jones, C. Saski, \u201cPolyploidy-Mediated Variations in Glutamate Receptor Proteins Linked to Fusarium Wilt Resistance in Upland Cotton\u201d, The Plant Journal, 122(1): e70125 (2025) doi: 10.1111\/tpj.70125<\/p>\n 25. R. K. Goutam, G. Huang, E. Medina, F. Ding, W. J. Edenfield, and H. Sanabria, \u201cImpact of Frequent ARID1A Mutations on Protein Stability: Insights into Cancer Pathogenesis\u201d, Scientific Reports, 15: 3072 (2025) doi: 10.1038\/s41598-025-87103-7<\/p>\n 24. J. Yan, Y. Wang, X. Fan, Y. Zou, F. Ding*, F. Huang*, Y. Sun*, \u201cDeciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin\u201d, Soft Matter, 20:693-703 (2024) doi:10.1039\/d3sm01332d<\/p>\n 23. Zheng C., Wei Y., Zhang P., Xu L., Zhang Z., Lin K., Hou J., Lv X., Ding Y., Chiu Y., Jain A., Islam N., Malovannaya A., Wu Y., Ding F., Xu H., Sun M., Chen X., and Chen Y., \u201cCRISPR\/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer\u201d, Journal of Clinical Investigation, 133(5):e159940 (2023) doi: 10.1172\/JCI159940<\/p>\n 22. G.L. Hamilton, N. Saikia, S. Basak, F.S. Welcome, F. Wu, J. Kubiak, C. Zhang, Y. Hao, C.A.M. Seidel, F. Ding*, H. Sanabria* and M.E. Bowen*, \u201cFuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding\u201d, eLife, 11: e77242, doi:10.7554\/eLife.77242 (2022)<\/p>\n 21. S. Basak, N. Saikia, D. Kwun, U. B. Choi, F. Ding, M. E. Bowen, \u201cDifferent Forms of Disorder in NMDA-Sensitive Glutamate Receptor Cytoplasmic Domains Are Associated with Differences in Condensate Formation\u201d, Biomolecules, 13(1):4 doi:10.3390\/biom13010004(2023)<\/p>\n 20. N. Saikia, I. S. Yanez-Orozco, R. Qiu, P. Hao, S. Milikisiyants, E. Ou, G. L. Hamilton, K. R. Weninger, T. Smirnova, H. Sanabria, and F. Ding, \u201cIntegrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25\u201d, Cell Reports Physical Science 2:100616 (2021) doi:10.1016\/j.xcrp.2021.100616<\/a><\/p>\n 19. H. Simon-Baram, D. Kleiner, F. Shmulevich, R. Zarivach, R. Zalk, H. Tang, F. Ding, S. Bershtein, \u201cSAMase of bacteriophage T3 inactivates E. coli\u2019s methionine S-adenosyltransferase by forming hetero-polymers\u201d, mBio, Vol. 12, No. 4 (2021) doi: 10.1128\/mBio.01242-21<\/a><\/p>\n 18. S. Basak, N. Saikia, L. Dougherty, Z. Guo, F. Wu, F. A. Mindlin, J. W. Lary, J. L. Cole, F. Ding & M. E. Bowen, \u201cProbing interdomain linkers and protein supertertiary structure in vitro and in live cells with fluorescent protein resonance energy transfer\u201d, J. Mol. Biol., 433(5): 166793 17. I.Y. Orozco , F. Mindlin , J. Ma , B. Levesque , B. Wang , M. Spencer , G. Hamilton , S.R. Adariani , F. Ding*, M. Bowen*, and H. Sanabria*, \u201cIdentifying Weak Interdomain Interactions that Stabilize the Supertertiary Structure of the N-Terminal Tandem PDZ Domains of PSD-95\u201d, Nature Communication 9: 3724, DOI: 10.1038\/s41467-018-06133-0<\/a>, (2018)<\/p>\n 16. Sun Y., Ding F., Ming D., \u201cNonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like \u03b2-Sandwich Protein\u201d, Int J Mol Sci., in press (2018) DOI: 10.3390\/ijms19051515 <\/a>.<\/p>\n 15. Shirvanyants, D., F. Ding, Tsao, D., Ramachandran, S. and Dokholyan, N. V. \u201cDMD: an efficient and versatile simulation method for fine protein characterization\u201d, Journal of Physical Chemistry B, in press [download]<\/a> (2012)<\/p>\n 14. F. Ding, D. Tsao, H. Nie, and N. V. Dokholyan, \u201cAb initio folding of proteins using all-atom discrete molecular dynamics\u201d Structure, 16: 1010-1018 (2008) [download]<\/a><\/p>\n 13. A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, H. E. Stanley, \u201cParallel folding pathways in the Src SH3 domain\u201d Journal of Molecular Biology, 373: 1348-1360 (2007)[download]<\/a><\/p>\n 12. Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, and N. V. Dokholyan, \u201cProtein folding: then and now\u201d Archives of Biochemistry and Biophysics, 469: 4-19 (2008)[download]<\/a><\/p>\n 11. S. Sharma, F. Ding, H. Nie, D. Watson, A. Unnithan, J. Lopp, D. Pozefsky, and N. V. Dokholyan, \u201ciFold: A platform for interactive folding simulations of proteins\u201d Bioinformatics, 22: 2693-2694 (2006) [download]<\/a> [service]<\/a><\/p>\n 10. F. Ding, W. Guo, N. V. Dokholyan, E. I. Shakhnovich, and J.-E. Shea, \u201cReconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations\u201d, J. Mol. Biol., 350: 1035-1050 (2005). [download]<\/a><\/p>\n 9. F. Ding, R. K. Jha, and N. V. Dokholyan, \u201cScaling behavior and structure of denatured proteins\u201d, Structure, 13: 1047-1054 (2005).[download]<\/a><\/p>\n 8. F. Ding, S. V. Buldyrev, and N. V. Dokholyan, \u201cFolding Trp-cage to NMR resolution native structure using a coarse-grained protein model\u201d, Biophys. J., 88: 147-155 (2005). [download]<\/a><\/p>\n 7. R. D. S. Dixon, Y. Chen, F. Ding, S. D. Khare, K. C. Prutzman, M. D. Schaller, S. L. Campbell, and N. V. Dokholyan, \u201cNew insights into FAK signaling and localization based on detection of a FAT domain folding intermediate\u201d Structure, 12: 2161-2171 (2004). [download]<\/a><\/p>\n 6. J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, \u201cMultiple folding pathways of the SH3 domain.\u201d Biophys. J. 87: 521-533 (2004). [download]<\/a><\/p>\n 5. S. D. Khare, F. Ding and N. V. Dokholyan, \u201cFolding of Cu,Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis.\u201d J. Mol. Biol, 334, 515-525, 2003 [download]<\/a><\/p>\n 4. Dokholyan N.V., Borreguero J.M., Buldyrev S.V., F. Ding, Stanley H.E. and Shakhnovich E.I., Identifying the importance of amino acids for protein folding from crystal structures, Methods in Enzymology Vol. 374: pp 618-640 Macromolecular crystallography D. Editors: C. W. Carter Jr. and R. M. Sweet (2003) [download]<\/a><\/p>\n 3. F. Ding, Borreguero J.M., Buldyrev S.V., Stangley H.E. and Dokholyan N.V., A mechanism for alpha-helix to beta-hairpin transition, Proteins: Structure, Function and Genetics, 53:220-228 (2003)[download]<\/a><\/p>\n 2. Dokholyan N.V., Li L., F. Ding, et al. Topological determinants of protein folding P NATL ACAD SCI USA, 99 (13): 8637-8641 JUN 25 2002 [download]<\/a><\/p>\n 1. F. Ding, Dokholyan V.N., Buldyrev V.S., Stanley H.E. and Shakhnovich E.I. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J., 86 (6): December 2002 [download]<\/a><\/p>\n","protected":false},"excerpt":{"rendered":" Topics: a) Protein folding thermodynamics and kinetics b) Protein folding transition states c) Protein folding pathways d) Protein conformational dynamics References: 26. S. Parris, J. Lovell, F. Ding, Z. Zhang, J. Olvey, J. Olvey II, J. Schmutz, J. Grimwood, A. Sreedasyam,S. Kumar, Z. Li, P. Joshi, J. Jenkins, C. Plott, A. Stewart, J. Webber, W. … <\/p>\n
\nReferences:<\/p>\n
\n(2021) doi: doi.org\/10.1016\/j.jmb.2020.166793<\/a><\/p>\n