Protein Structure and Dynamics


a) Protein folding thermodynamics and kinetics

b) Protein folding transition states

c) Protein folding pathways

d) Protein conformational dynamics


21. 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*, “Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding”, eLife, in press

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, “Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25”, Cell Reports Physical Science 2:100616 (2021) doi:10.1016/j.xcrp.2021.100616

19. H. Simon-Baram, D. Kleiner, F. Shmulevich, R. Zarivach, R. Zalk, H. Tang, F. Ding, S. Bershtein, “SAMase of bacteriophage T3 inactivates E. coli’s methionine S-adenosyltransferase by forming hetero-polymers”, mBio, Vol. 12, No. 4 (2021) doi: 10.1128/mBio.01242-21

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, “Probing interdomain linkers and protein supertertiary structure in vitro and in live cells with fluorescent protein resonance energy transfer”, J. Mol. Biol., 433(5): 166793
(2021) doi:

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*, “Identifying Weak Interdomain Interactions that Stabilize the Supertertiary Structure of the N-Terminal Tandem PDZ Domains of PSD-95”, Nature Communication 9: 3724, DOI: 10.1038/s41467-018-06133-0, (2018)

16. Sun Y., Ding F., Ming D., “Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Protein”, Int J Mol Sci., in press (2018) DOI: 10.3390/ijms19051515 .

15. Shirvanyants, D., F. Ding, Tsao, D., Ramachandran, S. and Dokholyan, N. V. “DMD: an efficient and versatile simulation method for fine protein characterization”, Journal of Physical Chemistry B, in press [download] (2012)

14. F. Ding, D. Tsao, H. Nie, and N. V. Dokholyan, “Ab initio folding of proteins using all-atom discrete molecular dynamics” Structure, 16: 1010-1018 (2008) [download]

13. A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, H. E. Stanley, “Parallel folding pathways in the Src SH3 domain” Journal of Molecular Biology, 373: 1348-1360 (2007)[download]

12. Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, and N. V. Dokholyan, “Protein folding: then and now” Archives of Biochemistry and Biophysics, 469: 4-19 (2008)[download]

11. S. Sharma, F. Ding, H. Nie, D. Watson, A. Unnithan, J. Lopp, D. Pozefsky, and N. V. Dokholyan, “iFold: A platform for interactive folding simulations of proteins” Bioinformatics, 22: 2693-2694 (2006) [download] [service]

10. F. Ding, W. Guo, N. V. Dokholyan, E. I. Shakhnovich, and J.-E. Shea, “Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations”, J. Mol. Biol., 350: 1035-1050 (2005). [download]

9. F. Ding, R. K. Jha, and N. V. Dokholyan, “Scaling behavior and structure of denatured proteins”, Structure, 13: 1047-1054 (2005).[download]

8. F. Ding, S. V. Buldyrev, and N. V. Dokholyan, “Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model”, Biophys. J., 88: 147-155 (2005). [download]

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, “New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate” Structure, 12: 2161-2171 (2004). [download]

6. J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, “Multiple folding pathways of the SH3 domain.” Biophys. J. 87: 521-533 (2004). [download]

5. S. D. Khare, F. Ding and N. V. Dokholyan, “Folding of Cu,Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis.” J. Mol. Biol, 334, 515-525, 2003 [download]

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]

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]

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]

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]