Protein Structure and Dynamics

Topics:

a) Protein folding thermodynamics and kinetics

b) Protein folding transition states

c) Protein folding pathways

d) Protein conformational dynamics


References:

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: doi.org/10.1016/j.jmb.2020.166793

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*, “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]