Feng Ding

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Direct molecular dynamics observation of protein folding transition state ensemble
    Feng Ding
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    Biophys J 83:3525-32. 2002
  2. ncbi request reprint Mechanism for the alpha-helix to beta-hairpin transition
    Feng Ding
    Center for Polymer Studies, Department of Physics, Boston University, Boston, Massachusetts 02215, USA
    Proteins 53:220-8. 2003
  3. ncbi request reprint Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
    Feng Ding
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    J Mol Biol 324:851-7. 2002
  4. pmc Multiple folding pathways of the SH3 domain
    Jose M Borreguero
    Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts, USA
    Biophys J 87:521-33. 2004
  5. pmc Fast complementation of split fluorescent protein triggered by DNA hybridization
    Vadim V Demidov
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 103:2052-6. 2006
  6. ncbi request reprint Simple but predictive protein models
    Feng Ding
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Trends Biotechnol 23:450-5. 2005
  7. ncbi request reprint Topological determinants of protein domain swapping
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599, USA
    Structure 14:5-14. 2006
  8. pmc Emergence of protein fold families through rational design
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    PLoS Comput Biol 2:e85. 2006
  9. ncbi request reprint iFold: a platform for interactive folding simulations of proteins
    Shantanu Sharma
    Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA
    Bioinformatics 22:2693-4. 2006
  10. ncbi request reprint Direct observation of protein folding, aggregation, and a prion-like conformational conversion
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
    J Biol Chem 280:40235-40. 2005

Collaborators

Detail Information

Publications31

  1. pmc Direct molecular dynamics observation of protein folding transition state ensemble
    Feng Ding
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    Biophys J 83:3525-32. 2002
    ..Our analysis reveals a set of key interactions between residues, conserved by evolution, that must be formed to enter the kinetic basin of attraction of the native state...
  2. ncbi request reprint Mechanism for the alpha-helix to beta-hairpin transition
    Feng Ding
    Center for Polymer Studies, Department of Physics, Boston University, Boston, Massachusetts 02215, USA
    Proteins 53:220-8. 2003
    ..For a certain range of side-chain interaction strengths, we find that the intermediate beta-hairpin state is destabilized and even disappears, suggesting an important role of the environment in the aggregation propensity of a peptide...
  3. ncbi request reprint Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
    Feng Ding
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    J Mol Biol 324:851-7. 2002
    ..Our simulations are consistent with a possible generic amyloidogenesis scenario...
  4. pmc Multiple folding pathways of the SH3 domain
    Jose M Borreguero
    Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts, USA
    Biophys J 87:521-33. 2004
    ....
  5. pmc Fast complementation of split fluorescent protein triggered by DNA hybridization
    Vadim V Demidov
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 103:2052-6. 2006
    ..The ability of our EGFP system to respond quickly to DNA hybridization should be useful for detecting the kinetics of many other types of pairwise interactions both in vitro and in living cells...
  6. ncbi request reprint Simple but predictive protein models
    Feng Ding
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Trends Biotechnol 23:450-5. 2005
    ..Here, we describe several recent studies that signify the predictive power of simplified protein models within the intuitive-modeling approach...
  7. ncbi request reprint Topological determinants of protein domain swapping
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599, USA
    Structure 14:5-14. 2006
    ..In particular, two distinct domain-swapped dimer conformations of the focal adhesion targeting domain of focal adhesion kinase were predicted computationally and were supported experimentally by data obtained from NMR analyses...
  8. pmc Emergence of protein fold families through rational design
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    PLoS Comput Biol 2:e85. 2006
    ..The conservation of amino acids in designed sequences recapitulates that of the naturally occurring sequences, thereby validating our computational design methodology...
  9. ncbi request reprint iFold: a platform for interactive folding simulations of proteins
    Shantanu Sharma
    Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA
    Bioinformatics 22:2693-4. 2006
    ....
  10. ncbi request reprint Direct observation of protein folding, aggregation, and a prion-like conformational conversion
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
    J Biol Chem 280:40235-40. 2005
    ..B. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 13363-13383) to account for prion infectivity...
  11. ncbi request reprint Scaling behavior and structure of denatured proteins
    Feng Ding
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
    Structure 13:1047-54. 2005
    ..In simulations, we observe that this protein exhibits a stable intermediate state, the size of which is consistent with the reported experimental observation...
  12. ncbi request reprint Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
    Feng Ding
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    J Mol Biol 350:1035-50. 2005
    ..A number of commonly used order parameters to identify the transition state for folding were investigated, with the number of native Cbeta contacts displaying the most satisfactory correlation with P(fold) values...
  13. ncbi request reprint New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate
    Richard D S Dixon
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Structure 12:2161-71. 2004
    ..The presence of this intermediate state in vivo may promote FAK signaling via the ERK/MAPK pathway and by release of FAK from focal adhesions...
  14. pmc Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model
    Feng Ding
    Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina 27599, USA
    Biophys J 88:147-55. 2005
    ..Our results also suggest that the success of folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulation studies may be mainly due to the special stabilizing features specific to this miniprotein...
  15. ncbi request reprint Identifying importance of amino acids for protein folding from crystal structures
    Nikolay V Dokholyan
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Methods Enzymol 374:616-38. 2003
  16. pmc Ab initio folding of proteins with all-atom discrete molecular dynamics
    Feng Ding
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
    Structure 16:1010-8. 2008
    ..The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes and applied to protein engineering and design of protein-protein interactions...
  17. pmc Probing protein aggregation using discrete molecular dynamics
    Shantanu Sharma
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Front Biosci 13:4795-808. 2008
    ....
  18. ncbi request reprint Self-templated growth of carbon-nanotube walls at high temperatures
    Jian Yu Huang
    Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
    Small 3:1735-9. 2007
  19. ncbi request reprint Modeling backbone flexibility improves protein stability estimation
    Shuangye Yin
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Structure 15:1567-76. 2007
    ..Unlike other methods, Eris also models the backbone flexibility, thereby allowing for determination of the mutation-induced backbone conformational changes. Eris is freely available via the web server at http://eris.dokhlab.org...
  20. ncbi request reprint The importance of strong carbon-metal adhesion for catalytic nucleation of single-walled carbon nanotubes
    Feng Ding
    Physics Department, Goteborg University, SE 412 96, Goteborg, Sweden
    Nano Lett 8:463-8. 2008
    ..The results highlight that first principles computations are vital for the understanding of the binding strength's role in the SWNT growth mechanism and are needed to get accurate force field parameters for MD...
  21. pmc iFoldRNA: three-dimensional RNA structure prediction and folding
    Shantanu Sharma
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Bioinformatics 24:1951-2. 2008
    ..We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses...
  22. pmc Topological determinants of protein folding
    Nikolay V Dokholyan
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 99:8637-41. 2002
    ....
  23. ncbi request reprint The length dependence of the polyQ-mediated protein aggregation
    Sunjay Barton
    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    J Biol Chem 282:25487-92. 2007
    ..These unfolded intermediates form aggregates through associations by interglutamine interactions...
  24. pmc Protein folding: then and now
    Yiwen Chen
    Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
    Arch Biochem Biophys 469:4-19. 2008
    ..We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases...
  25. ncbi request reprint Fidelity of the protein structure reconstruction from inter-residue proximity constraints
    Yiwen Chen
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599, USA
    J Phys Chem B 111:7432-8. 2007
    ....
  26. ncbi request reprint Eris: an automated estimator of protein stability
    Shuangye Yin
    Nat Methods 4:466-7. 2007
  27. pmc Multiscale modeling of nucleosome dynamics
    Shantanu Sharma
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
    Biophys J 92:1457-70. 2007
    ..Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA...
  28. pmc A structural model reveals energy transduction in dynein
    Adrian W R Serohijos
    Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27599, USA
    Proc Natl Acad Sci U S A 103:18540-5. 2006
    ..This study provides insights into the structure and function of dynein that can guide further experimental investigations into energy transduction in dynein...
  29. ncbi request reprint Atomistic simulations of catalyzed carbon nanotube growth
    Kim Bolton
    Department of Physics, Goteborg University, SE 412 96, Goteborg, Sweden
    J Nanosci Nanotechnol 6:1211-24. 2006
    ..These studies have deepened our understanding of the catalytic SWNT nucleation and growth mechanisms, but more accurate and efficient methods are required for a complete investigation at experimental growth conditions...
  30. ncbi request reprint Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis
    Sagar D Khare
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
    J Mol Biol 334:515-25. 2003
    ..To further characterize the folding of SOD1, we study the role of cysteine residues in folding and find that non-native disulfide bond formation may significantly alter SOD1 folding dynamics and aggregation propensity...
  31. pmc Active nuclear receptors exhibit highly correlated AF-2 domain motions
    Denise G Teotico
    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    PLoS Comput Biol 4:e1000111. 2008
    ..Taken together, our findings indicate that long-range motions within the LBD scaffold are critical to nuclear receptor function by promoting a mobile AF-2 state ready to bind coactivators...