Frontiers of Chemical Science and Engineering >
Molecular simulation of the interaction mechanism between CodY protein and DNA in Lactococcus lactis
Received date: 28 Mar 2018
Accepted date: 30 Apr 2018
Published date: 25 Feb 2019
Copyright
In Lactococcus lactis, the global transcriptional regulatory factor CodY can interact with the promoter DNA to regulate the growth, metabolism, environmental adaptation and other biological activities of the strains. In order to study the mechanism of interaction between CodY and its target DNA, molecular docking and molecular dynamics simulations were used to explore the binding process at molecular level. Through the calculations of the free energy of binding, hydrogen bonding and energy decomposition, nine key residues of CodY were identified, corresponding to SER184, SER186, SER208, THR217, ARG218, SER219, ASN223, LYS242 and GLY243, among which SER186, ARG218 and LYS242 play a vital role in DNA binding. Our research results provide important theoretical guidance for using wet-lab methods to study and optimize the metabolic network regulated by CodY.
Key words： CodY; DNA; molecular docking; molecular dynamics
Linchen Yuan , Hao Wu , Yue Zhao , Xiaoyu Qin , Yanni Li . Molecular simulation of the interaction mechanism between CodY protein and DNA in Lactococcus lactis[J]. Frontiers of Chemical Science and Engineering, 2019 , 13(1) : 133 -139 . DOI: 10.1007/s11705-018-1737-4
| 1 |
Zhang J, Zhong J. The journey of nisin development in China, a natural-green food preservative. Protein & Cell, 2015, 6(10): 709–711
|
| 2 |
Song A, In L, Lim S, Rahim R A. A review on Lactococcus lactis: From food to factory. Microbial Cell Factories, 2017, 16(1): 55
|
| 3 |
Papadimitriou K, Alegria A, Bron P A, Angelis M, Gobbetti M, Kleerebezem M. Stress physiology of lactic acid bacteria. Microbiology and Molecular Biology Reviews, 2016, 80(3): 837–890
|
| 4 |
McMahon D J, Oberg C J, Drake M A, Farkye N, Moyes L V, Arnold M R, Ganesan B, Steele J, Broadbent J R. Effect of sodium, potassium, magnesium, and calcium salt cations on pH, proteolysis, organic acids, and microbial populations during storage of full-fat cheddar cheese. Journal of Dairy Science, 2014, 97(8): 4780–4798
|
| 5 |
Laroute V, Yasaro C, Narin W, Mazzoli R, Pessione E, Loubiere P. GABA production in Lactococcus lactis is enhanced by arginine and co-addition of malate. Frontiers in Microbiology, 2016, 7: 1050
|
| 6 |
Delcour J, Ferain T, Deghorain M, Palumbo E, Hols P. The biosynthesis and functionality of the cell-wall of lactic acid bacteria. Antonie van Leeuwenhoek, 1999, 76(1/4): 159–184
|
| 7 |
Hartke A, Bouche S, Giard J C, Benachour A, Boutibonnes P, Auffray Y. The lactic acid stress response of Lactococcus lactis subsp. lactis. Current Microbiology, 1996, 33(3): 194–199
|
| 8 |
Belitsky B R, Sonenshein A L. Genome-wide identification of Bacillus subtilis CodY-binding sites at single-nucleotide resolution. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(17): 7026–7031
|
| 9 |
Yuan T, Guo Y K, Dong J K, Li T Y, Zhou T, Sun K W, Zhang M, Wu Q Y, Xie Z, Cai Y Z,
|
| 10 |
Levdikov V M, Blagova E, Young V L, Belitsky B R, Lebedev A, Sonenshein A L, Wilkinson A J. Structure of the branched-chain amino acid and GTP-sensing global regulator, CodY, from Bacillus subtilis. Journal of Biological Chemistry, 2017, 292(7): 2714–2728
|
| 11 |
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Klefer F, Cassarino T G, Bertonl M, Bordoli L,
|
| 12 |
Case D A, Darden T A, Cheatham T E III. AMBER 12. 2012
|
| 13 |
Adcock S A, Mccammon J A. Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 2006, 106(5): 1589–1615
|
| 14 |
Essmann U, Perera L, Berkowitz M, Darden T, Lee H, Pedersen L G. A smooth particle mesh Ewald method. Journal of Chemical Physics, 1998, 103(19): 8577–8593
|
| 15 |
Colovos C, Yeates T O. Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 1993, 2(9): 1511–1519
|
| 16 |
Wiederstein M, Slppl M J. ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 2007, 35(Web Server): W407–W410
|
| 17 |
Ercan O, Wels M, Smid E J, Kleerebezem M. Molecular and metabolic adaptations of Lactococcus lactis at near-zero growth rates. Applied and Environmental Microbiology, 2015, 81(1): 320–331
|
| 18 |
Dijk M V, Bonvin A M. 3D-DART: A DNA structure modeling server. Nucleic Acids Research, 2009, 37(Web Server): W235–W239
|
| 19 |
Dijk M V, Dijk A D, Hsu V, Boelens R, Bonvin A M. Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility. Nucleic Acids Research, 2006, 34(11): 3317–3325
|
| 20 |
Massova I, Kollman P A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 2000, 18(1): 113–135
|
| 21 |
Kottalam J, Case D A. Langevin modes of macromolecules: Applications to crambin and DNA hexamers. Biopolymers, 1990, 29(10-11): 1409–1421
|
| 22 |
Sharp K A, Honig B. Electrostatic interactions in macromolecules: Theory and applications. Annual Review of Biophysics and Biophysical Chemistry, 1990, 19(1): 301–332
|
| 23 |
Sitkoff D, Sharp K A, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. Journal of Physical Chemistry, 1994, 98(7): 1978–1988
|
| 24 |
Still W C, Tempczyk A, Hawley R C, Hendirckson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. Journal of the American Chemical Society, 1990, 112(16): 6127–6129
|
/
| 〈 |
|
〉 |