Premium
Interaction identification of Zif268 and TATA ZF proteins with GC‐/AT‐rich DNA sequence: A theoretical study
Author(s) -
Yang Bo,
Zhu Yanyan,
Wang Yan,
Chen Guangju
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21630
Subject(s) - van der waals force , chemistry , dna , solvation , molecular dynamics , binding energy , crystallography , zinc finger , implicit solvation , stereochemistry , computational chemistry , molecule , biochemistry , physics , gene , transcription factor , organic chemistry , nuclear physics
Molecular dynamics (MD) simulations for Zif268 (a zinc‐finger‐protein binding specifically to the GC‐rich DNA)‐d(A 1 G 2 C 3 G 4 T 5 G 6 G 7 G 8 C 9 A 10 C 11 ) 2 and TATA ZF (a zinc‐finger‐protein recognizing the AT‐rich DNA)‐d(A 1 C 2 G 3 C 4 T 5 A 6 T 7 A 8 A 9 A 10 A 11 G 12 G 13 ) 2 complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC‐rich and AT‐rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson‐Boltzmann surface area (MM‐PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268‐DNA complex is larger than that of TATA ZF ‐DNA one. The affinity between the zinc‐finger‐protein and DNA is mainly driven by more favorable van‐der‐Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van‐der‐Waals interactions and entropy components. The decomposition analysis of MM‐PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen‐bonds at the protein‐DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268‐DNA complex have been identified at some key contact sites. However, only the interhydrogen‐bonds between the residues of protein and DNA for TATA ZF ‐DNA complex have been found. The interactions of hydrogen‐bonds, electrostatistics and van‐der‐Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc‐finger‐proteins have also been discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011