PMID- 25204850
OWN - NLM
STAT- MEDLINE
DCOM- 20150626
LR  - 20141027
IS  - 1549-960X (Electronic)
IS  - 1549-9596 (Linking)
VI  - 54
IP  - 10
DP  - 2014 Oct 27
TI  - Truncated variants of the GCN4 transcription activator protein bind DNA with 
      dramatically different dynamical motifs.
PG  - 2869-75
LID - 10.1021/ci500448e [doi]
AB  - The yeast protein GCN4 is a transcriptional activator in the basic leucine zipper 
      (bZip) family, whose distinguishing feature is the "chopstick-like" homodimer of 
      alpha helices formed at the DNA-binding interface. While experiments have shown 
      that truncated versions of the protein retain biologically relevant DNA-binding 
      affinity, we present the results of a computational study revealing that these 
      variants show a wide variety of dynamical modes in their interaction with the 
      target DNA sequence. We have performed all-atom molecular dynamics simulations of 
      the full-length GCN4 protein as well as three truncated variants; our data 
      indicate that the truncated mutants show dramatically different correlation 
      patterns. We conclude that although the truncated mutants still retain 
      DNA-binding ability, the bZip interface present in the full-length protein 
      provides important stability for the protein-DNA complex.
FAU - McHarris, Danielle M
AU  - McHarris DM
AD  - Department of Chemistry and Biochemistry, Utica College , 1600 Burrstone Road, 
      Utica, New York 13502, United States.
FAU - Barr, Daniel A
AU  - Barr DA
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20140922
PL  - United States
TA  - J Chem Inf Model
JT  - Journal of chemical information and modeling
JID - 101230060
RN  - 0 (Basic-Leucine Zipper Transcription Factors)
RN  - 0 (DNA, Fungal)
RN  - 0 (GCN4 protein, S cerevisiae)
RN  - 0 (Recombinant Proteins)
RN  - 0 (Saccharomyces cerevisiae Proteins)
SB  - IM
MH  - Amino Acid Sequence
MH  - Basic-Leucine Zipper Transcription Factors/*chemistry/genetics/metabolism
MH  - Binding Sites
MH  - DNA, Fungal/*chemistry/metabolism
MH  - Hydrogen Bonding
MH  - *Molecular Dynamics Simulation
MH  - Molecular Sequence Data
MH  - Mutation
MH  - Protein Binding
MH  - *Protein Interaction Domains and Motifs
MH  - Protein Structure, Secondary
MH  - Recombinant Proteins/chemistry/genetics/metabolism
MH  - Saccharomyces cerevisiae/genetics/metabolism
MH  - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism
MH  - Thermodynamics
MH  - Transcription, Genetic
EDAT- 2014/09/11 06:00
MHDA- 2015/06/27 06:00
CRDT- 2014/09/11 06:00
PHST- 2014/09/11 06:00 [entrez]
PHST- 2014/09/11 06:00 [pubmed]
PHST- 2015/06/27 06:00 [medline]
AID - 10.1021/ci500448e [doi]
PST - ppublish
SO  - J Chem Inf Model. 2014 Oct 27;54(10):2869-75. doi: 10.1021/ci500448e. Epub 2014 
      Sep 22.