title: The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization.
abstract: We investigate the importance of the trigger sequence in the folding and dimerization of the GCN4 leucine zipper. We examine the role of the enhanced propensity of the amino acids in the trigger sequence to form an alpha-helix. Using computer simulations, we calculate heat capacities, free energy profiles, and the probability for successful dimerization as a function of the strength of the alpha-helical propensity of the trigger sequence. Our results elucidate the experimentally observed importance of the trigger sequence for dimerization and why it is not necessary for the trigger to have a specific "consensus" sequence of amino acids. We also find that a stronger trigger sequence not only increases the probability for dimerization but also changes the dimerization dynamics by introducing multiple intermediate states.
authors.affiliation: Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA. chapagap@fiu.edu
authors.forename: Prem P
authors.initials: PP
authors.lastname: Chapagain
authors.forename: Yanxin
authors.initials: Y
authors.lastname: Liu
authors.forename: Bernard S
authors.initials: BS
authors.lastname: Gerstman
mesh_terms: D000595:Amino Acid Sequence; D050976:Basic-Leucine Zipper Transcription Factors; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000737:chemistry*; D016350:Leucine Zippers; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011336:Probability; D017510:Protein Folding; D055503:Protein Multimerization; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D050976:Basic-Leucine Zipper Transcription Factors; D004268:DNA-Binding Proteins; C501391:GCN4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors