Probing the Viscosity of Aqueous Solutions Containing Ribosome-Bound Nascent Proteins

Abstract

Downstream regulatory element antagonist modulator (DREAM) is a member of the neuronal calcium sensors family and is expressed in the hippocampus. DREAM is involved in memory, learning, pain sensitivity, kinetics of potassium channels, calcium homeostasis, gene expression and enzymatic activity of presenilin. It has also been linked to pathologies such as Parkinson and Alzheimer's disease. The multifunctionality of this protein is due to its ability to interact with several intracellular partners such as presenilin, calmodulin, DNA and Kv channels. These interactions depend on the oligomerization state changes in DREAM which have been shown to be allosterically modulated upon Ca 2þ binding. The molecular mechanism of Ca 2þ regulation of DREAM interactions is yet to be determined, previous molecular dynamics data proposed that a hydrophobic residues network connecting the C-and N-terminal domains is involved interdomain communication since several hydrophobic residues sidechains reposition upon Ca 2þ binding, acting as molecular switch between the apo and the Ca 2þ bound state. The Trp169 residue may be a key residue in this interdomain communication as its position in the hydrophobic cavity between the N-and C-terminal domain and it is highly conserved among NCS proteins. To investigate the role of Trp169 in allosteric communication, we have mutated it to Ala and carry out molecular dynamics studies in the presence and absence of Ca 2þ using classical molecular dynamics and accelerated Gaussian molecular dynamic. These simulations show a different positioning of residues in the hydrophobic networks such as Tyr174 and Phe218, as well as an impact on the formation of the Glu 165-Lys 87 salt bridge, suggesting the crucial role of W169 residue in the reorientation of the amino acids in the hydrophobic network connecting the N-and Cterminal.