PhD Candidate

Maryam Saliminasab

Abstract

Microbial  rhodopsins  are  light-activated  retinal-binding  membrane  proteins,  performing  a  variety  of  ion  transporting  and  photosensory  functions  in  procaryotic  and  eukaryotic  cells.  They  display  several  cases  of  convergent  evolution,  where  the  same  function  is  produced  by unrelated  or  very  distant  protein  groups.  For  example, both schizorhodopsins and xenorhodopsins are inward proton pumps, while halorhodopsins and NTQ-rhodopsins  are  inward  chloride  pumps.  Here  we  present  another  possible  case  of  such  convergent  evolution,  describing biophysical  properties  of  a  new  group  of  sensory  rhodopsins,  not  related  to  the  well-known haloarchaeal  ones.  The  first  representative  of  this  group  was  identified  in  2004  (by  Kyndt,  Meyer,  and  Cusanovich) but none of the members had been expressed and characterized.The well-studied  haloarchaeal  sensory  rhodopsins  interacting  with  membrane-embedded  methyl-accepting  Htr  transducers are close relatives of halobacterial proton pump bacteriorhodopsin and have been studied extensively. In contrast, the new group of sensory rhodopsins we describe here is a relative of proteobacterial proton pumps, proteorhodopsins,  but  appear  to  interact  with  Htr-like  transducers  likewise.  This  interaction  is  likely  to  occur  through  an  unknown  mechanism,  as  they  do  not  conserve  the  residues  found  important  for  interaction  of  haloarchaeal  sensory rhodopsins  and  their  cognate  transducers.  Moreover,  the  new  sensory  rhodopsins  have  unique structural motifs and many unusual amino acid residues, including those around the retinal chromophore, most strikingly, a tyrosine in place of a carboxyl counterion of the retinal Schiff base on helix C. We describe spectroscopic properties and molecular dynamics simulations of these sensory rhodopsins, which report on their unique structure and hydrogen-bonded networks, their unusual retinal chromophore, and probe their interactions with  the  transducers.  To  characterize  their unique  sequence  motifs,  we  augment  the  spectroscopy  and  biochemistry data by structural modeling of the wild type and three mutants. Taken together, the experimental data,  bioinformatics  sequence  analyses,  and  structural  modeling  suggest  that  the  tyrosine/aspartate  complex counterion contributes to a complex water-mediated hydrogen-bond network that couples the protonated retinal Schiff base to an extracellular carboxylic dyad.

Examination Committee 

• Dr. Erica Pensini, Chair
• Dr. Leonid Brown, Advisor
• Dr. John Dutcher, Advisory Committee
• Dr. Derek O'Flaherty, Graduate Faculty
• Dr. Claudiu Gradinaru, External Examiner (University of Toronto, Mississauga)