Hi,
I am trying to model a large trans-membrane protein (ABCR; 2273 aa). The only reasonable template is P-glycoprotein.When I try to split ABCR I necessarily remove several trans-membrane domains (more details regarding ABCR structure can be found here "Posttranslational Modifications of the Photoreceptor-Specific ABC Transporter ABCA4" http://pubs.acs.org/doi/abs/10.1021/bi200774w ). The sequence represents 6+4 trans-membrane domains instead of 6+6 of the full protein. As a result the predicted structures either completely lack trans-membrane regions (very short a-helix regions separated by loops) or I-TASSER breaks some helical regions to arrive at desired 6+6.
Can you please give me an advise how to proceed?
Thank you
Stepan