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SUMMARY:StatMech Insights on Na+/I− Symporter transport cycle
DTSTART;VALUE=DATE-TIME:20260417T212000Z
DTEND;VALUE=DATE-TIME:20260417T214000Z
DTSTAMP;VALUE=DATE-TIME:20260409T051623Z
UID:indico-contribution-349@fisindico.uniandes.edu.co
DESCRIPTION:Speakers: Alfonso Leyva (Pontificia Universidad Javeriana)\nTh
 e intrinsic transmembrane protein known as sodium iodide symporter (NIS) f
 acilitates the active transport of iodide across the basolateral membrane 
 of thyroid follicular cells. Iodine is an essential molecule that is used 
 to produce the classical thyroid hormones.\nTo perform a molecular dynamic
 s (MD) simulation\, we used structures of apo-NIS and NIS with I− and an
  oxyanion (ReO4−) bound to it.  \nThe goal of our computational study wa
 s to explore the conformational space of NIS and gain insights into the co
 nformations it assumes over the course of its transport cycle.\nWe prepare
 d a realistic simulation system that included NIS Na+ + I− / Na+ + ReO4
 − complexes embedded in a central membrane with the mammalian lipid comp
 osition\, with two half-membrane leaflets on either side. We simulated the
  membrane potential by applying a constant external electrical field to th
 e system\, thereby bringing about the equivalent of a membrane potential. 
 We are using this system to conduct unbiased and enhanced dynamics (metady
 namics\, Deep-Tica)\, a NPT statistical ensemble\, with the program GROMAC
 S (2023.3) and a modified CHARMM36 force-field\, to include non-bonded int
 eractions between I− and the oxyanion ReO4−. In order to determine the
  effects of the potential on the outwardly open NIS events\, simulations w
 ere conducted with three different membrane potentials (0\, −70\, and 
 −140 mV) using the wild-type NIS with the anion and oxyanion bound to it
 \, and using a double mutant with interesting transport characteristics.\n
 The resulting MD trajectories are currently being analyzed using a Python 
 3.11 script and  some public  libraries such as  mdtraj (v1.9)\, MDanalysi
 s (v2.7)\, Pyemma (v2.5.12)\, mlcolvs and pytorch for deep-learning analys
 is. Metadynamics calculations of the transport of I−/ReO4− free energy
  along the transport path are currently being done for the different membr
 ane potentials\, using funnel bias metadynamics.\n\nhttps://fisindico.unia
 ndes.edu.co/event/23/contributions/349/
LOCATION:Universidad de los Andes ML-513
URL:https://fisindico.uniandes.edu.co/event/23/contributions/349/
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