Styret molekylær dynamisk undersøgelse af acetylcholin's transport gennem bindingskløften på acetylcholinesterase. Steered molecular dynamics investigation of the transport of acetylcholine through the active site gorge of acetylcholinesterase

Mette Korre Andersen & Camilla Helene Andreasen

Studenteropgave: Semesterprojekt

Abstrakt

#Vi ønsker at klarlægge, hvilke aminosyrer acetylcholin interagerer med, på vej mod bindingssitet i acetylcholinesterase, og dermed dels bestemme, hvad der medierer transporten gennem bindingskløften og hvad der holder acetylcholin fast i bindingssitet. For at undersøge dette, har vi udført en styret molekylær dynamisk simulering, hvor vi trækker acetylcholin ud af bindingskløften. Dette gøres under antagelse af, at det er de samme interaktioner acetylcholin vil indgå med aminosyrerne i acetylcholinesterase, uanset om den naturligt er på vej til bindingssitet, eller trækkes ud derfra. Simuleringen analyseres ved at sammenholde variationen i trækkraft som funktion af tid, med mulige interaktioner detekteret på øjebliksbilleder fra simuleringen. De mulige interaktioner evalueres på baggrund af afstandsdefinitioner, samt orienteringen af de elementer der indgår i interaktionen. Vi konkluderer, at det overvejende er aromatiske aminosyrer der medierer transporten af acetylcholin gennem kløften, via kation-π interaktioner mellem acetylcholins positive ladning og Trp84, Phe330, Tyr334 og Trp279. Ligeledes finder vi to negativt ladede aminosyrer, Asp72 og Glu199, nede i kløften, der ligeledes har vist sig at være vigtige for transporten. Trp84, Phe330, Glu199 og Gly119 er ansvarlig for fastholdelse af acetylcholin i bindingssitet i acetylcholinesterase. We intend to elucidate, with which amino acids acetylcholine interacts on the way towards the active site in acetylcholinesterase and thus both determine, what mediates the transportation through the active site gorge, and what binds acetylcholine in the active site. In order to examine this we have carried out a steered molecular dynamic simulation, in which we extract acetycholine from the active site gorge. This is done under the assumption that acetylcholine will interact with the same amino acids in acetylcholinesterase no matter if naturally it is on it’s way to the active site or if it is pulled out of it. The simulation has been analysed by means of a comparison of the variation of pulling force versus time, with possible interactions detected on snapshots from the simulation. The possible interactions are evaluated on the basis of definitions of distances of interaction, as well as the orientation of the elements involved. We conclude that it is mainly aromatic animo acids, which mediates the transportation of acetylcholine through the active site gorge by means of cation-π interactions between the positive charge of acetylcholine and Trp84, Phe330, Tyr334 and Trp279. We also find two negatively charged amino acids, Asp72 and Glu199, in the gorge, which have also proved to be important for the transportation. Trp84, Phe330, Glu199 and Gly119 is found to be responsible for the binding of acetylcholine in the active site of actylcholinesterase. It should be noted that the report is written in Danish.

UddannelserKemi, (Bachelor/kandidatuddannelse) Kandidat
SprogDansk
Udgivelsesdato1 jun. 2005

Emneord

  • acetylcholin
  • bindingskløft
  • transport
  • Acetylcholinesterase
  • Styret molekylær dynamik