Seminar CeNT 22.11.2019
18 listopada 2019

The Centre of New Technologies invites to a seminar by

Prof. Yuji Sugita
Chief Scientist at RIKEN Research Center in Tokyo, Japan

Title: Free-energy landscapes of protein-ligand bindings along the positional and orientational ligand coordinates

Date: November, 22nd (Friday), 2019 at 12 p.m.

Venue: Centre of New Technologies, Banacha 2C,
Lecture Hall 1130  (1st floor)

Host: Prof. Joanna Trylska


Protein-ligand binding is a slow process in solution and in a living cell. In the current study, we focus on the process between the encounter complex state and the canonical binding pose. Using all-atom MD simulations with enhanced conformational sampling algorithms, we could simulate the binding and unbinding events about hundred times. This simulation is sufficient to describe the free-energy landscape of protein-ligand binding processes. We observed the landscapes along the position coordinates as well as those along the ligand orientation coordinates. The former is a funnel like shape, while the latter is a more rugged „fork-shape” landscape. Based on the landscapes, we discuss molecular mechanisms for protein-ligand binding in solution.