Title:	AlphaFold2 modelling for structural data
DNr:	Berzelius-2023-85
Project Type:	LiU Berzelius
Principal Investigator:	Leonardo Monrroy <leonardo.monrroy@kemi.uu.se>
Affiliation:	Uppsala universitet
Duration:	2023-03-30 – 2023-10-01
Classification:	10602
Keywords:

Abstract

AlphaFold models can be used to complement experimental data and aid to solve and validate structures. With current advances of being able to manipulate AlphaFold new methods have been developed to not only sample standard structures but also an variety of conformation of structures. Combining this with experimental data can uncover new mechanisms and prove previously unexplained changes and behavior in proteins. Conventional methods to look at structural dynamics such as X-ray crystallography and cryo-EM have are limited to this by having either limited flexibility in the crystal or samples being to heterogeneous to model flexible regions while frozen. Combining this with conventional structural methods can push the limits and help uncovering new conformation that are supported by experimental data from NMR or X-ray solution scattering as example. For my project I would sample AlphaFold models of photoreceptor proteins using a dropout method to gain more diverse models and try to fit it to X-ray solution scattering model to explain dynamics that cannot be captured by conventional X-ray methods. These data sets can be used further also for developing new tools withing solution scattering or be applied in other structural fields such as cryo-em.