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GOKNOT TERMINATED

Modelling the formation of a gordian knot in Human Ubiquitin Hydrolase

Total Cost €

0

EC-Contrib. €

0

Partnership

0

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 GOKNOT project word cloud

Explore the words cloud of the GOKNOT project. It provides you a very rough idea of what is the project "GOKNOT" about.

center    models    gordian    metadynamics    relies    combines    atom    building    molecular    coarse    diseases    polypeptide    output    biophysical    biomedical    picture    dynamics    limitations    polymers    knotted    calculations    incomplete    devising    simplest    terminal    validation    bio    representation    advancements    modeling    description    intermediate    landscape    sampling    region    variationally    complemented    lifted    connected    limited    enhanced    introducing    parkinson    methodological    course    human    hydrolase    crossings    explicit    time    training    host    folding    full    protein    mostly    forms    model    computer    soft    nontrivial    action    effect    experiments    contributed    solvent    preferential    mechanisms    energy    strategy    grained    employ    proteins    alzheimer    computational    collaborations    knot    theoretical    ubiquitin    expertise    form    outline    generalize    topology    comprehension    simulations    backbone    free    trefoil   

Project "GOKNOT" data sheet

The following table provides information about the project.

Coordinator
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV 

Organization address
address: HOFGARTENSTRASSE 8
city: MUENCHEN
postcode: 80539
website: n.a.

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Germany [DE]
 Project website http://www2.mpip-mainz.mpg.de/
 Total cost 159˙460 €
 EC max contribution 159˙460 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2017
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2018
 Duration (year-month-day) from 2018-04-01   to  2020-03-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV DE (MUENCHEN) coordinator 159˙460.00

Map

 Project objective

The folding of knotted proteins is a challenging research topic of great biophysical interest. In this field, computer simulations have greatly contributed to advance our comprehension of the mechanisms that allow a polypeptide to form a knot during the folding. However, due to limitations in methods and resources, the state-of-the-art picture on the process is still incomplete, and mostly limited to the simplest nontrivial topology, the trefoil knot. In this Action I will investigate the folding of human Ubiquitin C-terminal Hydrolase, whose backbone forms a Gordian knot with five crossings. I will make use of a multi-scale Molecular Dynamics strategy that combines coarse grained and all-atom models with enhanced sampling. Using a coarse grained model I will outline a general picture of the folding, devising the preferential pathways and intermediate states. Then, building on this knowledge, I will employ a full-atom representation of the system, targeting the calculations in the most relevant region of the protein's free energy landscape. The effect of an explicit solvent description will be considered as well. The computational time limitations will be lifted by enhancing the sampling through the use of Metadynamics and Variationally Enhanced Sampling. The Action relies on my experience in enhanced sampling methods, that will be complemented by the training and expertise provided by the host institution, a leading center in coarse-grained modeling of bio-polymers and soft matter. In the course of the action I will establish two key collaborations, providing further expertise for the success of my simulations, and allowing the validation of my theoretical model with experiments. The output of the project will generalize the current picture on knotted protein folding, introducing important methodological advancements, and contributing to the knowledge on a system of great biomedical interest, connected to diseases such as Parkinson's and Alzheimer's.

 Publications

year authors and title journal last update
List of publications.
2018 Claudio Perego and Raffaello Potestio
Searching the optimal folding routes of a Complex Lasso protein
published pages: , ISSN: , DOI: 10.1101/507079
2019-05-08

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