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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.

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

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

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 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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