Aarhus University Seal / Aarhus Universitets segl

The fatgraph models of proteins and their applications in the protein folding problem

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandling

Standard

The fatgraph models of proteins and their applications in the protein folding problem. / Koyanagi, Yuki.

Aarhus Universitet, 2021. 143 s.

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandling

Harvard

APA

CBE

MLA

Vancouver

Author

Bibtex

@phdthesis{a85b91bbd941498a990de10be9deea4a,
title = "The fatgraph models of proteins and their applications in the protein folding problem",
abstract = "This thesis presents the results from my PhD studies at Aarhus University,supervised by Professor J{\o}rgen Ellegaard Andersen. The main focus of the PhDproject was to investigate applications of the fatgraph model of proteins, whichwas first proposed by Andersen and others [66]. The studies are exploratoryin nature, but are designed with a goal of tackling the protein folding problemusing the fatgraph model.In the first part of the thesis, a review of mathematical objects and theoriesrelated to the project is presented. It is followed by a review of the worksutilising fatgraphs in the study of another biological macromolecule, RNA. Wereview the recursion relations obtained by the so-called cut and join method,and by topological recursion.In the second part of the thesis, we present new results in relation to thestudy of protein structures. First the basic fatgraph model of proteins is in-troduced, and a recursion relations for the protein diagrams, obtained by cutand join method, are presented. We then discuss three experimental studies inapplications of fatgraph models. In the first project, we introduce a novel modelof proteins, which we call protein metastructures, and an associated topologicalmodel, which is a modification of the basic fatgraph model. These are used tostudy β-sheet topology of proteins, which is the configuration of β-strands inβ-sheets. We show that the proteins favour less complex β-sheet topologies bycomparing the data from the actual and simulated proteins. Some applicationsof the models are presented, including an example for combining the methodwith an existing program for predicting β-sheet topology. The second projecttakes inspiration from CASP assessment of model quality, and attempts to selectthe best structure from a set of candidate structures, which aim to reproducethe target protein structure from its primary sequence. We show the topolog-ical information contained in our model is enough to predict, if not the best,a structure close to the best candidate structure. The third project aims topredict local geometry of the proteins, expressed as a rotation between peptideunits (expressed as an element in the rotation group SO(3)) that are connectedby a hydrogen bond, from their topology. The topological information is ex-pressed as a pattern of other hydrogen bonds around the bond in question. Weshow that the rotation can be predicted to a high accuracy; close to 90% of thepredictions lie within a ball centred at the true rotation occupying 1% of theSO(3) space. We conclude the thesis by a brief discussion of potential futurechallenges and benefits of the use of fatgraph models in the protein structureresearch.",
author = "Yuki Koyanagi",
year = "2021",
month = mar,
language = "English",
publisher = "Aarhus Universitet",

}

RIS

TY - BOOK

T1 - The fatgraph models of proteins and their applications in the protein folding problem

AU - Koyanagi, Yuki

PY - 2021/3

Y1 - 2021/3

N2 - This thesis presents the results from my PhD studies at Aarhus University,supervised by Professor Jørgen Ellegaard Andersen. The main focus of the PhDproject was to investigate applications of the fatgraph model of proteins, whichwas first proposed by Andersen and others [66]. The studies are exploratoryin nature, but are designed with a goal of tackling the protein folding problemusing the fatgraph model.In the first part of the thesis, a review of mathematical objects and theoriesrelated to the project is presented. It is followed by a review of the worksutilising fatgraphs in the study of another biological macromolecule, RNA. Wereview the recursion relations obtained by the so-called cut and join method,and by topological recursion.In the second part of the thesis, we present new results in relation to thestudy of protein structures. First the basic fatgraph model of proteins is in-troduced, and a recursion relations for the protein diagrams, obtained by cutand join method, are presented. We then discuss three experimental studies inapplications of fatgraph models. In the first project, we introduce a novel modelof proteins, which we call protein metastructures, and an associated topologicalmodel, which is a modification of the basic fatgraph model. These are used tostudy β-sheet topology of proteins, which is the configuration of β-strands inβ-sheets. We show that the proteins favour less complex β-sheet topologies bycomparing the data from the actual and simulated proteins. Some applicationsof the models are presented, including an example for combining the methodwith an existing program for predicting β-sheet topology. The second projecttakes inspiration from CASP assessment of model quality, and attempts to selectthe best structure from a set of candidate structures, which aim to reproducethe target protein structure from its primary sequence. We show the topolog-ical information contained in our model is enough to predict, if not the best,a structure close to the best candidate structure. The third project aims topredict local geometry of the proteins, expressed as a rotation between peptideunits (expressed as an element in the rotation group SO(3)) that are connectedby a hydrogen bond, from their topology. The topological information is ex-pressed as a pattern of other hydrogen bonds around the bond in question. Weshow that the rotation can be predicted to a high accuracy; close to 90% of thepredictions lie within a ball centred at the true rotation occupying 1% of theSO(3) space. We conclude the thesis by a brief discussion of potential futurechallenges and benefits of the use of fatgraph models in the protein structureresearch.

AB - This thesis presents the results from my PhD studies at Aarhus University,supervised by Professor Jørgen Ellegaard Andersen. The main focus of the PhDproject was to investigate applications of the fatgraph model of proteins, whichwas first proposed by Andersen and others [66]. The studies are exploratoryin nature, but are designed with a goal of tackling the protein folding problemusing the fatgraph model.In the first part of the thesis, a review of mathematical objects and theoriesrelated to the project is presented. It is followed by a review of the worksutilising fatgraphs in the study of another biological macromolecule, RNA. Wereview the recursion relations obtained by the so-called cut and join method,and by topological recursion.In the second part of the thesis, we present new results in relation to thestudy of protein structures. First the basic fatgraph model of proteins is in-troduced, and a recursion relations for the protein diagrams, obtained by cutand join method, are presented. We then discuss three experimental studies inapplications of fatgraph models. In the first project, we introduce a novel modelof proteins, which we call protein metastructures, and an associated topologicalmodel, which is a modification of the basic fatgraph model. These are used tostudy β-sheet topology of proteins, which is the configuration of β-strands inβ-sheets. We show that the proteins favour less complex β-sheet topologies bycomparing the data from the actual and simulated proteins. Some applicationsof the models are presented, including an example for combining the methodwith an existing program for predicting β-sheet topology. The second projecttakes inspiration from CASP assessment of model quality, and attempts to selectthe best structure from a set of candidate structures, which aim to reproducethe target protein structure from its primary sequence. We show the topolog-ical information contained in our model is enough to predict, if not the best,a structure close to the best candidate structure. The third project aims topredict local geometry of the proteins, expressed as a rotation between peptideunits (expressed as an element in the rotation group SO(3)) that are connectedby a hydrogen bond, from their topology. The topological information is ex-pressed as a pattern of other hydrogen bonds around the bond in question. Weshow that the rotation can be predicted to a high accuracy; close to 90% of thepredictions lie within a ball centred at the true rotation occupying 1% of theSO(3) space. We conclude the thesis by a brief discussion of potential futurechallenges and benefits of the use of fatgraph models in the protein structureresearch.

M3 - Ph.D. thesis

BT - The fatgraph models of proteins and their applications in the protein folding problem

PB - Aarhus Universitet

ER -