La pedra rosetta de les proteïnes fluorescents: una descripció atomística

dc.contributor
Universitat Autònoma de Barcelona. Departament de Química
dc.contributor.author
Armengol Torrella, Pau
dc.date.accessioned
2017-11-17T19:41:22Z
dc.date.available
2017-11-17T19:41:22Z
dc.date.issued
2017-07-14
dc.identifier.isbn
9788449074424
en_US
dc.identifier.uri
http://hdl.handle.net/10803/456583
dc.description.abstract
Fluorescent Proteins have become a focus of scientific interest due to their applications in biomedical problems and bio-imaging. The growing interest in red fluorescent proteins demands a clear and systematic rationalization of the processes occurring in this complicated biosistems. In order to reach such a level of detail, a computational work has been done, using theories coming from Quantum Chemistry, Statistical Thermodynamics and Classical, Semi-classical and Quantum Dynamics. In a first step, and by means of molecular dynamics simulations integrated using the task-farming method, also developed in this work, in which we have applied Time Dependent Density Functional Theory calculations, we have been able to reproduce the absorption spectra of the selected proteins. The three green fluorescent proteins studied have been S65T/H148D-GFP, E222Q/H148D-GFP i wt-GFP. We have concluded that the proximity of a negative charge near the phenolic ring of the chromophore is presumably lowing the excitation energy, which increases the absorption wavelength. Regarding the second group of proteins, this time red fluorescent proteins, we have studied the mNeptune and mCardinal mutants, whose show their spectroscopic activity in the transparency window of the living mammal tissue. Using a similar methodology as the one used in the case of GFPs, we have been able to qualitatively reproduce the 4 nm red shift between the two mutants. In this sense, we have showed how the oxygen of the residue Phe62 is effectively interacting with the residue Gly41 in the case of mCardinal (interaction not found in mNeptune), which makes the former to be more red-shifted. In a second chapter, we have been able to reproduce and explain the experimental behavior observed for the mutant S65T-H148D, which is considered in this work as the Rosetta Stone of the fluorescent proteins, given that the knowledge obtained for it can be generalized to other proteins. In this sense, we have refuted the experimental supposition of the dramatic gain of acidity of the chromophore in the excited state and we have substituted it by a more dynamical view, in which there are structural factors that promote the proton transfer between the chromophore and the Asp148: (1) the spotted interaction between the residue Tyr146 and the chromophore, which stabilizes the photo-product and (2) the proper solvation of the proton acceptor, the residue Asp148. The solvation of this residue has to be adequate so it can accept the proton coming from the chromophore. Furthermore, by means of Quantum Dynamics calculations and non-adiabatic molecular dynamics simulations, we have been able to reproduce the time-scale for the proton transfer and the experimental emission time-resolved spectra. The first regime of relaxation has been associated to the main proton transfer and the second regime, which occurs in the picosecond time-scale, has been associated to the vibrational cooling, which involves (1) the separation of the residue Asp148 from the chromophore, (2) the loss of planarity of the second and (3) the interaction with the residue Tyr 148, which stabilizes the photoproduct.
en_US
dc.format.extent
167 p.
en_US
dc.format.mimetype
application/pdf
dc.language.iso
cat
en_US
dc.publisher
Universitat Autònoma de Barcelona
dc.rights.license
L'accés als continguts d'aquesta tesi queda condicionat a l'acceptació de les condicions d'ús establertes per la següent llicència Creative Commons: http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
*
dc.source
TDX (Tesis Doctorals en Xarxa)
dc.subject
Espectroscòpìa
en_US
dc.subject
Espectroscopia
en_US
dc.subject
Spectroscopy
en_US
dc.subject
Proteïnes fluorescents
en_US
dc.subject
Proteinas fluorescentes
en_US
dc.subject
Fluorescent proteins
en_US
dc.subject
Química teòrica
en_US
dc.subject
Química teórica
en_US
dc.subject
Theoretical chemistry
en_US
dc.subject.other
Ciències Experimentals
en_US
dc.title
La pedra rosetta de les proteïnes fluorescents: una descripció atomística
en_US
dc.type
info:eu-repo/semantics/doctoralThesis
dc.type
info:eu-repo/semantics/publishedVersion
dc.subject.udc
54
en_US
dc.contributor.authoremail
pau.armengol.t@gmail.com
en_US
dc.contributor.director
Gelabert Peiri, Ricard
dc.contributor.director
Moreno Ferrer, Miquel
dc.embargo.terms
cap
en_US
dc.rights.accessLevel
info:eu-repo/semantics/openAccess


Documentos

pat1de1.pdf

2.082Mb PDF

Este ítem aparece en la(s) siguiente(s) colección(ones)