María Del Carmen Marín

María Del Carmen Marín
The University of Tokyo | Todai · The Institute for Solid State Physics

Doctor of Chemical Sciences and Pharmacy

About

23
Publications
2,070
Reads
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259
Citations
Citations since 2017
20 Research Items
259 Citations
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20172018201920202021202220230102030405060
20172018201920202021202220230102030405060
Introduction
Investigation line: Development and application of accurate ab initio QM/MM methods for the investigating excited states and photochemical reactivity. Computational investigation of the “Primary event” in biological photoreceptors. Main Scientific Interests: Computational Photochemistry and Chemi-luminescence and Computational Researching of Fluorescence employing mutants.
Additional affiliations
January 2017 - July 2017
Università degli Studi di Siena
Position
  • Co-Supervisor Bachelor Thesis
Description
  • BSc Student: Gianmarco Bartalini. University of Siena (2017) Thesis title: Modeling of thermal modulation in cottoid fish rhodopsins
Education
November 2015 - November 2018
Università degli Studi di Siena
Field of study
  • Computational Chemistry
September 2014 - July 2015
University of Alcalá
Field of study
  • Nanotechnology
September 2010 - July 2014
Universidad de Jaén
Field of study
  • Scienze

Publications

Publications (23)
Article
Full-text available
DTG/DTS rhodopsin, which was named based on a three-residue motif (DTG or DTS) that is important for its function, is a light-driven proton-pumping microbial rhodopsin using a retinal chromophore. In contrast to other light-driven ion-pumping rhodopsins, DTG/DTS rhodopsin does not have a cytoplasmic proton donor residue such as Asp, Glu, or Lys. Be...
Article
Full-text available
Sub-picosecond photo-isomerization is the major primary process of energy conversion in retinal proteins and has as such been in the focus of extensive theoretical and experimental work over the past decades. In this review article, we revisit the long-standing question as to how the protein tunes the isomerization speed and quantum yield. We focus...
Chapter
The automatic building of quantum mechanical/molecular mechanical models (QM/MM) of rhodopsins has been recently proposed. This is a prototype of an approach that will be expanded to make possible the systematic computational investigation of biological photoreceptors. QM/MM models represent useful tools for biophysical studies and for protein engi...
Article
This article introduces Web-ARM, a specialized, on-line available, tool designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows to rapidly build models of rhodopsins with a documented quality and to predict trends in UV-Vis absorption maximum wavelengths, ba...
Article
Full-text available
Microbial rhodopsins are photoreceptive membrane proteins that transport various ions using light energy. While they are widely used in optogenetics to optically control neuronal activity, rhodopsins that function with longer-wavelength light are highly demanded because of their low phototoxicity and high tissue penetration. Here, we achieve a 40-n...
Article
The Automatic Rhodopsin Modeling (ARM) protocol, has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild-type and mutant rhodopsins. However, in its present version, the input preparation requires a few hour long user's manipulation of the template protei...
Article
A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-containing rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodops...
Article
Full-text available
We report new experimental results on the ultrafast photo-isomerization of ASR - PSBR where, unlike other retinal proteins, point mutations lead to a 2-fold increase of the photo-isomerization speed for the all-trans isomer. Prominent low-frequency vibrational coherences are reported for both the excited and photo-product ground states.
Article
The engineering of microbial rhodopsins with enhanced fluorescence is of great importance in the expanding field of optogenetics. Here we report the discovery of two mutants (W76S/Y179F and L83Q) of a sensory rhodopsin from the cyanobacterium Anabaena PCC7120 with opposite fluorescence behavior. In fact, while W76S/Y179F displays, with respect to t...
Poster
Full-text available
Protein engineering of microbial rhodopsins with enhanced fluorescence has been successful in the generation of variants with improved properties for applications in the expanding field of optogenetics1. These systems exhibit a significant change in the fluorescence as a consequence of action potential variation along the neuron membrane. Archaerho...
Article
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40~nm in absorption maxima and only 18~nm in emission. The five proteins -- Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa -- carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic in...
Article
Anabaena Sensory Rhodopsin is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-...
Article
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR...
Article
A novel atomistic methodology to perform free energy geometry optimization of a retinal chromophore covalently bound to any rhodopsin-like protein cavity is presented and benchmarked by computing the absorption maxima wavelengths (λmax) of distant rhodopsin systems. The optimization is achieved by computing the Nagaoka's Free Energy Gradient (FEG)...
Article
Full-text available
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40~nm in absorption maxima and only 18~nm in emission. The five proteins -- Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa -- carry exactly the same chromophore and differ just in a few mutations. Thus they form an ideal set for mechanistic in...
Poster
Full-text available
ARM is a protocol for the automatic, fast and congruous construction of uncharged gas-phase QM/MM models of rhodopsin-like photoreceptors and of their mutants. In its present implementation, the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on...
Article
Full-text available
We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information...
Article
The unzipping of temperature-induced multi-walled carbon nanotubes (MWCNTs) to yield graphene oxide nanoribbons (GONRs) has been studied. These carbon nanomaterials consisting of MWCNTs and unzipped MWCNTs have been synthesized, thoroughly characterized, and subsequently evaluated for electrochemical sensing. Three temperatures (55, 65 and 75 °C) y...

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