Yoelvis Orozco-GonzalezGeorgia State University | GSU · Department of Chemistry
Yoelvis Orozco-Gonzalez
Ph.D. Physics
About
31
Publications
2,353
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400
Citations
Citations since 2017
Introduction
Additional affiliations
October 2017 - present
Position
- PostDoc Position
Description
- Software Developer applied to study Biological and molecular systems
October 2015 - September 2017
Position
- PostDoc Position
Description
- Software Developer applied to study Biological and molecular systems
October 2014 - September 2015
Position
- PostDoc Position
Description
- Computational Chemical Physics and software Developer applied to study Biological and molecular systems
Education
August 2008 - July 2012
Publications
Publications (31)
Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-argini...
Remarkable interest is associated with the interpretation of the Prodan fluorescent spectrum. A sequential hybrid Quantum Mechanics/Molecular Mechanics method was used to establish that the fluorescent emission occurs from two different excited states, resulting in a broad asymmetric emission spectrum. The absorption spectra in several solvents wer...
Prodan is a fluorescent probe used to monitor biological systems such as lipid membrane,
proteins and DNA. Remarkable interest is associated to the interpretation of its fluorescent spectrum.
In this paper the sequential hybrid Quantum Mechanics/Molecular Mechanics (S-QM/MM) method was used to establish that the fluorescent emission occurs from two...
The photocycle of a reversible photoisomerizing rhodopsin mimic (M2) is investigated. This system, based on the cellular retinoic acid binding protein, is structurally different from natural rhodopsin systems; but exhibits a similar isomerization upon light irradiation. More specifically, M2 displays a 15-cis to all-trans conversion of retinal prot...
Flavins are versatile molecules due to their ability to exist in multiple redox and protonation states. At physiological conditions, they are usually encountered either as oxidized quinones, neutral semiquinones, anionic semiquinones, neutral hydroquinones, or anionic hydroquinones. We compute the electronic near-UV/vis spectra for flavin in each o...
The neutral flavin semiquinone radical stabilized in the active site of nitronate monooxygenase shows novel fluorescence behavior. It displays a broad UV–visible absorption spectrum in the near‐UV and visible light range and emits red fluorescence when excited with yellow and red light. Such fluorescence is not observed when using excitation light...
The mechanism by which the absorption wavelength of a molecule is modified by a protein is known as spectral tun-ing. Spectral tuning is often achieved by electrostatic interactions that stabilize/destabilize or modify the shape of the excited and ground-state potential energy surfaces of the chromophore. We present a protocol for the construction...
Fluorescent cofactors like flavins can be exploited to probe their local environment with spatial and temporal resolution. While the fluorescence properties of oxidized and two‐electron reduced states of flavins have been studied extensively, this is not the case for the one‐electron reduced state. Both the neutral and anionic semiquinones have pro...
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.
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...
The manuscript reports on two mutations of the photo-sensory protein Anabaena Sensory Rhodopsin and how these mutations modify the fluorescence quantum yield with respect to the wild-type protein. Experimental results are presented and explained theoretically on the basis of mixing of the S1 and S2 excited states. This mixing modulated by electrost...
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...
The light-induced double-bond isomerization of the visual pigment rhodopsin operates a molecular-level optomechanical energy transduction, which triggers a crucial protein structure change. In fact, rhodopsin isomerization occurs according to a unique, ultrafast mechanism that preserves mode-specific vibrational coherence all the way from the react...
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-...
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...
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)...
Spectral data show that the photoisomerization of retinal protonated Schiff base (rPSB) chromophores occurs on a 100 fs timescale or less in vertebrate rhodopsins, it is several times slower in microbial rhodopsins and it is between one and two order of magnitude slower in solution. These timescale variations have been attributed to specific modifi...
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...
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...
There is current considerable interest in the properties of semiconducting metal oxide nanoparticle substrates because of their utility in surface-enhanced Raman scattering, dye-sensitized solar cells, and photo-catalysis. While the enhancement of Raman activities of molecules adsorbed on these nanoparticles is due to a large increase in the polari...
The flavonoids have been the target of several experimental works due to its influence in the human health as antioxidant elements. The fluorescence properties of these compounds have been widely studied due to the large Stokes shifts experimentally observed and the variety of processes that lead to the fluorescence. In the present work it is theor...
The photophysics of the 1-nitronaphthalene molecular system, after the absorption transition to the first singlet excited state, is theoretically studied for investigating the ultrafast multiplicity change to the triplet manifold. The consecutive transient absorption spectra experimentally observed in this molecular system are also studied. To iden...
The importance of the HSO(2) system in atmospheric and combustion chemistry has motivated several works dedicated to the study of associated structures and chemical reactions. Nevertheless controversy still exists in connection with the reaction SH + O(2)→ H + SO(2) and also related to the role of the HSOO isomers in the potential energy surface (P...
Electronic polarization of the acetone molecule in the excited n → π∗ state is considered and its influence on the solvent shift in the emission spectrum is analyzed. Using an iterative procedure the electronic polarizations of both the ground and the excited states are included and compared with previous results obtained with Car–Parrinello dynami...
A full dimensional quasiclassical trajectory study of the OH+SO reaction is presented with the aim of investigating the role of the reactants rotational energy in the reactivity. Different energetic combinations with one and both reactants rotationally excited are studied. A passive method is used to correct zero-point-energy leakage in the classic...
Sumario. Se reporta por primera vez una superficie de energía potencial (SEP) global para el SO 3 en el estado electró-nico más bajo en forma de triplete, utilizando el método de expansión doble de muchos cuerpos (DMBE). Se emplearon funciones previamente reportadas utilizando la misma teoría para los fragmentos diatómicos y triatómicos, además de...
Projects
Projects (2)
Light-responsive proteins have evolved to use light to drive complex processes ranging from photosynthesis to vision. These systems not only serve as an inspiration for technology but have also been implemented directly in biotechnologies such as bioimaging, biosensing, optogenetics, and photodynamic therapy. However, engineering photoreceptors for use in biotechnology requires a fundamental understanding of how these systems operate on a molecular level. To this end, we use quantum mechanics and molecular mechanics to understand how biological systems respond to light. A family of proteins we are currently interested in are light-oxygen-voltage (LOV) domains.
QM/MM geometry optimization of chromophore-protein complexes using the ASEC free energy gradient
