Sebastian Ayala-Ruano

Sebastian Ayala-Ruano
Universidad San Francisco de Quito (USFQ) · College of Science and Engineering

Bachelor of Engineering (Biotechnology)

About

17
Publications
972
Reads
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11
Citations
Introduction
I am a focused and motivated young researcher that has worked in Bioinformatics for four years at different laboratories. Phylogenetics and Structural Bioinformatics have been the main topics of this research experience. However, my current interests are devoted to Network Science, Complex Systems, and Machine Learning to understand different biological phenomena. Also, I am involved in various initiatives to empower Bioinformatics in Ecuador and Latin America.
Additional affiliations
June 2019 - August 2019
Gwangju Institute of Science and Technology
Position
  • Research Intern
Description
  • Performed a computational study of a missense mutation from Cereblon protein using Molecular Dynamics simulations, and other bioinformatics tools.
August 2018 - present
Universidad de Las Américas
Position
  • Research Intern
Description
  • Identified impact of horizontal gene transfer in the genome of Streptomyces clavuligerus using Phylogeny, RNAseq data, and other bioinformatics tools.
January 2017 - present
Universidad San Francisco de Quito (USFQ)
Position
  • Research Assistant
Description
  • Developed computational workflows to understand biological questions. Documented procedures and results with a high degree of accuracy and precision.
Education
January 2015 - December 2020
January 2015 - December 2020
Universidad San Francisco de Quito (USFQ)
Field of study
  • Computer Science

Publications

Publications (17)
Article
Full-text available
Streptomyces clavuligerus is a Gram‐positive bacterium that is a high producer of secondary metabolites with industrial applications. The production of antibiotics such as clavulanic acid or cephamycin has been extensively studied in this species; nevertheless, other aspects, such as evolution or ecology, have received less attention. Furthermore,...
Article
Full-text available
The jasmonic acid (JA) signaling pathway is one of the primary mechanisms that allow plants to respond to a variety of biotic and abiotic stressors. Within this pathway, the JAZ repressor proteins and the basic helix-loop-helix (bHLH) transcription factor MYC3 play a critical role. JA is a volatile organic compound with an essential role in plant i...
Article
Full-text available
Since 2014, the ISCB Latin American Student Council Symposium (LA-SCS) serves as the main biannual activity where students from all levels, postdocs and early researchers from the entire Latin American region can gather to discuss recent advances in the fields of bioinformatics and computational biology. This time we faced a major unexpected obstac...
Thesis
Full-text available
La proteína Cereblon (CRBN) es el receptor de los sustratos que se unen al complejo CRL4CRBN E3 ubiquitina ligasa, cuya función es controlar la degradación selectiva de proteínas durante varios procesos celulares. Se han reportado varias mutaciones de CRBN asociadas con casos clínicos de discapacidad intelectual. Una de estas mutaciones se produjo...
Preprint
Full-text available
Antimicrobial peptides (AMPs) are small bioactive chemicals that have appeared as promising compounds to treat a wide range of diseases. The effectiveness of AMPs resides in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the AMPs’ chemical space (AMPCS) is huge, it is estimated that the...
Preprint
Antimicrobial peptides (AMPs) have appeared as promising compounds to treat a wide range of diseases. Their clinical potentialities reside in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the hugeness of the AMPs’ chemical space (AMPCS), represented by more than 1065 unique sequences o...
Presentation
Full-text available
The jasmonic acid (JA) signaling pathway is one of the primary mechanisms that allow plants to respond to a variety of biotic and abiotic stressors. Within this pathway, the JAZ repressor proteins and the basic helix-loop-helix (bHLH) transcription factor MYC3 play a critical role. JA is a volatile organic compound with an essential role in plant i...
Preprint
Antimicrobial peptides (AMPs) are small bioactive chemicals that have appeared as promising compounds to treat a wide range of diseases. The effectiveness of AMPs resides in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the AMPs’ chemical space (AMPCS) is huge, it is estimated that the...
Presentation
Full-text available
La vía de señalización del ácido jasmónico es uno de los principales mecanismos que permiten a las plantas responder ante estresores bióticos y abióticos. Dentro de esta vía, las proteínas represoras JAZ y el factor de transcripción MYC3 juegan un rol crítico. El objetivo principal de este estudio fue identificar la base molecular de la interacción...
Presentation
Full-text available
Streptomyces clavuligerus is a bacterium that produces a lot of secondary metabolites. The production of antibiotics has been extensively studied in this specie; nevertheless, other aspects, such as evolution or ecology, have received less attention. Thus, we studied the impact of horizontal gene transfer in the S. clavuligerus genome. To perform t...
Data
The file contains the structure (all-atom predicted structure) for the MYC3 transcription factor JID-TAD Domain bound to each of the TIFY family's proteins (only the Jas domain). Details of construction and validation of these structures are described in our article "The molecular basis of JAZ-MYC coupling, a protein-protein interface essential for...
Presentation
Full-text available
Streptomyces clavuligerus is a bacterium that produces a lot of secondary metabolites. The production of antibiotics has been extensively studied in this species; nevertheless, other aspects, such as evolution or ecology, have received less attention. Thus, we studied the impact of horizontal gene transfer in the S. clavuligerus genome. To perform...
Poster
Full-text available
Las plantas poseen un intrincado sistema de defensa, que involucra procesos metabólicos y mecanismos moleculares, que trabajan en conjunto para garantizar su supervivencia. Un compuesto clave en este sistema es el ácido jasmónico (JA), que induce respuestas en contra de ataques de herbivoría. Así, cuando la concentración de JA aumenta, se activa la...
Poster
Full-text available
Poster presentation as a result of the Global Intern Program at the Gwangju Institute of Science and Technology, South Korea.

Questions

Question (1)
Question
I am performing a molecular dynamics simulation from CRBN protein (PDB ID: 4tz4), which contain a ZN binding site composed of four cysteines. The main goal is understanding the chemical and biological changes in the Zn binding site from this protein when Cys391-to-Arg (C391R) substitution occur. For this, we performed the geometry optimization of the complex of four cysteines and Zn using DFT calculations on Gaussian 16 suite. Then, we put the coordinates obtained through DFT on the PDB format, and we will perform molecular dynamics simulation to obtain results in the perspective of the whole protein.
Now, I am using Gromacs to perform the MD simulation, but there is an error on my simulation during the NVT stabilization. This is the error message:
"Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1# Wrote pdb files with previous and current coordinates ^Mstep 0 WARNING: Listed nonbonded interaction between particles 4204 and 4221 at distance 4.402 which is larger than the table limit 2.029 nm.
This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason."
I am thinking about the reason for this error, and this could be because the force field which I am using to perform the simulation (amber03), but I am not sure about that. It is proper to mention that the atoms in which there is the error are the C of the residues (Lys324 and Gly325) which are between two of the Cys that form the Zn binding site.
Please, can anyone help me with this issue? Thank you very much

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