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  • Open access
  • 12 Reads
Assessing the effect of calcium and magnesium ions in the structural stability of the protein kinase A through molecular dynamics simulations

Protein kinase A (PKA) is part of the big family of protein kinases, whose role consists in catalyzing the transfer of a phosphate group from an ATP molecule to a peptide substrate. While Mg2+ is the preferred cofactor in kinases, it has been proven experimentally than other divalent metals such as Ca2+ can also promote the phosphoryl transfer but not with the same efficiency achieved with Mg2+. Recent crystallographic and kinetic data for PKA have shown that the presence of Ca2+ would allow the transfer of a phosphate group from ATP to the substrate SP20 but the products would be trapped at the active site of the enzyme. Based on these experimental results, the main goal of this research was to determine how the retention of the products occurs and to identify which interactions in the presence of Ca2+ overstabilize the final state of the catalysis in PKA. In order to get a better understanding of these events, PKA in its product state was evaluated through molecular dynamics simulations using two previously crystallized systems, one using the ion Mg2+ as a cofactor, and other using the Ca2+ ion. The results obtained suggest that the stable coordination of seven ligands around Ca2+ not only allows to the phosphorylated substrate to coordinate Ca1, but also Ca2, interaction not present in the crystal structure. By means of structural analysis, it was corroborated that in PKA with Ca2+ there is a reduced mobility of the glycine-rich loop, moiety whose function is to cover the active site by hydrogen bonds that interact with the phosphorylated substrate. In this way, it was identified that the residues Thr51 and Ser53 located in this loop form hydrogen bonds with the substrate pSP20 which are more stable in the system with Ca2+ compared to Mg2+. These results were supported by binding energy calculations, using the MMPBSA method. Overall, this information provides a better understanding of the structural mechanism by which Ca2+ inhibits the activity of protein kinase A and gives new insights into the possible regulatory mechanism of Ca2+ on protein kinases.

  • Open access
  • 26 Reads

The increasing use of hydrocarbons has generated several environmental problems due to accidents during the extraction, transportation, refining, storage and use of said compounds. Diesel is a complex mixture of alkanes and aromatics, which due to its wide use has become a very frequent pollutant of water and soil. Therefore, it is necessary to explore alternatives for the degradation of said pollutants. The purpose of this work is to analyze the optimal conditions for the degradation of diesel by bacterial consortiums from polluted soils, as well as to evaluate the production of surfactants. The bacterial consortiums (J3 and S3) were obtained from soil samples and selected in diesel as the sole carbon source, in addition, the data of the growth kinetics obtained to date in different concentrations of diesel indicate that the two bacterial consortiums use it more at 3 and 4%. On the other hand, at a pH of 7 and 8 in the presence of 3% of diesel, better bacterial growth was observed. Also, the S3 consortium showed good growth at NaCl levels of 4%. For the case of the production of surfactants only the J3 consortium, production was produced with an E24 emulsion index of 38%, which was also recorded by the hemolytic activity of the bacterial supernatant and by the collapse of the oil drop. On the other hand, the consortia are able to grow in pentadecane and citronellol, while they do not grow in naphthalene and pyrene as the sole source of carbon. Although they are partial results, they reflect the potential of these consortiums for the degradation of linear hydrocarbons, so studies are being conducted to quantify diesel degradation, identify the members of each consortium and characterize the surfactants produced.

  • Open access
  • 43 Reads
Machine learning techniques and the identification of new potentially active compounds against Leishmania infantum.

Leishmaniasis is defined as a set of diseases of very varied clinical presentation produced by obligate intracellular parasites belonging to the genus Leishmania. They have been classified by the World Health Organization in category I of infectious diseases and are part of neglected tropical pathologies. Leishmania infantum mainly affects children under five years of age and has been associated with an increase in the appearance of cutaneous and visceral leishmaniasis. The search for new therapeutic alternatives remains a challenge and in silico studies are alternative tools to solve this problem. With the main objective of identify potentially effective compounds against Leishmania infantum through in silico studies, artificial Intelligence techniques implemented in the WEKA program and molecular descriptors 0D-2D of DRAGON software are used in this research. A new database was created and the clusters analysis (AC) k-means was used to design the training and prediction series. Four models were obtained with the following techniques: IBk, J48, MLP and SMO that reached percentages of classification higher than 80% for training and prediction series, whose predictive power was confirmed through external and internal validation procedures. The use of the models obtained in the virtual screening of the international database DrugBank and synthesis compounds allowed the optimal identification of 120 new potentially active compounds against Leishmania infantum amastigote form.

  • Open access
  • 34 Reads
Analysis of chemical composition of Cissus incisa leaves by GC/MS

The human being since ancient times has sought in plants to cure their various diseases. The plants used for traditional medicine contain a wide range of substances that can be used to treat chronic and infectious diseases. Phytochemical researchers have great interest in the selection of medicinal plants for new therapies. In the present study, the bioactive components of the leaves of Cissus incisa have been identified using gas chromatography-mass spectrum (GC-MS). Sixteen compounds were identified in hexane extract. β-Sitosterol (19.445%) was the predominant compound in the hexane extract, which is a well-known biologically active compound. All compounds are reported for the first time in the species. The present investigation is the base for a later phytochemical study. With which it is possible to isolate different metabolites of biological interest.

  • Open access
  • 195 Reads

MOL2NET: FROM MOLECULES TO NETWORKS (PROC. BOOK), ISBN: 978-3-03842-820-6, 2019, Vol. 4, 2985 pp.

Conference: Proceedings of the conference MOL2NET International Conference on Multidisciplinary Sciences (4th edition), 2018 is part of a year-round worldwide conference series hosted by MDPI Sciforum, Basel, Switzerland. This conference series has had organized more than 20 associated workshop series in universities worldwide: USA, France, Portugal, Spain, China, Chile, Brazil, India, etc. These workshop series run in person and/or online. Some of these workshops are the SRI-10 St Thomas University (STU)- Miami Dade College (MDC), Miami, USA; USINEWS-02 University of Minnesota, USA; BIOCHEMPHYS-01 CNAM, Paris, France; WCUCW, West Coast University, Miami, USA; IWMEDIC UDC, Coruña, Spain, LAWSCI-02, UPV/EHU, Bilbao, Spain, etc. Workshops allow both in person and/or online only publication of papers, research highlights of previous papers, letters, short reviews, etc.
Topics: The topics are multidisciplinary covering, but not limited to, Chemistry (All areas), Physics, Biology, Ecology, Statistics, Bioinformatics, Education, Nanotechnology, Materials, Computational, Complex Networks, Legal, and Social sciences, etc.
Statistics: This edition hosted >10 workshops that attracted >300 communications submitted by >700 authors. We organized 7 special issues published in JCR journals (MDPI editorial) such as Molecules, Entropy, and Appl. Sci. We also organized 3 bootcamps, hand-training, or capstone courses in MDC, Miami, WCU Miami, and UPV/EHU Bilbao.
Proceedings Book: The present book of proceedings have been released in two versions. The first is a short version without communications including links to online versions of all communications (only 94 pages). The second one is the long version including full text of all communications and abstracts (2985 pages). Download short version from MDPI AG Sciforum publisher link: We released long versiong to Researchgate public repository: Thank you very much to all colleagues for your kind support.

  • Open access
  • 26 Reads
Characterization and overexpression of a glucanase from a newly isolated B. subtilis strain

Glucanases are enzymes that hydrolysis glucans which are the major cell wall components in cereals. A newly isolated bacteria, assigned as Bacillus subtilis HB2, produces a monomeric glucanase (GLU HB2) of a molecular mass of 75 kDa. GLU HB2 has an optimal activity at pH 5 and 55°C. It is extremely stable at a broad range of pH and temperature up to 65°C, in presence of 5 mM of CaCl2. In order to overcome the enzymatic inhibition problem observed in wild-type strains, GluHB2 gene was integrated into the genome of B. subtilis HB2 and the recombinant strain was named HB2G. The correlation of glucanase production with bacterial growth shows that the level of expression of HB2G remains low and relatively comparable to the wild-type strain. But in terms of productivity, the HB2G strain is more productive throughout bacterial culture. This low production and growth of the recombinant strain can be attributed to the toxicity of the overexpression of the glucanase gene under a constitutive promoter.

  • Open access
  • 37 Reads
PANELFIT-LAWSci-02 Workshop: H2020 Challenges in Law, Technology, Life, and Social Sciences

Dear colleagues worldwide,

Welcome to the workshop PANELFIT-LAWSci-02, H2020 Challenges in Law, Technology, Life, and Social Sciences; which was held from 2018-Nov-01 to 2019-Jan-25, MDPI AG, SciForum Platform, Basel, Switzerland. This workshop is associated to the European Commission Project PANELFIT H2020. In this sense, the workshop series will help to attract the attention of the pubic worldwide over the topics of the project. The project is concerned about changes in the regulation of ICT research and innovation are opening up a new scenario. It is expected that stakeholders, policy makers, and end users adapt to them as soon as possible. This, however, might be hard, especially for SMEs. PANELFIT is firmly committed to facilitating this adaptation process by producing a set of editable, open access Guidelines, validated by two data protection agencies. Once produced, they will serve as operational standards able to reduce the ethical and legal issues posed by ICT technologies while promoting innovation and market growth, enabling high-quality job creation and ensuring an adequate level of privacy and security/cybersecurity.
Furthermore, we will produce a complementary set of six outcomes to 1) suggest possible concrete improvements to the current regulatory and governance framework, both at the EU and the national level, 2) create mutual learning and support tools and to promote networking among stakeholders and policy makers and 3) increase the quantity and quality of the information available to policy makers, professionals, researchers, journalists and the public.

All these outcomes will be produced by a co-creation process involving policy makers, stakeholders, and end-users. They will all participate in the creation of the main outcomes of the project through a range of engagement activities that includes workshops, public consultations, encounters, surveys, etc. This will be combined with a strong communication and dissemination strategy that includes numerous activities, such as webinars, MOOC courses, public debates, a constant use of a web site and social networks and the creation of a Platform for Mutual Learning, which is meant to become the reference forum for the discussion of the issues at stake even after the end of the project. The participation in PANELFIT of the European Data Journalism Network, with an aggregated web audience of almost 70 million monthly visits will help us reach this aim.

In this sense, LAWSci workshop series associated this year to PANELFIT Project in order to promote multidisciplinary collaborations and debate in the frontiers of Law, Technology, Life, and Social Sciences. The interaction between bio-science and ICTs has forged great developments in many fields. However, the appreciation of these discoveries is sadly, all too often, accompanied by a lack of understanding of the legal implications. This conference series aims to provide a reference to the various legal avenues that are available for the protection of scientific advances, but also the legal instruments to protect society from unwanted effects. It constitutes a study of some of the legal implications of bioscience and ICT advances, weighing their impact on society and the law's role in shaping that effect.

The presentations will be focused on legal trends in different fields covering, but not limited to: patentability in plants and human genomics, clinical procedures’ standards, patients’ personal data protection, informed consent, regulatory issues in drug discovery, biomedical research legislation, toxicology, medico-legal problems such as healthcare malpractice, medical insurance or ethics in medical practice, software protection in chemo-informatics, bioinformatics, medical informatics, and social sciences, taxes in the biotechnology industry and causality/liability in environmental pollution, criminology, etc. The conference will run on-line and free, saving traveling and participation costs (subscriptions, open publication, participation in forum, certificates, etc., are free of cost).

  • Open access
  • 40 Reads
The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field

Due to the recent increase in computing power, the molecular modeling community has been focused on improving the accuracy and overall quality of biomolecular simulations. These technological improvements centered on the development of new force fields and simulation packages, allowed for more complex and heavier systems to be tackled, while maintaining, or even improving simulations speed. Some force fields, such as GROMOS, have been parameterized and validated using a reaction field (RF), charge groups and a twin-range cutoff scheme (0.8 and 1.4 nm) to treat long range electrostatics [1]. However, in GROMACS software package, the use of group-based cutoff scheme will be deprecated in future versions. As to properly use the newer and faster versions of this simulation package coupled with GROMOS 54A7 and RF, it is crucial to assess the impact on the system sampling when using a single atomistic cutoff (based on the Verlet method) instead of the twin-range group-based scheme.

We reproduced the GROMOS parameterization procedure [1] with both schemes and measured very similar hydration free energy values of small amino acid side chains analogs between both protocols [2]. However, we observed a small, yet significant, difference on the conformational spaces of G1-PAMAM and DMPC when using the atomistic cutoff scheme [2]. The DMPC Al values decrease to a region outside the experimental range, which is not surprising since the force field parameters were optimized for a group-based scheme. Nevertheless, the structural properties for both systems are better converged for the used atomistic cutoff range (1.4-2.0 nm) relative to the group-based cutoff simulation set [2]. The use of a single atomistic cutoff scheme seems a viable approach for MD simulations of biomolecules using G54A7 force field, even if in some cases, new calibration protocols are needed.

(1) Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25, 1656–1676

(2) Silva, T. F. D., Vila-Viçosa, D., Reis, P. B. P. S., Victor, B. L., Diem, M., Oostenbrink, C., and Machuqueiro, M. (2018) "The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field", J. Chem. Theory Comput., 14, 5823-5833