Pub Date : 2018-12-17DOI: 10.3390/mol2net-04-05922
Pedro R. Magalhães, Diogo Vila-Viçosa, Tomás F D Silva, M. Machuqueiro
{"title":"pH effects on PG/PC and PS/PC lipid binary mixtures","authors":"Pedro R. Magalhães, Diogo Vila-Viçosa, Tomás F D Silva, M. Machuqueiro","doi":"10.3390/mol2net-04-05922","DOIUrl":"https://doi.org/10.3390/mol2net-04-05922","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85352554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/mol2net-04-05925
A. Santiago, Carlos Soto, H. Fraire, B. Dorronsoro
Graphical Abstract Abstract. High-Performance Computing (HPC) is a growing necessity of our technological society, HPC demands high loads of parallel computing jobs, an optimal scheduling of the parallel applications tasks is a priority to meet the demands of its users on time. Branch-and-bound (BB) Algorithms and Mathematical Programming (MP) solve complex optimization problems in an optimal manner, some MP or BB even have parallel computing capabilities, making them suitable solutions to solve realworld problems. In this paper, we propose two exact algorithms, a BB and an MP Model for scheduling precedence-constrained applications, on heterogeneous computing systems, as far as we known the first ones on his kind presented in the state of the art. One major contribution of the work is the proposed formulations of the objective function in both methods. Experimental results obtained more than twenty optimal values for synthetic applications from the literature.
{"title":"Optimal Scheduling for Precedence-Constrained Applications on Heterogeneous Machines","authors":"A. Santiago, Carlos Soto, H. Fraire, B. Dorronsoro","doi":"10.3390/mol2net-04-05925","DOIUrl":"https://doi.org/10.3390/mol2net-04-05925","url":null,"abstract":"Graphical Abstract Abstract. High-Performance Computing (HPC) is a growing necessity of our technological society, HPC demands high loads of parallel computing jobs, an optimal scheduling of the parallel applications tasks is a priority to meet the demands of its users on time. Branch-and-bound (BB) Algorithms and Mathematical Programming (MP) solve complex optimization problems in an optimal manner, some MP or BB even have parallel computing capabilities, making them suitable solutions to solve realworld problems. In this paper, we propose two exact algorithms, a BB and an MP Model for scheduling precedence-constrained applications, on heterogeneous computing systems, as far as we known the first ones on his kind presented in the state of the art. One major contribution of the work is the proposed formulations of the objective function in both methods. Experimental results obtained more than twenty optimal values for synthetic applications from the literature.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75762381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-06005
N. Cerqueira, A. Pina, S. Sousa
.
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{"title":"Application of QM/MM Methods in the Study of PNPOx","authors":"N. Cerqueira, A. Pina, S. Sousa","doi":"10.3390/MOL2NET-04-06005","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06005","url":null,"abstract":".","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78569468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-06007
João P. Luís, Ana I Mata, N. Alves, Carlos J. V. Simões, João Pereira-Vaz, Daniela C. Vaz, V. Duque, R. Brito
One of the main challenges facing the development of effective anti HIV-1 medicines relates to the high mutation rate of essential enzymes, such as HIV-1 Protease (HIV1Pr).[1] Pereira Vaz et al. [2] first reported a threonine insertion at position 35 (E35E_T), in the HIV1Pr coding region, among treatment-naive subtype C infected individuals. Undetectable viral loads were attained after antiretroviral therapy in such individuals, with no associated major mutations, implying null contribution of E35E_T to viral resistance. Interestingly, a new study suggests a potential additive effect of position 35 insertions when in presence of major mutations – ultimately leading to resistance to HIV1Pr inhibitors in higher extent. [3] In order to study the role of the E35E_T insertion in the structure and ligand-binding propensity of HIV1Pr, homology models were generated from subtype B and subtype C base sequences, using available X-ray structures corresponding to highest identity sequences as template. Fifty (50)-nanoseconds Molecular Dynamics (MD) simulations were then performed for unbound and bound (HIV1PR:darunavir complex) structures of the wild-type form and a single‑point major mutation variant of HIV1PR – in all cases in presence and absence of E35_T. Combining simple measurements like the root mean square (RMS) deviations and fluctuations, applied to the whole protein and to its two functional flap regions, with principal component analysis (PCA) of the multiple MD trajectories, we herein contrast the behaviour of all systems in attempt to dissect the putative role of E35E_T in the resistance towards HIV1PR inhibitors.
{"title":"Influence of codon 35 amino acid insertion in HIV-1 protease: insights from molecular dynamics","authors":"João P. Luís, Ana I Mata, N. Alves, Carlos J. V. Simões, João Pereira-Vaz, Daniela C. Vaz, V. Duque, R. Brito","doi":"10.3390/MOL2NET-04-06007","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06007","url":null,"abstract":"One of the main challenges facing the development of effective anti HIV-1 medicines relates to the high mutation rate of essential enzymes, such as HIV-1 Protease (HIV1Pr).[1] Pereira Vaz et al. [2] first reported a threonine insertion at position 35 (E35E_T), in the HIV1Pr coding region, among treatment-naive subtype C infected individuals. Undetectable viral loads were attained after antiretroviral therapy in such individuals, with no associated major mutations, implying null contribution of E35E_T to viral resistance. Interestingly, a new study suggests a potential additive effect of position 35 insertions when in presence of major mutations – ultimately leading to resistance to HIV1Pr inhibitors in higher extent. [3] \u0000In order to study the role of the E35E_T insertion in the structure and ligand-binding propensity of HIV1Pr, homology models were generated from subtype B and subtype C base sequences, using available X-ray structures corresponding to highest identity sequences as template. Fifty (50)-nanoseconds Molecular Dynamics (MD) simulations were then performed for unbound and bound (HIV1PR:darunavir complex) structures of the wild-type form and a single‑point major mutation variant of HIV1PR – in all cases in presence and absence of E35_T. \u0000Combining simple measurements like the root mean square (RMS) deviations and fluctuations, applied to the whole protein and to its two functional flap regions, with principal component analysis (PCA) of the multiple MD trajectories, we herein contrast the behaviour of all systems in attempt to dissect the putative role of E35E_T in the resistance towards HIV1PR inhibitors.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85417128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-06004
N. Cerqueira, Henrique S. Fernandes, S. Sousa
The 5,10-methylenetetrahydrofolate (5,10-mTHF) is a cofactor essential for the synthesis of purines and thymidine, which are crucial for the cell viability.[1] The α-elimination of ʟ-serine, catalyzed by the serine hydroxymethyltransferase (SHMT), is the primary source of 5,10-mTHF in the cell. However, the catalytic mechanism behind the synthesis of 5,10-mTHF was unknown, and two divergent theories were proposed for the mechanism. Some authors suggested that the final steps of the 5,10-mTHF synthesis occur in the cytoplasm whereas other authors showed some evidence that the reaction must occur inside the SHMT. [2] In this study, we addressed the entire catalytic mechanism of the PLP-dependent enzyme SHMT using a QM/MM approach and the mechanism of 5,10-mTHF synthesis in aqueous solution. The calculations were prepared and analyzed using molUP [3] for VMD and run on Gaussian09 and ORCA. This work [4] resulted in the entire e detailed catalytic mechanism of SHMT. The results showed that both hypotheses for the synthesis of 5,10-mTHF shared the two first steps where the -OH group is transferred from the serine to the THF. These reactions occur inside the SHMT and have a ∆G‡ of 18.0 and 2.0 kcal/mol. Then, the reaction can proceed inside the enzyme through 5 sequential steps or in the cytoplasm where only 3 steps are needed. The calculations showed that the mechanism is kinetic and thermodynamically favorable by 0.8 and 24.3 kcal/mol, respectively, when it takes place inside the SHMT. Although the reaction is not impossible in solution, it is very improbable that the THF intermediate might be released to the cytoplasm to overcome a set of reactions that are less favorable when compared to the ones that would occur in the SHMT. Reference [1] Froese, D. S.; et al., Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nature comm 2018, 9 (1), 2261-2261. [2] Schirch, V.; et al, Serine hydroxymethyltransferase revisited. Curr Opin Chem Biol 2005, 9 (5), 482-7. [3] Fernandes, H. S.; et al., molUP: A VMD plugin to handle QM and ONIOM calculations using the Gaussian software. J Comput Chem 2018, 39 (19), 1344-1353. [4] Fernandes, H. S.; et al., Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catalysis 2018, 10096-10110. Acknowledgments FCT (SFRH/BD/115396/2016, IF/01310/2013, IF/00052/2014 e PTDC/QUI-QFI/31689/2017)
{"title":"Is the 5,10-methylenetetrahydrofolate cofactor synthesized through a non-enzymatic or enzymatic mechanism?","authors":"N. Cerqueira, Henrique S. Fernandes, S. Sousa","doi":"10.3390/MOL2NET-04-06004","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06004","url":null,"abstract":"The 5,10-methylenetetrahydrofolate (5,10-mTHF) is a cofactor essential for the synthesis of purines and thymidine, which are crucial for the cell viability.[1] The α-elimination of ʟ-serine, catalyzed by the serine hydroxymethyltransferase (SHMT), is the primary source of 5,10-mTHF in the cell. However, the catalytic mechanism behind the synthesis of 5,10-mTHF was unknown, and two divergent theories were proposed for the mechanism. Some authors suggested that the final steps of the 5,10-mTHF synthesis occur in the cytoplasm whereas other authors showed some evidence that the reaction must occur inside the SHMT. [2] \u0000In this study, we addressed the entire catalytic mechanism of the PLP-dependent enzyme SHMT using a QM/MM approach and the mechanism of 5,10-mTHF synthesis in aqueous solution. The calculations were prepared and analyzed using molUP [3] for VMD and run on Gaussian09 and ORCA. \u0000This work [4] resulted in the entire e detailed catalytic mechanism of SHMT. The results showed that both hypotheses for the synthesis of 5,10-mTHF shared the two first steps where the -OH group is transferred from the serine to the THF. These reactions occur inside the SHMT and have a ∆G‡ of 18.0 and 2.0 kcal/mol. Then, the reaction can proceed inside the enzyme through 5 sequential steps or in the cytoplasm where only 3 steps are needed. The calculations showed that the mechanism is kinetic and thermodynamically favorable by 0.8 and 24.3 kcal/mol, respectively, when it takes place inside the SHMT. Although the reaction is not impossible in solution, it is very improbable that the THF intermediate might be released to the cytoplasm to overcome a set of reactions that are less favorable when compared to the ones that would occur in the SHMT. \u0000 \u0000Reference \u0000[1] Froese, D. S.; et al., Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nature comm 2018, 9 (1), 2261-2261. \u0000[2] Schirch, V.; et al, Serine hydroxymethyltransferase revisited. Curr Opin Chem Biol 2005, 9 (5), 482-7. \u0000[3] Fernandes, H. S.; et al., molUP: A VMD plugin to handle QM and ONIOM calculations using the Gaussian software. J Comput Chem 2018, 39 (19), 1344-1353. \u0000[4] Fernandes, H. S.; et al., Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catalysis 2018, 10096-10110. \u0000 \u0000Acknowledgments \u0000FCT (SFRH/BD/115396/2016, IF/01310/2013, IF/00052/2014 e PTDC/QUI-QFI/31689/2017)","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76395178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/MOL2NET-04-05920
Viviana Quevedo, Bernabé Ortega-Tenezaca
{"title":"Use of integrated software, applied to the elaboration of didactic material for students with hearing disability at the basic intercultural education center of deaf","authors":"Viviana Quevedo, Bernabé Ortega-Tenezaca","doi":"10.3390/MOL2NET-04-05920","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-05920","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74338328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-17DOI: 10.3390/mol2net-04-06008
M. F. Matus, I. Palomo, C. Vilos
{"title":"COMPUTATIONAL STUDY OF HYBRID PLA-PEG NANOPARTICLES AS ANTIPLATELET DRUG CARRIERS","authors":"M. F. Matus, I. Palomo, C. Vilos","doi":"10.3390/mol2net-04-06008","DOIUrl":"https://doi.org/10.3390/mol2net-04-06008","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83711611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-16DOI: 10.3390/mol2net-04-05914
A. Akremi, Mouna Jlidi, Adel Haj Brahim, M. Ali, L. Daoud, Houda Hmani, S. Bejar, Naser Aliye Feto, Mamdouh Ben Ali
{"title":"Isolation of Erwinia amylovora Bacteriophage from Soil and Pear Trees Plant Tissues","authors":"A. Akremi, Mouna Jlidi, Adel Haj Brahim, M. Ali, L. Daoud, Houda Hmani, S. Bejar, Naser Aliye Feto, Mamdouh Ben Ali","doi":"10.3390/mol2net-04-05914","DOIUrl":"https://doi.org/10.3390/mol2net-04-05914","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90212384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-16DOI: 10.3390/mol2net-04-05918
N. Semmar, M. Farman, Asma Hammami, A. Sarraj-Laabidi
{"title":"Mini-review on the applications and perspectives of a new simplex machine learning approach in chemistry and biology","authors":"N. Semmar, M. Farman, Asma Hammami, A. Sarraj-Laabidi","doi":"10.3390/mol2net-04-05918","DOIUrl":"https://doi.org/10.3390/mol2net-04-05918","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90464254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-12-16DOI: 10.3390/mol2net-04-05915
N. Charanraj
{"title":"LIVER CANCER IN CHILDREN","authors":"N. Charanraj","doi":"10.3390/mol2net-04-05915","DOIUrl":"https://doi.org/10.3390/mol2net-04-05915","url":null,"abstract":"","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81745140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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