Pub Date : 2018-12-20DOI: 10.3390/mol2net-04-06093
J. Dias, Tomás F D Silva, M. Machuqueiro
{"title":"The pH-dependent membrane stability and insertion mechanism of GALA peptide","authors":"J. Dias, Tomás F D Silva, M. Machuqueiro","doi":"10.3390/mol2net-04-06093","DOIUrl":"https://doi.org/10.3390/mol2net-04-06093","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":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79766797","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 : 2018-12-20DOI: 10.3390/MOL2NET-04-06086
P. Fernandes, Pedro Paiva, S. Sousa, M. Ramos
{"title":"Exploring the Catalytic Mechanism of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase","authors":"P. Fernandes, Pedro Paiva, S. Sousa, M. Ramos","doi":"10.3390/MOL2NET-04-06086","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06086","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":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85103055","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}
In the 40’s, Erwin Chargaff was the first to observe the parity between Adenines (A) and Timinies (T) and Citosines (C) and Guanines (G), in the molecule of DNA. In the 60’s, Chargaff found a second parity rule. This time in a single strand of DNA. The amounts of A’s and T’s, and the amounts of C’s and G’s is similar. The explanation of the first rule is the complementary nature of the double stranded helix of the DNA molecule. However, for the 2nd rule, a biological explanation has remained a mystery. In the last 40 years, a generalization of the second rule was proposed, to explain the 2nd rule as a particular case. This generalization states that for any given k-mer and its reverse complement (RC), the number of times both are found is similar in a single strand of DNA. Two measures have been proposed to test the generalized Chargaff’s 2nd rule (gC2r), both include an artifact regarding the length of the genomes. This has led the authors to think there is a minimum length of a genome and a maximum k-mer for compliance. We propose a new way to measure the compliance of any given genome to the gC2r. The measure is the proportion of the genome which complies with gC2r. The compliance is measured per pair of kmer/k-merRC, using the natural logarithm of the number of times the k-mer is found, divided by the number of times its reverse complement is found in the genome or ln(#k-mer/k-merRC). This measure is independent of the size of the analyzed k-mer and the size of the genome. This measure has been implemented in a software, ChargaffCracker, which can rapidly analyze sequences and deliver a statistical report. We have generated random genomes based on the proportions and lengths of biological prokaryote genome sequences and compared them. We conclude hypothesizing that: 1. The compliance of the gC2r is a consequence, not cause of the 2nd rule and; 2. Although Chargaff’s 2nd rule might be a consequence of transpositions and inversions, the limits of compliance of the gC2r is a property of the sequence model of genomes, not of the biology of organisms. However, this property might have been selected to fulfill biological needs in genome evolution.
{"title":"A proposed new measure to verify the general version of Chargaff 2nd rule.","authors":"Camilo Fuentes Beals, Gonzalo Riadi Mahias, Karen Y. Oróstica, Ignacio Vidal","doi":"10.3390/MOL2NET-04-06090","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06090","url":null,"abstract":"In the 40’s, Erwin Chargaff was the first to observe the parity between Adenines (A) and Timinies (T) and Citosines (C) and Guanines (G), in the molecule of DNA. In the 60’s, Chargaff found a second parity rule. This time in a single strand of DNA. The amounts of A’s and T’s, and the amounts of C’s and G’s is similar. The explanation of the first rule is the complementary nature of the double stranded helix of the DNA molecule. However, for the 2nd rule, a biological explanation has remained a mystery. In the last 40 years, a generalization of the second rule was proposed, to explain the 2nd rule as a particular case. This generalization states that for any given k-mer and its reverse complement (RC), the number of times both are found is similar in a single strand of DNA. Two measures have been proposed to test the generalized Chargaff’s 2nd rule (gC2r), both include an artifact regarding the length of the genomes. This has led the authors to think there is a minimum length of a genome and a maximum k-mer for compliance. We propose a new way to measure the compliance of any given genome to the gC2r. The measure is the proportion of the genome which complies with gC2r. The compliance is measured per pair of kmer/k-merRC, using the natural logarithm of the number of times the k-mer is found, divided by the number of times its reverse complement is found in the genome or ln(#k-mer/k-merRC). This measure is independent of the size of the analyzed k-mer and the size of the genome. This measure has been implemented in a software, ChargaffCracker, which can rapidly analyze sequences and deliver a statistical report. We have generated random genomes based on the proportions and lengths of biological prokaryote genome sequences and compared them. We conclude hypothesizing that: 1. The compliance of the gC2r is a consequence, not cause of the 2nd rule and; 2. Although Chargaff’s 2nd rule might be a consequence of transpositions and inversions, the limits of compliance of the gC2r is a property of the sequence model of genomes, not of the biology of organisms. However, this property might have been selected to fulfill biological needs in genome evolution.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88651227","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 : 2018-12-20DOI: 10.3390/mol2net-04-06089
Juliana F. Rocha, David S. Freitas, Jennifer Noro, C. Teixeira, Cristina E. A. Sousa, S. Sousa, M. Alves, N. Cerqueira
{"title":"Combined experimental and computational studies devoted to the synthesis of 1,4-lactones","authors":"Juliana F. Rocha, David S. Freitas, Jennifer Noro, C. Teixeira, Cristina E. A. Sousa, S. Sousa, M. Alves, N. Cerqueira","doi":"10.3390/mol2net-04-06089","DOIUrl":"https://doi.org/10.3390/mol2net-04-06089","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":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89156731","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 : 2018-12-20DOI: 10.3390/MOL2NET-04-06088
C. Teixeira, S. Sousa, N. Cerqueira
{"title":"Unraveling the catalytic mechanism of Tryptophan synthase, a drug target against Mycobacterium tuberculosis","authors":"C. Teixeira, S. Sousa, N. Cerqueira","doi":"10.3390/MOL2NET-04-06088","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06088","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":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80896998","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 : 2018-12-19DOI: 10.3390/mol2net-04-06083
J. A. Morales, A. Mulholland, R. A. Fritz, M. Kamp, J. Spencer
{"title":"Understanding the covalent inhibition of Clavulanate against β-lactamases (TEM-1 and KPC-2) with QM/MM screening methods.","authors":"J. A. Morales, A. Mulholland, R. A. Fritz, M. Kamp, J. Spencer","doi":"10.3390/mol2net-04-06083","DOIUrl":"https://doi.org/10.3390/mol2net-04-06083","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":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90672470","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 : 2018-12-19DOI: 10.3390/MOL2NET-04-06081
Bernabé Ortega-Tenezaca, Viviana F Quevedo-Tumailli, Lenin Ochoa Carrión, Ronny Rodríguez Cabrera, Luis Uvidia Armijo
{"title":"MVVM design pattern for asynchronous events in information system","authors":"Bernabé Ortega-Tenezaca, Viviana F Quevedo-Tumailli, Lenin Ochoa Carrión, Ronny Rodríguez Cabrera, Luis Uvidia Armijo","doi":"10.3390/MOL2NET-04-06081","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06081","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":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86927526","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 : 2018-12-19DOI: 10.3390/MOL2NET-04-06082
Nuno F. B. Oliveira, Inês D. S. Pires, M. Machuqueiro
{"title":"New phosphorylated amino acid parametrization to correctly reproduce their acid/base equilibria, including in protein binding events","authors":"Nuno F. B. Oliveira, Inês D. S. Pires, M. Machuqueiro","doi":"10.3390/MOL2NET-04-06082","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06082","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":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74849118","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 : 2018-12-19DOI: 10.3390/MOL2NET-04-06079
Rita P. Magalhães, Tatiana F. Vieira, Henrique S. Fernandes, N. Cerqueira, André Melo, M. Simões, S. Sousa
Biofilms can be prevalent in natural, industrial and hospital settings and are associated to ca. 80% of all human infections 1. The increased antimicrobial resistance and mutation rate of bacteria in biofilms contributes to the development of antibiotic resistance, greatly limiting the therapeutic options to a variety of infections, posing a critical problem to the biomedical sector. Preventing biofilm formation could dramatically reduce the effects of infectious diseases 2. Quorum-sensing (QS) is the cell-to-cell communication in bacteria and contributes to the formation of organized structural communities of bacteria in biofilms 3. Several different microbial-derived signaling molecule types and receptors have been recently identified, offering a very appealing opportunity for rational design of new drugs. This work reports the creation of a database containing all the available experimental X-ray structures for all the synthases and receptors known to be involved in quorum sensing and includes also structural and biological information on all the known compounds with demonstrated inhibitory activity against each of these protein targets. This database will provide useful atomic-level information for researchers working on this field with direct application in drug design and development efforts through docking, virtual screening, molecular dynamics and QSAR techniques. Worthington, R. J.; Richards, J. J.; Melander, C., Small molecule control of bacterial biofilms. Organic & biomolecular chemistry 2012, 10 (37), 7457-74. Subhadra, B.; Kim, D. H.; Woo, K.; Surendran, S.; Choi, C. H., Control of Biofilm Formation in Healthcare: Recent Advances Exploiting Quorum-Sensing Interference Strategies and Multidrug Efflux Pump Inhibitors. Materials (Basel, Switzerland) 2018, 11 (9). Banerjee, G.; Ray, A. K., Quorum-sensing network-associated gene regulation in Gram-positive bacteria. Acta microbiologica et immunologica Hungarica 2017, 64 (4), 439-453.
{"title":"Creation of a Structural Database for Inhibition of Biofilm Formation","authors":"Rita P. Magalhães, Tatiana F. Vieira, Henrique S. Fernandes, N. Cerqueira, André Melo, M. Simões, S. Sousa","doi":"10.3390/MOL2NET-04-06079","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06079","url":null,"abstract":"Biofilms can be prevalent in natural, industrial and hospital settings and are associated to ca. 80% of all human infections 1. The increased antimicrobial resistance and mutation rate of bacteria in biofilms contributes to the development of antibiotic resistance, greatly limiting the therapeutic options to a variety of infections, posing a critical problem to the biomedical sector. Preventing biofilm formation could dramatically reduce the effects of infectious diseases 2. \u0000 Quorum-sensing (QS) is the cell-to-cell communication in bacteria and contributes to the formation of organized structural communities of bacteria in biofilms 3. Several different microbial-derived signaling molecule types and receptors have been recently identified, offering a very appealing opportunity for rational design of new drugs. \u0000 This work reports the creation of a database containing all the available experimental X-ray structures for all the synthases and receptors known to be involved in quorum sensing and includes also structural and biological information on all the known compounds with demonstrated inhibitory activity against each of these protein targets. \u0000 This database will provide useful atomic-level information for researchers working on this field with direct application in drug design and development efforts through docking, virtual screening, molecular dynamics and QSAR techniques. \u0000 Worthington, R. J.; Richards, J. J.; Melander, C., Small molecule control of bacterial biofilms. Organic & biomolecular chemistry 2012, 10 (37), 7457-74. \u0000 Subhadra, B.; Kim, D. H.; Woo, K.; Surendran, S.; Choi, C. H., Control of Biofilm Formation in Healthcare: Recent Advances Exploiting Quorum-Sensing Interference Strategies and Multidrug Efflux Pump Inhibitors. Materials (Basel, Switzerland) 2018, 11 (9). \u0000 Banerjee, G.; Ray, A. K., Quorum-sensing network-associated gene regulation in Gram-positive bacteria. Acta microbiologica et immunologica Hungarica 2017, 64 (4), 439-453.","PeriodicalId":20475,"journal":{"name":"Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77178392","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 : 2018-12-19DOI: 10.3390/MOL2NET-04-06084
Sateesh Kumar Vemula, R. Jadi, Sridhar Gummadi, Raja Sridhar Rao. Ponugoti
{"title":"Development and characterization of isradipine compression coated controlled release mini-tablets","authors":"Sateesh Kumar Vemula, R. Jadi, Sridhar Gummadi, Raja Sridhar Rao. Ponugoti","doi":"10.3390/MOL2NET-04-06084","DOIUrl":"https://doi.org/10.3390/MOL2NET-04-06084","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":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80919189","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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