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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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2
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Braga C, Martelli CMT, Souza WV, Luna CF, Albuquerque MDFPM, Mariz CA, Morais CNL, Brito CAA, Melo CFCA, Lins RD, Drexler JF, Jaenisch T, Marques ETA, Viana IFT. Seroprevalence of Dengue, Chikungunya and Zika at the epicenter of the congenital microcephaly epidemic in Northeast Brazil: A population-based survey. PLoS Negl Trop Dis 2023; 17:e0011270. [PMID: 37399197 DOI: 10.1371/journal.pntd.0011270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The four Dengue viruses (DENV) serotypes were re-introduced in Brazil's Northeast region in a couple of decades, between 1980's and 2010's, where the DENV1 was the first detected serotype and DENV4 the latest. Zika (ZIKV) and Chikungunya (CHIKV) viruses were introduced in Recife around 2014 and led to large outbreaks in 2015 and 2016, respectively. However, the true extent of the ZIKV and CHIKV outbreaks, as well as the risk factors associated with exposure to these viruses remain vague. METHODS We conducted a stratified multistage household serosurvey among residents aged between 5 and 65 years in the city of Recife, Northeast Brazil, from August 2018 to February 2019. The city neighborhoods were stratified and divided into high, intermediate, and low socioeconomic strata (SES). Previous ZIKV, DENV and CHIKV infections were detected by IgG-based enzyme linked immunosorbent assays (ELISA). Recent ZIKV and CHIKV infections were assessed through IgG3 and IgM ELISA, respectively. Design-adjusted seroprevalence were estimated by age group, sex, and SES. The ZIKV seroprevalence was adjusted to account for the cross-reactivity with dengue. Individual and household-related risk factors were analyzed through regression models to calculate the force of infection. Odds Ratio (OR) were estimated as measure of effect. PRINCIPAL FINDINGS A total of 2,070 residents' samples were collected and analyzed. The force of viral infection for high SES were lower as compared to low and intermediate SES. DENV seroprevalence was 88.7% (CI95%:87.0-90.4), and ranged from 81.2% (CI95%:76.9-85.6) in the high SES to 90.7% (CI95%:88.3-93.2) in the low SES. The overall adjusted ZIKV seroprevalence was 34.6% (CI95%:20.0-50.9), and ranged from 47.4% (CI95%:31.8-61.5) in the low SES to 23.4% (CI95%:12.2-33.8) in the high SES. The overall CHIKV seroprevalence was 35.7% (CI95%:32.6-38.9), and ranged from 38.6% (CI95%:33.6-43.6) in the low SES to 22.3% (CI95%:15.8-28.8) in the high SES. Surprisingly, ZIKV seroprevalence rapidly increased with age in the low and intermediate SES, while exhibited only a small increase with age in high SES. CHIKV seroprevalence according to age was stable in all SES. The prevalence of serological markers of ZIKV and CHIKV recent infections were 1.5% (CI95%:0.1-3.7) and 3.5% (CI95%:2.7-4.2), respectively. CONCLUSIONS Our results confirmed continued DENV transmission and intense ZIKV and CHIKV transmission during the 2015/2016 epidemics followed by ongoing low-level transmission. The study also highlights that a significant proportion of the population is still susceptible to be infected by ZIKV and CHIKV. The reasons underlying a ceasing of the ZIKV epidemic in 2017/18 and the impact of antibody decay in susceptibility to future DENV and ZIKV infections may be related to the interplay between disease transmission mechanism and actual exposure in the different SES.
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Affiliation(s)
- Cynthia Braga
- Department of Parasitology, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Celina M T Martelli
- Department of Public Health, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Wayner V Souza
- Department of Public Health, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Carlos F Luna
- Department of Public Health, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | - Carolline A Mariz
- Department of Parasitology, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Clarice N L Morais
- Department of Virology, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Carlos A A Brito
- Department of Clinical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Roberto D Lins
- Department of Virology, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
| | - Thomas Jaenisch
- Section Clinical Tropical Medicine, Department of Infectious Diseases, Heidelberg University Hospital, Germany
- German Centre for Infection Research (DZIF), Heidelberg Site, Heidelberg, Germany
- Center for Global Health, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Ernesto T A Marques
- Department of Virology, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Isabelle F T Viana
- Department of Virology, Institute Aggeu Magalhães, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
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3
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Maciel L, Ferraz MVF, Oliveira AA, Lins RD, dos Anjos J, Guido RVC, Soares TA. Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses. ACS Bio Med Chem Au 2023; 3:211-222. [PMID: 37101811 PMCID: PMC10125267 DOI: 10.1021/acsbiomedchemau.2c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 04/28/2023]
Abstract
Arboviral infections such as Zika, chikungunya, dengue, and yellow fever pose significant health problems globally. The population at risk is expanding with the geographical distribution of the main transmission vector of these viruses, the Aedes aegypti mosquito. The global spreading of this mosquito is driven by human migration, urbanization, climate change, and the ecological plasticity of the species. Currently, there are no specific treatments for Aedes-borne infections. One strategy to combat different mosquito-borne arboviruses is to design molecules that can specifically inhibit a critical host protein. We obtained the crystal structure of 3-hydroxykynurenine transaminase (AeHKT) from A. aegypti, an essential detoxification enzyme of the tryptophan metabolism pathway. Since AeHKT is found exclusively in mosquitoes, it provides the ideal molecular target for the development of inhibitors. Therefore, we determined and compared the free binding energy of the inhibitors 4-(2-aminophenyl)-4-oxobutyric acid (4OB) and sodium 4-(3-phenyl-1,2,4-oxadiazol-5-yl)butanoate (OXA) to AeHKT and AgHKT from Anopheles gambiae, the only crystal structure of this enzyme previously known. The cocrystallized inhibitor 4OB binds to AgHKT with K i of 300 μM. We showed that OXA binds to both AeHKT and AgHKT enzymes with binding energies 2-fold more favorable than the crystallographic inhibitor 4OB and displayed a 2-fold greater residence time τ upon binding to AeHKT than 4OB. These findings indicate that the 1,2,4-oxadiazole derivatives are inhibitors of the HKT enzyme not only from A. aegypti but also from A. gambiae.
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Affiliation(s)
- Larissa
G. Maciel
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, 50740-560 Recife, Brazil
| | - Matheus V. F. Ferraz
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, 50740-560 Recife, Brazil
- Aggeu
Magalhães Institute, Oswaldo Cruz
Foundation, 50740-465 Recife, Brazil
| | - Andrew A. Oliveira
- São
Carlos Institute of Physics, University
of São Paulo, 13563-120 São Carlos, Brazil
| | - Roberto D. Lins
- Aggeu
Magalhães Institute, Oswaldo Cruz
Foundation, 50740-465 Recife, Brazil
| | - Janaína
V. dos Anjos
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, 50740-560 Recife, Brazil
| | - Rafael V. C. Guido
- São
Carlos Institute of Physics, University
of São Paulo, 13563-120 São Carlos, Brazil
| | - Thereza A. Soares
- Department
of Chemistry, University of São Paulo, 055508-090 Ribeirão
Preto, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
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4
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Ferraz MVF, Neto JCS, Lins RD, Teixeira ES. An artificial neural network model to predict structure-based protein-protein free energy of binding from Rosetta-calculated properties. Phys Chem Chem Phys 2023; 25:7257-7267. [PMID: 36810523 DOI: 10.1039/d2cp05644e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The prediction of the free energy (ΔG) of binding for protein-protein complexes is of general scientific interest as it has a variety of applications in the fields of molecular and chemical biology, materials science, and biotechnology. Despite its centrality in understanding protein association phenomena and protein engineering, the ΔG of binding is a daunting quantity to obtain theoretically. In this work, we devise a novel Artificial Neural Network (ANN) model to predict the ΔG of binding for a given three-dimensional structure of a protein-protein complex with Rosetta-calculated properties. Our model was tested using two data sets, and it presented a root-mean-square error ranging from 1.67 kcal mol-1 to 2.45 kcal mol-1, showing a better performance compared to the available state-of-the-art tools. Validation of the model for a variety of protein-protein complexes is showcased.
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Affiliation(s)
- Matheus V F Ferraz
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, FIOCRUZ, Recife, PE, Brazil.,Department of Fundamental Chemistry, Federal University of Pernambuco, UFPE, Recife, PE, Brazil.,Heidelberg Institute for Theoretical Studies, HITS, Heidelberg, Germany
| | - José C S Neto
- Recife Center for Advanced Studies and Systems, CESAR, Recife, PE, Brazil.
| | - Roberto D Lins
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, FIOCRUZ, Recife, PE, Brazil.,Department of Fundamental Chemistry, Federal University of Pernambuco, UFPE, Recife, PE, Brazil
| | - Erico S Teixeira
- Recife Center for Advanced Studies and Systems, CESAR, Recife, PE, Brazil.
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5
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Santos RCM, Lucena DMS, Loponte HFBR, Alisson-Silva F, Dias WB, Lins RD, Todeschini AR. GM2/GM3 controls the organizational status of CD82/Met microdomains: further studies in GM2/GM3 complexation. Glycoconj J 2022; 39:653-661. [PMID: 35536494 DOI: 10.1007/s10719-022-10061-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
At cell surface gangliosides might associate with signal transducers proteins, grown factor receptors, integrins, small G-proteins and tetraspanins establishing microdomains, which play important role in cell adhesion, cell activation, motility, and growth. Previously, we reported that GM2 and GM3 form a heterodimer that interacts with the tetraspanin CD82, controlling epithelial cell mobility by inhibiting integrin-hepatocyte growth factor-induced cMet tyrosine kinase signaling. By using molecular dynamics simulations to study the molecular basis of GM2/GM3 interaction we demonstrate, here, that intracellular levels of Ca2+ mediate GM2/GM3 complexation via electrostatic interaction with their carboxyl groups, while hydrogen bonds between the ceramide groups likely aid stabilizing the complex. The presence of GM2/GM3 complex alters localization of CD82 on cell surface and therefore downstream signalization. These data contribute for the knowledge of how glycosylation may control signal transduction and phenotypic changes.
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Affiliation(s)
- Ronan C M Santos
- Carlos Chagas Filho Biophysics' Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela M S Lucena
- Carlos Chagas Filho Biophysics' Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hector F B R Loponte
- Carlos Chagas Filho Biophysics' Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Frederico Alisson-Silva
- Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Wagner B Dias
- Carlos Chagas Filho Biophysics' Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Roberto D Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, 50740-465, Brazil
| | - Adriane R Todeschini
- Carlos Chagas Filho Biophysics' Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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6
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Loeffler FF, Viana IFT, Fischer N, Coêlho DF, Silva CS, Purificação AF, Araújo CMCS, Leite BHS, Durães-Carvalho R, Magalhães T, Morais CNL, Cordeiro MT, Lins RD, Marques ETA, Jaenisch T. Identification of a Zika NS2B epitope as a biomarker for severe clinical phenotypes. RSC Med Chem 2021; 12:1525-1539. [PMID: 34671736 DOI: 10.1039/d1md00124h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/17/2021] [Indexed: 01/04/2023] Open
Abstract
The identification of specific biomarkers for Zika infection and its clinical complications is fundamental to mitigate the infection spread, which has been associated with a broad range of neurological sequelae. We present the characterization of antibody responses in serum samples from individuals infected with Zika, presenting non-severe (classical) and severe (neurological disease) phenotypes, with high-density peptide arrays comprising the Zika NS1 and NS2B proteins. The data pinpoints one strongly IgG-targeted NS2B epitope in non-severe infections, which is absent in Zika patients, where infection progressed to the severe phenotype. This differential IgG profile between the studied groups was confirmed by multivariate data analysis. Molecular dynamics simulations and circular dichroism have shown that the peptide in solution presents itself in a sub-optimal conformation for antibody recognition, which led us to computationally engineer an artificial protein able to stabilize the NS2B epitope structure. The engineered protein was used to interrogate paired samples from mothers and their babies presenting Zika-associated microcephaly and confirmed the absence of NS2B IgG response in those samples. These findings suggest that the assessment of antibody responses to the herein identified NS2B epitope is a strong candidate biomarker for the diagnosis and prognosis of Zika-associated neurological disease.
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Affiliation(s)
- Felix F Loeffler
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems Potsdam Germany
| | - Isabelle F T Viana
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Nico Fischer
- Section Clinical Tropical Medicine, Department of Infectious Diseases, Heidelberg University Hospital Germany
| | - Danilo F Coêlho
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil.,Department of Fundamental Chemistry, Federal University of Pernambuco Recife PE Brazil
| | - Carolina S Silva
- Department of Chemical Engineering, Federal University of Pernambuco Recife PE Brazil
| | - Antônio F Purificação
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Catarina M C S Araújo
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Bruno H S Leite
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | | | - Tereza Magalhães
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Clarice N L Morais
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Marli T Cordeiro
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Roberto D Lins
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil
| | - Ernesto T A Marques
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation Recife PE Brazil.,Department of Infectious Diseases and Microbiology, University of Pittsburgh Pittsburgh PA USA
| | - Thomas Jaenisch
- Section Clinical Tropical Medicine, Department of Infectious Diseases, Heidelberg University Hospital Germany .,German Centre for Infection Research (DZIF) Heidelberg Site Heidelberg Germany
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7
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Resende PC, Naveca FG, Lins RD, Dezordi FZ, Ferraz MVF, Moreira EG, Coêlho DF, Motta FC, Paixão ACD, Appolinario L, Lopes RS, Mendonça ACDF, da Rocha ASB, Nascimento V, Souza V, Silva G, Nascimento F, Neto LGL, da Silva FV, Riediger I, Debur MDC, Leite AB, Mattos T, da Costa CF, Pereira FM, dos Santos CA, Rovaris DB, Fernandes SB, Abbud A, Sacchi C, Khouri R, Bernardes AFL, Delatorre E, Gräf T, Siqueira MM, Bello G, Wallau GL. The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein. Virus Evol 2021; 7:veab069. [PMID: 34532067 PMCID: PMC8438916 DOI: 10.1093/ve/veab069] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/29/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022] Open
Abstract
Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. Importantly, we detected the community transmission of different P.1 lineages bearing NTD indels ∆69-70 (which can impact several SARS-CoV-2 diagnostic protocols), ∆144 and ins214ANRN, and a new VOI N.10 derived from the B.1.1.33 lineage carrying three NTD deletions (∆141-144, ∆211, and ∆256-258). These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil generates new viral lineages that might be more resistant to antibody neutralization than parental variants of concern.
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Affiliation(s)
| | | | - Roberto D Lins
- Department of Virology, Instituto Aggeu Magalhães, FIOCRUZ-Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-465, Brazil
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães, FIOCRUZ-Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-465, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães FIOCRUZ-Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-465, Brazil
| | - Matheus V. F Ferraz
- Department of Virology, Instituto Aggeu Magalhães, FIOCRUZ-Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-465, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-560, Brazil
| | - Emerson G Moreira
- Department of Virology, Instituto Aggeu Magalhães, FIOCRUZ-Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-465, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Av. Professor Moraes Rego, s/n – Cidade Universitária, Recife 50.740-560, Brazil
| | | | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Anna Carolina Dias Paixão
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Luciana Appolinario
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Ana Carolina da Fonseca Mendonça
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Alice Sampaio Barreto da Rocha
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Rua Teresina, 476. Adrianópolis, Manaus 69.057-070, Brazil
| | - Victor Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Rua Teresina, 476. Adrianópolis, Manaus 69.057-070, Brazil
| | - George Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Rua Teresina, 476. Adrianópolis, Manaus 69.057-070, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Rua Teresina, 476. Adrianópolis, Manaus 69.057-070, Brazil
| | - Lidio Gonçalves Lima Neto
- Laboratório Central de Saúde Pública do Estado do Maranhão (LACEN-MA), Rua João Luís, Bairro Diamente, Sao Luis 65020-320, Brazil
| | - Fabiano Vieira da Silva
- Laboratório Central de Saúde Pública do Estado do Maranhão (LACEN-MA), Rua João Luís, Bairro Diamente, Sao Luis 65020-320, Brazil
| | - Irina Riediger
- Laboratório Central de Saúde Pública do Estado do Paraná (LACEN-PR), Rua Ubaldino do Amaral 545 - Alto da XV, Curitiba 80060-190, Brazil
| | - Maria do Carmo Debur
- Laboratório Central de Saúde Pública do Estado do Paraná (LACEN-PR), Rua Ubaldino do Amaral 545 - Alto da XV, Curitiba 80060-190, Brazil
| | - Anderson Brandao Leite
- Laboratório Central de Saúde Pública do Estado do Alagoas (LACEN-AL), Av. Marechal Castelo Branco, 1773 Jatiúca, Alagoas, 57030340 Brazil
| | - Tirza Mattos
- Laboratório Central de Saúde Pública do Amazonas (LACEN-AM), Rua Emílio Moreira, 528 - Centro, Manaus 69020-040, Brazil
| | - Cristiano Fernandes da Costa
- Fundação de Vigilância em Saúde do Amazonas, Av. Torquato Tapajós, 4.010 Colônia Santo Antônio, Manaus 69.093-018, Brazil
| | - Felicidade Mota Pereira
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Rua Waldemar Falcão, 123 - Bairro Brotas, Salvador 40295-001, Brazil
| | - Cliomar Alves dos Santos
- Laboratório Central de Saúde Pública do Estado de Sergipe (LACEN-SE), Rua Campo do Brito, 551 - Bairro São José, Aracajú, Sergipe 49020-380, Brazil
| | - Darcita Buerger Rovaris
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Avenida Rio Branco, 152 – Fundos, Florianópolis, Santa Catarina 88015-201, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Avenida Rio Branco, 152 – Fundos, Florianópolis, Santa Catarina 88015-201, Brazil
| | | | - Claudio Sacchi
- Instituto Adolfo Lutz, Av. Dr. Arnaldo, 351, São Paulo 01246-000, Brazil
| | | | - André Felipe Leal Bernardes
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Rua Conde Pereira Carneiro, 80 - Gameleira, Belo Horizonte 30510-010, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Av. Fernando Ferrari, 514 - Goiabeira, Alegre 29075-910, Brazil
| | | | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Av. Brasil, 4365 - Manguinhos, Rio de Janeiro 21040-900, Brazil
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8
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Sonon P, Brito Ferreira ML, Santos Almeida R, Saloum Deghaide NH, Henrique Willcox G, Guimarães EL, da Purificação Júnior AF, Cordeiro MT, Antunes de Brito CA, de Albuquerque MDFM, Lins RD, Donadi EA, Lucena-Silva N. Differential Frequencies of HLA-DRB1, DQA1, and DQB1 Alleles and Haplotypes Are Observed in the Arbovirus-Related Neurological Syndromes. J Infect Dis 2021; 224:517-525. [PMID: 33320259 DOI: 10.1093/infdis/jiaa764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/11/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND We took advantage of the 2015-2016 Brazilian arbovirus outbreak (Zika [ZIKV]/dengue/chikungunya viruses) associated with neurological complications to type HLA-DRB1/DQA1/DQB1 variants in patients exhibiting neurological complications and in bone marrow donors from the same endemic geographical region. METHODS DRB1/DQA1/DQB1 loci were typed using sequence-specific oligonucleotides. In silico studies were performed using X-ray resolved dimer constructions. RESULTS The DQA1*01, DQA1*05, DQB1*02, or DQB1*06 genotypes/haplotypes and DQA1/DQB1 haplotypes that encode the putative DQA1/DQB1 dimers were overrepresented in the whole group of patients and in patients exhibiting peripheral neurological spectrum disorders (PSD) or encephalitis spectrum disorders (ESD). The DRB1*04, DRB1*13, and DQA1*03 allele groups protected against arbovirus neurological manifestation, being underrepresented in whole group of patients and ESD and PSD groups. Genetic and in silico studies revealed that DQA1/DQB1 dimers (1) were primarily associated with susceptibility to arbovirus infections; (2) can bind to a broad range of ZIKV peptides (235 of 1878 peptides, primarily prM and NS2A); and (3) exhibited hydrophilic and highly positively charged grooves when compared to the DRA1/DRB1 cleft. The protective dimer (DRA1/DRB1*04) bound a limited number of ZIKV peptides (40 of 1878 peptides, primarily prM). CONCLUSION Protective haplotypes may recognize arbovirus peptides more specifically than susceptible haplotypes.
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Affiliation(s)
- Paulin Sonon
- Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | - Renata Santos Almeida
- Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | | | | | | | - Marli Tenório Cordeiro
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | | | - Roberto D Lins
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Eduardo A Donadi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Norma Lucena-Silva
- Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
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9
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Ferraz MVF, Moreira EG, Coêlho DF, Wallau GL, Lins RD. Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies. Chem Commun (Camb) 2021; 57:6094-6097. [PMID: 34037640 DOI: 10.1039/d1cc01747k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 VOC immune evasion is mainly due to lower cross-reactivity from previously elicited class I/II neutralizing antibodies, while increased affinity to hACE2 plays a minor role. The affinity between antibodies and VOCs is impacted by remodeling of the electrostatic surface potential of the Spike RBDs. The P.3 variant is a putative VOC.
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10
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Santos ALS, Braga-Silva LA, Gonçalves DS, Ramos LS, Oliveira SSC, Souza LOP, Oliveira VS, Lins RD, Pinto MR, Muñoz JE, Taborda CP, Branquinha MH. Repositioning Lopinavir, an HIV Protease Inhibitor, as a Promising Antifungal Drug: Lessons Learned from Candida albicans-In Silico, In Vitro and In Vivo Approaches. J Fungi (Basel) 2021; 7:jof7060424. [PMID: 34071195 PMCID: PMC8229492 DOI: 10.3390/jof7060424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/20/2022] Open
Abstract
The repurposing strategy was applied herein to evaluate the effects of lopinavir, an aspartic protease inhibitor currently used in the treatment of HIV-infected individuals, on the globally widespread opportunistic human fungal pathogen Candida albicans by using in silico, in vitro and in vivo approaches in order to decipher its targets on fungal cells and its antifungal mechanisms of action. Secreted aspartic proteases (Saps) are the obviously main target of lopinavir. To confirm this hypothesis, molecular docking assays revealed that lopinavir bound to the Sap2 catalytic site of C. albicans as well as inhibited the Sap hydrolytic activity in a typically dose-dependent manner. The inhibition of Saps culminated in the inability of C. albicans yeasts to assimilate the unique nitrogen source (albumin) available in the culture medium, culminating with fungal growth inhibition (IC50 = 39.8 µM). The antifungal action of lopinavir was corroborated by distinct microscopy analyses, which evidenced drastic and irreversible changes in the morphology that justified the fungal death. Furthermore, our results revealed that lopinavir was able to (i) arrest the yeasts-into-hyphae transformation, (ii) disturb the synthesis of neutral lipids, including ergosterol, (iii) modulate the surface-located molecules, such as Saps and mannose-, sialic acid- and N-acetylglucosamine-containing glycoconjugates, (iv) diminish the secretion of hydrolytic enzymes, such as Saps and esterase, (v) negatively influence the biofilm formation on polystyrene surface, (vi) block the in vitro adhesion to epithelial cells, (vii) contain the in vivo infection in both immunocompetent and immunosuppressed mice and (viii) reduce the Sap production by yeasts recovered from kidneys of infected animals. Conclusively, the exposed results highlight that lopinavir may be used as a promising repurposing drug against C. albicans infection as well as may be used as a lead compound for the development of novel antifungal drugs.
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Affiliation(s)
- André L. S. Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
- Programa de Pós-Graduação em Bioquímica (PPGBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil
- Correspondence: (A.L.S.S.); (M.H.B.); Tel.: +55-21-3938-0366 (A.L.S.S.)
| | - Lys A. Braga-Silva
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
- Programa de Pós-Graduação em Bioquímica (PPGBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil
| | - Diego S. Gonçalves
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
- Programa de Pós-Graduação em Bioquímica (PPGBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil
| | - Lívia S. Ramos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
| | - Simone S. C. Oliveira
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
| | - Lucieri O. P. Souza
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
| | - Vanessa S. Oliveira
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife 50740-465, Brazil; (V.S.O.); (R.D.L.)
| | - Roberto D. Lins
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife 50740-465, Brazil; (V.S.O.); (R.D.L.)
| | - Marcia R. Pinto
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense (UFF), Niterói 24210-130, Brazil;
| | - Julian E. Muñoz
- MICROS Group, Medicine Traslacional Institute, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Carlos P. Taborda
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo 05508-060, Brazil;
- Laboratório de Micologia Médica—LIM53/IMTSP, Universidade de São Paulo (USP), São Paulo 05508-000, Brazil
| | - Marta H. Branquinha
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil; (L.A.B.-S.); (D.S.G.); (L.S.R.); (S.S.C.O.); (L.O.P.S.)
- Correspondence: (A.L.S.S.); (M.H.B.); Tel.: +55-21-3938-0366 (A.L.S.S.)
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11
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Rusu VH, Santos DES, Poleto MD, Galheigo MM, Gomes ATA, Verli H, Soares TA, Lins RD. Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations. J Chem Inf Model 2020; 60:5923-5927. [PMID: 33213140 DOI: 10.1021/acs.jcim.0c01168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). The linear least-squares regression method is used to generate sets of parameters that best satisfy the fitting. Rotational Profiler is free to use, analytical, and force field/package independent. The formalism is herein described, and its usage, in an interactive and automated manner, is made available as a Web server at http://rotprof.lncc.br.
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Affiliation(s)
- Victor H Rusu
- Swiss National Supercomputing Centre, Lugano, Ticino 6900, Switzerland
| | - Denys E S Santos
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Pernambuco 50740-640, Brazil
| | - Marcelo D Poleto
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Marcelo M Galheigo
- Brazilian National Scientific Computing Laboratory, Petrópolis, Rio de Janeiro 25651-075, Brazil
| | - Antônio T A Gomes
- Brazilian National Scientific Computing Laboratory, Petrópolis, Rio de Janeiro 25651-075, Brazil
| | - Hugo Verli
- Center for Biotechnology, Federal University of Rio Grande do Sul, Rio Grande do Sul 91500-970, Brazil
| | - Thereza A Soares
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Pernambuco 50740-640, Brazil
| | - Roberto D Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco 50740-465, Brazil
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12
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Aprà E, Bylaska EJ, de Jong WA, Govind N, Kowalski K, Straatsma TP, Valiev M, van Dam HJJ, Alexeev Y, Anchell J, Anisimov V, Aquino FW, Atta-Fynn R, Autschbach J, Bauman NP, Becca JC, Bernholdt DE, Bhaskaran-Nair K, Bogatko S, Borowski P, Boschen J, Brabec J, Bruner A, Cauët E, Chen Y, Chuev GN, Cramer CJ, Daily J, Deegan MJO, Dunning TH, Dupuis M, Dyall KG, Fann GI, Fischer SA, Fonari A, Früchtl H, Gagliardi L, Garza J, Gawande N, Ghosh S, Glaesemann K, Götz AW, Hammond J, Helms V, Hermes ED, Hirao K, Hirata S, Jacquelin M, Jensen L, Johnson BG, Jónsson H, Kendall RA, Klemm M, Kobayashi R, Konkov V, Krishnamoorthy S, Krishnan M, Lin Z, Lins RD, Littlefield RJ, Logsdail AJ, Lopata K, Ma W, Marenich AV, Martin Del Campo J, Mejia-Rodriguez D, Moore JE, Mullin JM, Nakajima T, Nascimento DR, Nichols JA, Nichols PJ, Nieplocha J, Otero-de-la-Roza A, Palmer B, Panyala A, Pirojsirikul T, Peng B, Peverati R, Pittner J, Pollack L, Richard RM, Sadayappan P, Schatz GC, Shelton WA, Silverstein DW, Smith DMA, Soares TA, Song D, Swart M, Taylor HL, Thomas GS, Tipparaju V, Truhlar DG, Tsemekhman K, Van Voorhis T, Vázquez-Mayagoitia Á, Verma P, Villa O, Vishnu A, Vogiatzis KD, Wang D, Weare JH, Williamson MJ, Windus TL, Woliński K, Wong AT, Wu Q, Yang C, Yu Q, Zacharias M, Zhang Z, Zhao Y, Harrison RJ. NWChem: Past, present, and future. J Chem Phys 2020; 152:184102. [PMID: 32414274 DOI: 10.1063/5.0004997] [Citation(s) in RCA: 275] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.
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Affiliation(s)
- E Aprà
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - E J Bylaska
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - W A de Jong
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - N Govind
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - K Kowalski
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Valiev
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - H J J van Dam
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Y Alexeev
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - J Anchell
- Intel Corporation, Santa Clara, California 95054, USA
| | - V Anisimov
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - F W Aquino
- QSimulate, Cambridge, Massachusetts 02139, USA
| | - R Atta-Fynn
- Department of Physics, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - J Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - N P Bauman
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - J C Becca
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - D E Bernholdt
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | | | - S Bogatko
- 4G Clinical, Wellesley, Massachusetts 02481, USA
| | - P Borowski
- Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - J Boschen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - J Brabec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 18223 Prague 8, Czech Republic
| | - A Bruner
- Department of Chemistry and Physics, University of Tennessee at Martin, Martin, Tennessee 38238, USA
| | - E Cauët
- Service de Chimie Quantique et Photophysique (CP 160/09), Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Y Chen
- Facebook, Menlo Park, California 94025, USA
| | - G N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - C J Cramer
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Daily
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M J O Deegan
- SKAO, Jodrell Bank Observatory, Macclesfield SK11 9DL, United Kingdom
| | - T H Dunning
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - M Dupuis
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - K G Dyall
- Dirac Solutions, Portland, Oregon 97229, USA
| | - G I Fann
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S A Fischer
- Chemistry Division, U. S. Naval Research Laboratory, Washington, DC 20375, USA
| | - A Fonari
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - H Früchtl
- EaStCHEM and School of Chemistry, University of St. Andrews, St. Andrews KY16 9ST, United Kingdom
| | - L Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Col. Vicentina, Iztapalapa, C.P. 09340 Ciudad de México, Mexico
| | - N Gawande
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - S Ghosh
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 5545, USA
| | - K Glaesemann
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A W Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - J Hammond
- Intel Corporation, Santa Clara, California 95054, USA
| | - V Helms
- Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany
| | - E D Hermes
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA
| | - K Hirao
- Next-generation Molecular Theory Unit, Advanced Science Institute, RIKEN, Saitama 351-0198, Japan
| | - S Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - M Jacquelin
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - L Jensen
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B G Johnson
- Acrobatiq, Pittsburgh, Pennsylvania 15206, USA
| | - H Jónsson
- Faculty of Physical Sciences, University of Iceland, Reykjavík, Iceland and Department of Applied Physics, Aalto University, FI-00076 Aalto, Espoo, Finland
| | - R A Kendall
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Klemm
- Intel Corporation, Santa Clara, California 95054, USA
| | - R Kobayashi
- ANU Supercomputer Facility, Australian National University, Canberra, Australia
| | - V Konkov
- Chemistry Program, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - S Krishnamoorthy
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Krishnan
- Facebook, Menlo Park, California 94025, USA
| | - Z Lin
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - R D Lins
- Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | | | - A J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, Wales CF10 3AT, United Kingdom
| | - K Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - W Ma
- Institute of Software, Chinese Academy of Sciences, Beijing, China
| | - A V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Martin Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México City, Mexico
| | - D Mejia-Rodriguez
- Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida 32611, USA
| | - J E Moore
- Intel Corporation, Santa Clara, California 95054, USA
| | - J M Mullin
- DCI-Solutions, Aberdeen Proving Ground, Maryland 21005, USA
| | - T Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - D R Nascimento
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - J A Nichols
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - P J Nichols
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - J Nieplocha
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - B Palmer
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A Panyala
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - T Pirojsirikul
- Department of Chemistry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - B Peng
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - R Peverati
- Chemistry Program, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J Pittner
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., 18223 Prague 8, Czech Republic
| | - L Pollack
- StudyPoint, Boston, Massachusetts 02114, USA
| | | | - P Sadayappan
- School of Computing, University of Utah, Salt Lake City, Utah 84112, USA
| | - G C Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - W A Shelton
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | | | - D M A Smith
- Intel Corporation, Santa Clara, California 95054, USA
| | - T A Soares
- Dept. of Fundamental Chemistry, Universidade Federal de Pernambuco, Recife, Brazil
| | - D Song
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Swart
- ICREA, 08010 Barcelona, Spain and Universitat Girona, Institut de Química Computacional i Catàlisi, Campus Montilivi, 17003 Girona, Spain
| | - H L Taylor
- CD-adapco/Siemens, Melville, New York 11747, USA
| | - G S Thomas
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - V Tipparaju
- Cray Inc., Bloomington, Minnesota 55425, USA
| | - D G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | - T Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Á Vázquez-Mayagoitia
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - P Verma
- 1QBit, Vancouver, British Columbia V6E 4B1, Canada
| | - O Villa
- NVIDIA, Santa Clara, California 95051, USA
| | - A Vishnu
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - K D Vogiatzis
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - D Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong 250014, China
| | - J H Weare
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - M J Williamson
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - T L Windus
- Department of Chemistry, Iowa State University and Ames Laboratory, Ames, Iowa 50011, USA
| | - K Woliński
- Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - A T Wong
- Qwil, San Francisco, California 94107, USA
| | - Q Wu
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Yang
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Q Yu
- AMD, Santa Clara, California 95054, USA
| | - M Zacharias
- Department of Physics, Technical University of Munich, 85748 Garching, Germany
| | - Z Zhang
- Stanford Research Computing Center, Stanford University, Stanford, California 94305, USA
| | - Y Zhao
- State Key Laboratory of Silicate Materials for Architectures, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - R J Harrison
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
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13
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Santos DES, Pontes FJS, Lins RD, Coutinho K, Soares TA. SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. J Chem Inf Model 2019; 60:473-484. [DOI: 10.1021/acs.jcim.9b00569] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Denys E. S. Santos
- Departmento Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil
| | - Frederico J. S. Pontes
- Departmento Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil
| | - Roberto D. Lins
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, 50740-465 Cidade Universitária, Recife, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo, Brazil
| | - Thereza A. Soares
- Departmento Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil
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14
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Durães-Carvalho R, Ludwig-Begall LF, Salemi M, Lins RD, Marques ETA. Influence of directional positive Darwinian selection-driven evolution on arboviruses Dengue and Zika virulence and pathogenesis. Mol Phylogenet Evol 2019; 140:106607. [PMID: 31473337 DOI: 10.1016/j.ympev.2019.106607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/29/2019] [Indexed: 12/25/2022]
Abstract
Dengue (DENV) and Zika (ZIKV) viruses are antigenically and evolutionarily related; immunological cross-reactions between them have been associated to both cross-protection and infection-enhanced mechanisms. Here, DENV-1-4 and ZIKV were investigated through Bayesian coalescent-based approaches and selection-driven Darwinian evolution methods using robust datasets. Our findings show that both DENV and ZIKV, driven essentially by directional positive selection, have undergone evolution and diversification and that their entire polyproteins are subject to an intense directional evolution. Interestingly, positively selected codons mapped here are directly associated to DENV-1-2 virulence as well as the ZIKV burgeoning 2015-16 outbreak in the Americas, therefore, having impact on the pathogenesis of these viruses. Biochemical prediction analysis focusing on markers involved in virulence and viral transmission dynamics identified alterations in N-Glycosylation-, Phosphorylation- and Palmitoylation-sites in ZIKV sampled from different countries, hosts and isolation sources. Taking into account both DENV-ZIKV co-circulation either into and/or out of flavivirus-endemic regions, as well as recombination and quasispecies scenarios, these results indicate the action of a selection-driven evolution affecting the biology, virulence and pathogenesis of these pathogens in a non-randomized environment.
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Affiliation(s)
- Ricardo Durães-Carvalho
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE 50740-465, Brazil.
| | - Louisa F Ludwig-Begall
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, University of Liège, Belgium
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, United States
| | - Roberto D Lins
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE 50740-465, Brazil
| | - Ernesto T A Marques
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Recife, PE 50740-465, Brazil; Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, United States
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15
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Coêlho DF, Ferraz MVF, Marques ETA, Lins RD, Viana IFT. The influence of biotinylation on the ability of a computer designed protein to detect B-cells producing anti-HIV-1 2F5 antibodies. J Mol Graph Model 2019; 93:107442. [PMID: 31479948 DOI: 10.1016/j.jmgm.2019.107442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
Abstract
Antibodies against the HIV-1 2F5 epitope are known as one of the most powerful and broadly protective anti-HIV antibodies. Therefore, vaccine strategies that include the 2F5 epitope in their formulation require a robust method to detect specific anti-2F5 antibody production by B cells. Towards this goal, we have biotinylated a previously reported computer-designed protein carrying the HIV-1 2F5 epitope aiming the further development of a platform to detect human B-cells expressing anti-2F5 antibodies through flow cytometry. Biophysical and immunological properties of our devised protein were characterized by computer simulation and experimental methods. Biotinylation did not affect folding and improved protein stability and solubility. The biotinylated protein exhibited similar binding affinity trends compared to its unbiotinylated counterpart and was recognized by anti-HIV-1 2F5 antibodies expressed on the surface of patient-derived peripheral blood mononuclear cells. Moreover, we present a high affinity marker for the identification of epitope-specific B cells that can be used to measure the efficacy of vaccine strategies based on the HIV-1 envelope protein.
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Affiliation(s)
- Danilo F Coêlho
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil; Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-540, Brazil
| | - Matheus V F Ferraz
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil; Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-540, Brazil
| | - Ernesto T A Marques
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil; Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Roberto D Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil; Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-540, Brazil.
| | - Isabelle F T Viana
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil.
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16
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Polêto MD, Rusu VH, Grisci BI, Dorn M, Lins RD, Verli H. Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities. Front Pharmacol 2018; 9:395. [PMID: 29740321 PMCID: PMC5928326 DOI: 10.3389/fphar.2018.00395] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/05/2018] [Indexed: 11/13/2022] Open
Abstract
The identification of lead compounds usually includes a step of chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and quantitative (QSAR) approaches, offering models of the putative ligand-receptor interactions. In both scenarios, our understanding of which interactions functional groups can perform is mostly based on their chemical nature (such as electronegativity, volume, melting point, lipophilicity etc.) instead of their dynamics in aqueous, biological solutions (solvent accessibility, lifetime of hydrogen bonds, solvent structure etc.). As a consequence, it is challenging to predict from 2D structures which functional groups will be able to perform interactions with the target receptor, at which intensity and relative abundance in the biological environment, all of which will contribute to ligand potency and intrinsic activity. With this in mind, the aim of this work is to assess properties of aromatic rings, commonly used for drug design, in aqueous solution through molecular dynamics simulations in order to characterize their chemical features and infer their impact in complexation dynamics. For this, common aromatic and heteroaromatic rings were selected and received new atomic charge set based on the direction and module of the dipole moment from MP2/6-31G* calculations, while other topological terms were taken from GROMOS53A6 force field. Afterwards, liquid physicochemical properties were simulated for a calibration set composed by nearly 40 molecules and compared to their respective experimental data, in order to validate each topology. Based on the reliance of the employed strategy, we expanded the dataset to more than 100 aromatic rings. Properties in aqueous solution such as solvent accessible surface area, H-bonds availability, H-bonds residence time, and water structure around heteroatoms were calculated for each ring, creating a database of potential interactions, shedding light on features of drugs in biological solutions, on the structural basis for bioisosterism and on the enthalpic/entropic costs for ligand-receptor complexation dynamics.
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Affiliation(s)
- Marcelo D Polêto
- Grupo de Bioinformática Estrutural, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Victor H Rusu
- Swiss National Supercomputing Centre, Lugano, Switzerland
| | - Bruno I Grisci
- Instituto de Informática, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcio Dorn
- Instituto de Informática, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Roberto D Lins
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
| | - Hugo Verli
- Grupo de Bioinformática Estrutural, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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17
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Seo S, Lee DW, Ahn JS, Cunha K, Filippidi E, Ju SW, Shin E, Kim BS, Levine ZA, Lins RD, Israelachvili JN, Waite JH, Valentine MT, Shea JE, Ahn BK. Significant Performance Enhancement of Polymer Resins by Bioinspired Dynamic Bonding. Adv Mater 2017; 29:10.1002/adma.201703026. [PMID: 28833661 PMCID: PMC5640498 DOI: 10.1002/adma.201703026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Indexed: 05/09/2023]
Abstract
Marine mussels use catechol-rich interfacial mussel foot proteins (mfps) as primers that attach to mineral surfaces via hydrogen, metal coordination, electrostatic, ionic, or hydrophobic bonds, creating a secondary surface that promotes bonding to the bulk mfps. Inspired by this biological adhesive primer, it is shown that a ≈1 nm thick catecholic single-molecule priming layer increases the adhesion strength of crosslinked polymethacrylate resin on mineral surfaces by up to an order of magnitude when compared with conventional primers such as noncatecholic silane- and phosphate-based grafts. Molecular dynamics simulations confirm that catechol groups anchor to a variety of mineral surfaces and shed light on the binding mode of each molecule. Here, a ≈50% toughness enhancement is achieved in a stiff load-bearing polymer network, demonstrating the utility of mussel-inspired bonding for processing a wide range of polymeric interfaces, including structural, load-bearing materials.
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Affiliation(s)
- Sungbaek Seo
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Biomaterials Science, Pusan National University, Miryang, 627-706, South Korea
| | - Dong Woog Lee
- Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea
- Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Jin Soo Ahn
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Dental Research Institute and Biomaterials Science, Dentistry, Seoul National University, Seoul, 110-749, South Korea
| | - Keila Cunha
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-670, Brazil
- Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Emmanouela Filippidi
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Mechanical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Sung Won Ju
- Dental Research Institute and Biomaterials Science, Dentistry, Seoul National University, Seoul, 110-749, South Korea
| | - Eeseul Shin
- Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea
| | - Byeong-Su Kim
- Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea
| | - Zachary A Levine
- Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Roberto D Lins
- Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-670, Brazil
- Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil
| | - Jacob N Israelachvili
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - J Herbert Waite
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
| | - Megan T Valentine
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Mechanical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Joan Emma Shea
- Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - B Kollbe Ahn
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
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18
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Santos DES, Pol-Fachin L, Lins RD, Soares TA. Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes. J Chem Inf Model 2017; 57:2181-2193. [DOI: 10.1021/acs.jcim.7b00271] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Denys E. S. Santos
- Department
of Fundamental Chemistry, Federal University of Pernambuco, 50740-560 Recife, Brazil
| | - Laércio Pol-Fachin
- Department
of Fundamental Chemistry, Federal University of Pernambuco, 50740-560 Recife, Brazil
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50740-465 Recife, Brazil
| | - Roberto D. Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50740-465 Recife, Brazil
| | - Thereza A. Soares
- Department
of Fundamental Chemistry, Federal University of Pernambuco, 50740-560 Recife, Brazil
- Department
of Chemistry, Umeå Center for Microbial Research, Umeå University, 90.187 Umeå, Sweden
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19
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Freire MLC, Pol-Fachin L, Coêlho DF, Viana IFT, Magalhães T, Cordeiro MT, Fischer N, Loeffler FF, Jaenisch T, Franca RF, Marques ETA, Lins RD. Mapping Putative B-Cell Zika Virus NS1 Epitopes Provides Molecular Basis for Anti-NS1 Antibody Discrimination between Zika and Dengue Viruses. ACS Omega 2017; 2:3913-3920. [PMID: 30023708 PMCID: PMC6044859 DOI: 10.1021/acsomega.7b00608] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 05/18/2023]
Abstract
B-cell epitope sequences from Zika virus (ZIKV) NS1 protein have been identified using epitope prediction tools. Mapping these sequences onto the NS1 surface reveals two major conformational epitopes and a single linear one. Despite an overall average sequence identity of ca. 55% between the NS1 from ZIKV and the four dengue virus (DENV) serotypes, epitope sequences were found to be highly conserved. Nevertheless, nonconserved epitope-flanking residues are responsible for a dramatically divergent electrostatic surface potential on the epitope regions of ZIKV and DENV2 serotypes. These findings suggest that strategies for differential diagnostics on the basis of short linear NS1 sequences are likely to fail due to immunological cross-reactions. Overall, results provide the molecular basis of differential discrimination between Zika and DENVs by NS1 monoclonal antibodies.
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Affiliation(s)
| | - Laércio Pol-Fachin
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, Recife 50740-670, Brazil
| | - Danilo F. Coêlho
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, Recife 50740-670, Brazil
| | | | - Tereza Magalhães
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
| | - Marli T. Cordeiro
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
| | - Nico Fischer
- Department
of Infectious Diseases, Section Clinical Tropical Medicine, Heidelberg University Hospital, INF 324, Heidelberg 69120, Germany
- HEiKA
- Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Felix F. Loeffler
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- HEiKA
- Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Thomas Jaenisch
- Department
of Infectious Diseases, Section Clinical Tropical Medicine, Heidelberg University Hospital, INF 324, Heidelberg 69120, Germany
- HEiKA
- Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Rafael F. Franca
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
| | - Ernesto T. A. Marques
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
- Center for
Vaccine Research, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States
- E-mail: . Tel +1 (412) 624.4440 (E.T.A.M.)
| | - Roberto D. Lins
- Aggeu
Magalhães Institute, Oswaldo Cruz Foundation, Recife 50740-465, Brazil
- Department
of Fundamental Chemistry, Federal University
of Pernambuco, Recife 50740-670, Brazil
- E-mail: . Tel +55 (81) 2123.7848 (R.D.L.)
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20
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Casillas-Ituarte NN, Cruz CHB, Lins RD, DiBartola AC, Howard J, Liang X, Höök M, Viana IFT, Sierra-Hernández MR, Lower SK. Amino acid polymorphisms in the fibronectin-binding repeats of fibronectin-binding protein A affect bond strength and fibronectin conformation. J Biol Chem 2017; 292:8797-8810. [PMID: 28400484 DOI: 10.1074/jbc.m117.786012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/08/2017] [Indexed: 11/06/2022] Open
Abstract
The Staphylococcus aureus cell surface contains cell wall-anchored proteins such as fibronectin-binding protein A (FnBPA) that bind to host ligands (e.g. fibronectin; Fn) present in the extracellular matrix of tissue or coatings on cardiac implants. Recent clinical studies have found a correlation between cardiovascular infections caused by S. aureus and nonsynonymous SNPs in FnBPA. Atomic force microscopy (AFM), surface plasmon resonance (SPR), and molecular simulations were used to investigate interactions between Fn and each of eight 20-mer peptide variants containing amino acids Ala, Asn, Gln, His, Ile, and Lys at positions equivalent to 782 and/or 786 in Fn-binding repeat-9 of FnBPA. Experimentally measured bond lifetimes (1/koff) and dissociation constants (Kd = koff/kon), determined by mechanically dissociating the Fn·peptide complex at loading rates relevant to the cardiovascular system, varied from the lowest-affinity H782A/K786A peptide (0.011 s, 747 μm) to the highest-affinity H782Q/K786N peptide (0.192 s, 15.7 μm). These atomic force microscopy results tracked remarkably well to metadynamics simulations in which peptide detachment was defined solely by the free-energy landscape. Simulations and SPR experiments suggested that an Fn conformational change may enhance the stability of the binding complex for peptides with K786I or H782Q/K786I (Kdapp = 0.2-0.5 μm, as determined by SPR) compared with the lowest-affinity double-alanine peptide (Kdapp = 3.8 μm). Together, these findings demonstrate that amino acid substitutions in Fn-binding repeat-9 can significantly affect bond strength and influence the conformation of Fn upon binding. They provide a mechanistic explanation for the observation of nonsynonymous SNPs in fnbA among clinical isolates of S. aureus that cause endovascular infections.
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Affiliation(s)
| | - Carlos H B Cruz
- the Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50.740-465, Brazil, and
| | - Roberto D Lins
- the Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50.740-465, Brazil, and
| | | | | | - Xiaowen Liang
- the Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030
| | - Magnus Höök
- the Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030
| | - Isabelle F T Viana
- the Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, 50.740-465, Brazil, and
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21
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Taylor ES, Pol-Fachin L, Lins RD, Lower SK. Conformational stability of the epidermal growth factor (EGF) receptor as influenced by glycosylation, dimerization and EGF hormone binding. Proteins 2017; 85:561-570. [PMID: 28019699 PMCID: PMC5835389 DOI: 10.1002/prot.25220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 12/18/2022]
Abstract
The epidermal growth factor receptor (EGFR) is an important transmembrane glycoprotein kinase involved the initiation or perpetuation of signal transduction cascades within cells. These processes occur after EGFR binds to a ligand [epidermal growth factor (EGF)], thus inducing its dimerization and tyrosine autophosphorylation. Previous publications have highlighted the importance of glycosylation and dimerization for promoting proper function of the receptor and conformation in membranes; however, the effects of these associations on the protein conformational stability have not yet been described. Molecular dynamics simulations were performed to characterize the conformational preferences of the monomeric and dimeric forms of the EGFR extracellular domain upon binding to EGF in the presence and absence of N-glycan moieties. Structural stability analyses revealed that EGF provides the most conformational stability to EGFR, followed by glycosylation and dimerization, respectively. The findings also support that EGF-EGFR binding takes place through a large-scale induced-fitting mechanism. Proteins 2017; 85:561-570. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Eric S. Taylor
- Department of Geology, Kent State University, North Canton, Ohio 44720
| | - Laercio Pol-Fachin
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Recife, Pernambuco 50740-465, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Pernambuco 50740-560, Brazil
| | - Roberto D. Lins
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Recife, Pernambuco 50740-465, Brazil
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, Pernambuco 50740-560, Brazil
| | - Steven K. Lower
- School of Environment and Natural Resources, Ohio State University, 275 Mendenhall Laboratory, Columbus, Ohio 43210
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22
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Taylor ES, Pol-Fachin L, Lins RD, Lower SK. Cover Image, Volume 85, Issue 4. Proteins 2017. [DOI: 10.1002/prot.25275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Eric S. Taylor
- Department of Geology; Kent State University; North Canton Ohio 44720
| | - Laercio Pol-Fachin
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation; Recife Pernambuco 50740-465 Brazil
- Department of Fundamental Chemistry; Federal University of Pernambuco; Recife Pernambuco 50740-560 Brazil
| | - Roberto D. Lins
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation; Recife Pernambuco 50740-465 Brazil
- Department of Fundamental Chemistry; Federal University of Pernambuco; Recife Pernambuco 50740-560 Brazil
| | - Steven K. Lower
- School of Environment and Natural Resources; Ohio State University; 275 Mendenhall Laboratory Columbus Ohio 43210
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23
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Das S, Lee BH, Linstadt RTH, Cunha K, Li Y, Kaufman Y, Levine ZA, Lipshutz BH, Lins RD, Shea JE, Heeger AJ, Ahn BK. Molecularly Smooth Self-Assembled Monolayer for High-Mobility Organic Field-Effect Transistors. Nano Lett 2016; 16:6709-6715. [PMID: 27673480 DOI: 10.1021/acs.nanolett.6b03860] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite the need for molecularly smooth self-assembled monolayers (SAMs) on silicon dioxide surfaces (the most common dielectric surface), current techniques are limited to nonideal silane grafting. Here, we show unique bioinspired zwitterionic molecules forming a molecularly smooth and uniformly thin SAM in "water" in <1 min on various dielectric surfaces, which enables a dip-coating process that is essential for organic electronics to become reality. This monomolecular layer leads to high mobility of organic field-effect transistors (OFETs) based on various organic semiconductors and source/drain electrodes. A combination of experimental and computational techniques confirms strong adsorption (Wad > 20 mJ m-2), uniform thickness (∼0.5 or ∼1 nm) and orientation (all catechol head groups facing the oxide surface) of the "monomolecular" layers. This robust (strong adsorption), rapid, and green SAM represents a promising advancement toward the next generation of nanofabrication compared to the current nonuniform and inconsistent polysiloxane-based SAM involving toxic chemicals, long processing time (>10 h), or heat (>80 °C).
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Affiliation(s)
| | | | | | - Keila Cunha
- Fundamental Chemistry, Federal University of Pernambuco , Recife, Pernambuco 50740-670, Brazil
| | | | - Yair Kaufman
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev , Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel
| | | | | | - Roberto D Lins
- Fundamental Chemistry, Federal University of Pernambuco , Recife, Pernambuco 50740-670, Brazil
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Recife, Pernambuco 50740-465, Brazil
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Cunha KC, Rusu VH, Viana IFT, Marques ETA, Dhalia R, Lins RD. Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations. Biopolymers 2016; 103:351-61. [PMID: 25677872 DOI: 10.1002/bip.22626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/31/2015] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
Molecular dynamics and de novo techniques, associated to quality parameter sets, have excelled at determining the structure of small proteins with high accuracy. To achieve a detailed description of protein conformations, these methods must critically assess the thermodynamic features of the molecular ensembles. Here, a comparison of the conformational ensemble generated by molecular dynamics and de novo techniques were carried out for six Top7-based proteins carrying gp41 HIV-1 epitopes. The native Top7, a highly stable computationally designed protein, was used as benchmark. Structural stability, flexibility, and secondary structure content were assessed. The consistency of the latter was compared to experimental circular dichroism spectra for all proteins. While both methods are capable to identify the stable from unstable chimeric proteins, the sampled conformational space and flexibility differ significantly in both methods. Molecular dynamics simulations seem to better describe secondary structure content and identify regions responsible for conformational instability. The de novo method, as implemented in Rosetta-a prime tool for protein design, overestimates secondary structure content. On the other hand, its empirical energy function is capable to predict the threshold for protein stability.
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Affiliation(s)
- Keila C Cunha
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-560, Brazil
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25
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Affiliation(s)
- Victor H. Rusu
- Department
of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring
Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820, United States
- Departamento
de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
| | - Riccardo Baron
- Department
of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring
Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820, United States
| | - Roberto D. Lins
- Departamento
de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
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26
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Pol-Fachin L, Verli H, Lins RD. Extension and validation of the GROMOS 53A6(GLYC) parameter set for glycoproteins. J Comput Chem 2014; 35:2087-95. [PMID: 25196137 DOI: 10.1002/jcc.23721] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/23/2014] [Accepted: 08/09/2014] [Indexed: 11/08/2022]
Abstract
An extension of the GROMOS 53A6GLYC force field for carbohydrates to encompass glycoprotein linkages is presented. The set includes new atomic charges and incorporates adequate torsional potential parameters for N-, S-, C-, P-, and O-glycosydic linkages, offering compatibility with the GROMOS force field family for proteins. Validation included the description of glycosydic linkage geometries between amino acid and monosaccharide residues, comparison of NMR-derived protein-carbohydrate and carbohydrate-carbohydrate nuclear overhauser effect (NOE) signals for glycoproteins and the effects of glycosylation on protein flexibility and dynamics.
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Affiliation(s)
- Laercio Pol-Fachin
- Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil, 91500-970; Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil, 50670-540
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27
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Fernandes AMAP, Fernandes GD, Barrera-Arellano D, de Sá GF, Lins RD, Eberlin MN, Alberici RM. Desorption/ionization efficiencies of triacylglycerols and phospholipids via EASI-MS. J Mass Spectrom 2014; 49:335-341. [PMID: 24809895 DOI: 10.1002/jms.3366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/03/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
Knowledge of the major effects governing desorption/ionization efficiency is required for the development and application of ambient mass spectrometry. Although all triacylglycerols (TAG) have the same favorable protonation and cationization sites, their desorption/ionization efficiencies can vary dramatically during easy ambient sonic-spray ionization because of structural differences in the carbon chain. To quantify this somewhat surprising and drastic effect, we have performed a systematic investigation of desorption/ionization efficiencies as a function of unsaturation and length for TAG as well as for diacylglycerols, monoacylglycerols and several phospholipids (PL). Affinities for Na(+) as a function of unsaturation level have also been assayed via comprehensive metadynamics calculations to understand the influence of this phenomenon on the ionization efficiency. The results suggest that dipole-dipole interactions within a carbon chain tuned by unsaturation sites govern ionization efficiency of TAG and PL.
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Affiliation(s)
- Anna Maria A P Fernandes
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, 13083-970, SP, Brazil
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28
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Nadvorny D, da Silva JBP, Lins RD. Anionic Form of Usnic Acid Promotes Lamellar to Nonlamellar Transition in DPPC and DOPC Membranes. J Phys Chem B 2014; 118:3881-6. [DOI: 10.1021/jp412176f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniela Nadvorny
- Fundamental
Chemistry Department, Federal University of Pernambuco, Recife PE 50.740-540, Brazil
| | - João Bosco P. da Silva
- Fundamental
Chemistry Department, Federal University of Pernambuco, Recife PE 50.740-540, Brazil
| | - Roberto D. Lins
- Fundamental
Chemistry Department, Federal University of Pernambuco, Recife PE 50.740-540, Brazil
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29
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Nascimento A, Pontes FJS, Lins RD, Soares TA. Hydration, ionic valence and cross-linking propensities of cations determine the stability of lipopolysaccharide (LPS) membranes. Chem Commun (Camb) 2014; 50:231-3. [DOI: 10.1039/c3cc46918b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Rusu VH, Horta VAC, Horta BAC, Lins RD, Baron R. MDWiZ: a platform for the automated translation of molecular dynamics simulations. J Mol Graph Model 2013; 48:80-6. [PMID: 24434017 DOI: 10.1016/j.jmgm.2013.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 11/17/2022]
Abstract
A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.
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Affiliation(s)
- Victor H Rusu
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
| | - Vitor A C Horta
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Computational Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Bruno A C Horta
- Department of Electrical Engineering, Pontíficia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil; Department of Biotechnology and Biological Sciences, Centro Universitário Estadual da Zona Oeste, Rio de Janeiro, Brazil
| | - Roberto D Lins
- Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil
| | - Riccardo Baron
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA.
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31
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de Carvalho RV, Lopez-Ferrer D, Guimarães KS, Lins RD. IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol. J Comput Chem 2013; 34:1707-18. [PMID: 23609240 DOI: 10.1002/jcc.23299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/17/2013] [Accepted: 03/25/2013] [Indexed: 11/06/2022]
Abstract
Introduction of ion mobility mass spectrometry (IMS/MS) into the proteomic workflow provides an orthogonal separation to the widely used LC-MS platforms. IMS also provides structural information that could facilitate peptide identification. However, the lack of tools capable of predictive power in a high-throughput fashion makes peptide global profiling quite challenging. To target this issue, a computational workflow was developed based on biophysical principles to predict the collision cross-section area (CCS) of peptides as measured from IMS/MS experiments. Hosted on a web server, it allows the user to input a primary sequence (query) and retrieve information on peptide structure, sequence, and corresponding CCS. The current version is designed to identify peptide sequences up to 23 residues in length, in its higher charge state, based on a match of the molecule m/z and CCS. The protocol was validated against a 128-sequences-dataset and CCS predicted within 2.8% average error.
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Affiliation(s)
- Ranieri V de Carvalho
- Center of Informatics, Federal University of Pernambuco, Recife, PE, 50740-560, Brazil
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32
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Viana IFT, Soares TA, Lima LFO, Marques ETA, Krieger MA, Dhalia R, Lins RD. De novo design of immunoreactive conformation-specific HIV-1 epitopes based on Top7 scaffold. RSC Adv 2013. [DOI: 10.1039/c3ra41562g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Pol-Fachin L, Rusu VH, Verli H, Lins RD. GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates. J Chem Theory Comput 2012; 8:4681-90. [PMID: 26605624 DOI: 10.1021/ct300479h] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules.
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Affiliation(s)
- Laercio Pol-Fachin
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Victor H Rusu
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil
| | - Hugo Verli
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.,College of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto D Lins
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil
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34
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Kirschner KN, Lins RD, Maass A, Soares TA. A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation. J Chem Theory Comput 2012; 8:4719-31. [DOI: 10.1021/ct300534j] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl N. Kirschner
- Fraunhofer-Institute for Algorithms
and Scientific Computing (SCAI), Department of Bioinformatics, Schloss
Birlinghoven, 53754 Sankt Augustin, Germany
| | - Roberto D. Lins
- Department of Fundamental Chemistry,
Federal University of Pernambuco, Cidade Universitária, Recife,
PE 50740-560 Brazil
| | - Astrid Maass
- Fraunhofer-Institute for Algorithms
and Scientific Computing (SCAI), Department of Simulation Engineering,
Schloss Birlinghoven, 53754 Sankt Augustin, Germany
| | - Thereza A. Soares
- Department of Fundamental Chemistry,
Federal University of Pernambuco, Cidade Universitária, Recife,
PE 50740-560 Brazil
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35
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Pontes FJS, Rusu VH, Soares TA, Lins RD. The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View. J Chem Theory Comput 2012; 8:3830-8. [DOI: 10.1021/ct300084v] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Frederico J. S. Pontes
- Department of Fundamental
Chemistry, Federal University
of Pernambuco, Cidade Universitária, Recife, PE 50740-560 Brazil
| | - Victor H. Rusu
- Department of Fundamental
Chemistry, Federal University
of Pernambuco, Cidade Universitária, Recife, PE 50740-560 Brazil
| | - Thereza A. Soares
- Department of Fundamental
Chemistry, Federal University
of Pernambuco, Cidade Universitária, Recife, PE 50740-560 Brazil
| | - Roberto D. Lins
- Department of Fundamental
Chemistry, Federal University
of Pernambuco, Cidade Universitária, Recife, PE 50740-560 Brazil
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36
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Gomes DEB, Lins RD, Pascutti PG, Lei C, Soares TA. Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding. J Phys Chem B 2011; 115:15389-98. [PMID: 22098575 DOI: 10.1021/jp208787g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F), and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK(a) calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolylmethylphosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK(a) calculations for the substrate-bound and unbound enzyme showed a significant pK(a) shift from standard values (ΔpK(a) = ±3 units) for residues His254 and Arg275. MD simulations of protonated His254 revealed a dynamic hydrogen bond network connecting the catalytic residue Asp301 via His254 to Asp232, Asp233, Arg275, and Asp235, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between Asp301 and His254 were persistent in the OPH-paraoxon complex but not in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue His254, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the open to the closed substate promoting a tighter binding of paraoxon.
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Affiliation(s)
- Diego E B Gomes
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil
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Franca EF, Freitas LCG, Lins RD. Chitosan molecular structure as a function of N-acetylation. Biopolymers 2011; 95:448-60. [PMID: 21328576 DOI: 10.1002/bip.21602] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 01/14/2011] [Accepted: 01/17/2011] [Indexed: 11/10/2022]
Abstract
Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with ϕ and ψ values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3-HO3((n)) ···O5((n +) (1)) hydrogen bond, which in turn controls particle aggregation.
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Affiliation(s)
- Eduardo F Franca
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, MG 38400-902, Brazil
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38
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Lins RD, Devanathan R, Dupuis M. Modeling the Nanophase Structural Dynamics of Phenylated Sulfonated Poly Ether Ether Ketone Ketone (Ph-SPEEKK) Membranes As a Function of Hydration. J Phys Chem B 2011; 115:1817-24. [DOI: 10.1021/jp110331m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roberto D. Lins
- Department of Fundamental Chemistry, Federal University of Pernambuco (UFPE), Recife, PE, 50740-540, Brazil
| | - Ram Devanathan
- Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Michel Dupuis
- Chemical & Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Gomes DE, Lins RD, Pascutti PG, Lei C, Soares TA. The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces. J Phys Chem B 2010; 114:531-40. [PMID: 19938866 PMCID: PMC2818561 DOI: 10.1021/jp9083635] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme organophosphorous hydrolase (OPH) catalyzes the hydrolysis of a wide variety of organophosphorous compounds with high catalytic efficiency and broad substrate specificity. The immobilization of OPH in functionalized mesoporous silica (FMS) surfaces increases significantly its catalytic specific activity, as compared to the enzyme in solution, with important applications for the detection and decontamination of insecticides and chemical warfare agents. Experimental measurements of immobilization efficiency as a function of the charge and coverage percentage of different functional groups have been interpreted as electrostatic forces being the predominant interactions underlying the adsorption of OPH onto FMS surfaces. Explicit solvent molecular dynamics simulations have been performed for OPH in bulk solution and adsorbed onto two distinct interaction potential models of the FMS functional groups to investigate the relative contributions of nonbonded interactions to the conformational dynamics and adsorption of the protein. Our results support the conclusion that electrostatic interactions are responsible for the binding of OPH to the FMS surface. However, these results also show that van der Waals forces are detrimental for interfacial adhesion. In addition, it is found that OPH adsorption onto the FMS models favors a protein conformation whose active site is fully accessible to the substrate, in contrast to the unconfined protein.
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Affiliation(s)
- Diego E.B. Gomes
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil
| | - Roberto D. Lins
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
- Departamento de Química Fundamental, CCEN, UFPE, 50590-470, Recife PE, Brazil
| | - Pedro G. Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil
| | - Chenghong Lei
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
| | - Thereza A. Soares
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
- Departamento de Química Fundamental, CCEN, UFPE, 50590-470, Recife PE, Brazil
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40
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Ferreira R, Lai K, Lins RD. Prebiotic chemical kinetics imprint on positional codon usage. J BRAZIL CHEM SOC 2010. [DOI: 10.1590/s0103-50532010000600022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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41
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Oliveira OV, Freitas LCG, Straatsma TP, Lins RD. Interaction between the CBM of Cel9A fromThermobifida fuscaand cellulose fibers. J Mol Recognit 2009; 22:38-45. [DOI: 10.1002/jmr.925] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Franca EF, Lins RD, Freitas LCG, Straatsma TP. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution. J Chem Theory Comput 2008; 4:2141-9. [DOI: 10.1021/ct8002964] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eduardo F. Franca
- Pacific Northwest National Laboratory, Richland, Washington 99352, and Departamento de Química, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Roberto D. Lins
- Pacific Northwest National Laboratory, Richland, Washington 99352, and Departamento de Química, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Luiz C. G. Freitas
- Pacific Northwest National Laboratory, Richland, Washington 99352, and Departamento de Química, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - T. P. Straatsma
- Pacific Northwest National Laboratory, Richland, Washington 99352, and Departamento de Química, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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43
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Lower BH, Lins RD, Oestreicher Z, Straatsma TP, Hochella MF, Shi L, Lower SK. In vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype. Environ Sci Technol 2008; 42:3821-3827. [PMID: 18546729 DOI: 10.1021/es702688c] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the peptide-metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for Ser-Pro-Ser at a hematite surface. These simulations show that hydrogen bonding occurs between the two serine amino acids and the hydroxylated hematite surface and that the presence of proline between the hydroxide residues restricts the peptide flexibility, thereby inducing a structural-binding motif. A search of published sequence data revealed that the binding motif (Ser/Thr-Pro-Ser/Thr) is adjacent to the terminal heme-binding domain of both OmcA and MtrC, which are outer membrane cytochromes from the metal-reducing bacterium Shewanella oneidensis MR-1. The entire five amino acid consensus sequence (Ser/Thr-hydrophobic/ aromatic-Ser/Thr-Pro-Ser/Thr) was also found as multiple copies in the primary sequences of metal-oxide binding proteins Sil1 and Sil2 from Thalassiosira pseudonana. We suggest that this motif constitutes a natural metal-oxide binding archetype that could be exploited in enzyme-based biofuel cell design and approaches to synthesize tailored metal-oxide nanostructures.
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Affiliation(s)
- Brian H Lower
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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44
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Soares TA, Straatsma TP, Lins RD. Influence of the B-band O-antigen chain in the structure and electrostatics of the lipopolysaccharide membrane of Pseudomonas aeruginosa. J BRAZIL CHEM SOC 2008. [DOI: 10.1590/s0103-50532008000200018] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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45
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Lins RD, Vorpagel ER, Guglielmi M, Straatsma TP. Computer Simulation of Uranyl Uptake by the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa. Biomacromolecules 2007; 9:29-35. [DOI: 10.1021/bm700609r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto D. Lins
- Computational Biology and Bioinformatics, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, and Laboratory of Computational Chemistry, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Erich R. Vorpagel
- Computational Biology and Bioinformatics, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, and Laboratory of Computational Chemistry, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Matteo Guglielmi
- Computational Biology and Bioinformatics, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, and Laboratory of Computational Chemistry, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - T. P. Straatsma
- Computational Biology and Bioinformatics, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, and Laboratory of Computational Chemistry, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
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46
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Pereira CS, Moura AFD, Freitas LCG, Lins RD. Revisiting the internal conformational dynamics and solvation properties of cyclodextrins. J BRAZIL CHEM SOC 2007. [DOI: 10.1590/s0103-50532007000500012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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47
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Abstract
Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen-bonding pattern of the intermolecular beta-sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side-chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the beta-sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed.
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Affiliation(s)
- Daniel Trzesniak
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland
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48
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Lins RD, Röthlisberger U. Influence of Long-Range Electrostatic Treatments on the Folding of the N-Terminal H4 Histone Tail Peptide. J Chem Theory Comput 2006; 2:246-50. [DOI: 10.1021/ct0501699] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roberto D. Lins
- École Polytechnique Fédérale de Lausane, Institute of Chemical Sciences and Engineering, CH-1015 Lausanne, Switzerland
| | - Ursula Röthlisberger
- École Polytechnique Fédérale de Lausane, Institute of Chemical Sciences and Engineering, CH-1015 Lausanne, Switzerland
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von Lilienfeld OA, Lins RD, Rothlisberger U. Variational particle number approach for rational compound design. Phys Rev Lett 2005; 95:153002. [PMID: 16241723 DOI: 10.1103/physrevlett.95.153002] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Indexed: 05/05/2023]
Abstract
Within density functional theory, a variational particle number approach for rational compound design (RCD) is presented. An expression for RCD is obtained in terms of minimization of a suitably defined energy penalty functional whose gradients are the nuclear and the electronic chemical potential. Using combined quantum and molecular mechanics, a nonpeptidic anticancer drug candidate is designed.
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Affiliation(s)
- O Anatole von Lilienfeld
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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50
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Soares TA, Hünenberger PH, Kastenholz MA, Kräutler V, Lenz T, Lins RD, Oostenbrink C, van Gunsteren WF. An improved nucleic acid parameter set for the GROMOS force field. J Comput Chem 2005; 26:725-37. [PMID: 15770662 DOI: 10.1002/jcc.20193] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson-Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves.
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Affiliation(s)
- Thereza A Soares
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland
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