Search Results - "Cino, Elio A."

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations by Cino, Elio A, Choy, Wing-Yiu, Karttunen, Mikko

“…We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using…”
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Effects of molecular crowding on the dynamics of intrinsically disordered proteins by Cino, Elio A, Karttunen, Mikko, Choy, Wing-Yiu

“…Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in…”
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Targeting the Prion-like Aggregation of Mutant p53 to Combat Cancer by Silva, Jerson L, Cino, Elio A, Soares, Iaci N, Ferreira, Vitor F, A. P. de Oliveira, Guilherme

“…Conspectus Prion-like behavior of several amyloidogenic proteins has been demonstrated in recent years. Despite having functional roles in some cases,…”
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Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds by Cino, Elio A., Soares, Iaci N., Pedrote, Murilo M., de Oliveira, Guilherme A. P., Silva, Jerson L.

“…The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic…”
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Aggregation and Prion-Like Properties of Misfolded Tumor Suppressors: Is Cancer a Prion Disease? by Costa, Danielly C F, de Oliveira, Guilherme A P, Cino, Elio A, Soares, Iaci N, Rangel, Luciana P, Silva, Jerson L

“…Prion diseases are disorders that share several characteristics that are typical of many neurodegenerative diseases. Recently, several studies have extended…”
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Aggregation-primed molten globule conformers of the p53 core domain provide potential tools for studying p53C aggregation in cancer by Pedrote, Murilo M., de Oliveira, Guilherme A.P., Felix, Adriani L., Mota, Michelle F., Marques, Mayra de A., Soares, Iaci N., Iqbal, Anwar, Norberto, Douglas R., Gomes, Andre M.O., Gratton, Enrico, Cino, Elio A., Silva, Jerson L.

“…The functionality of the tumor suppressor p53 is altered in more than 50% of human cancers, and many individuals with cancer exhibit amyloid-like buildups of…”
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Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response by Cino, Elio A, Wong-ekkabut, Jirasak, Karttunen, Mikko, Choy, Wing-Yiu

“…Intrinsically disordered proteins (IDPs) are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP…”
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The Status of p53 Oligomeric and Aggregation States in Cancer by de Oliveira, Guilherme A P, Petronilho, Elaine C, Pedrote, Murilo M, Marques, Mayra A, Vieira, Tuane C R G, Cino, Elio A, Silva, Jerson L

“…Despite being referred to as the guardian of the genome, when impacted by mutations, p53 can lose its protective functions and become a renegade. The malignant…”
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PyAutoFEP: An Automated Free Energy Perturbation Workflow for GROMACS Integrating Enhanced Sampling Methods by Carvalho Martins, Luan, Cino, Elio A, Ferreira, Rafaela Salgado

“…Free energy perturbation (FEP) calculations are now routinely used in drug discovery to estimate the relative FEB (RFEB) of small molecules to a biomolecular…”
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Curvature-based sorting of eight lipid types in asymmetric buckled plasma membrane models by Cino, Elio A., Tieleman, D. Peter

“…Curvature is a fundamental property of biological membranes and has essential roles in cellular function. Bending of membranes can be induced by their lipid…”
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Curvature Footprints of Transmembrane Proteins in Simulations with the Martini Force Field by Cino, Elio A., Tieleman, D. Peter

“…Membranes play essential roles in biological systems and are tremendously diverse in the topologies and chemical and elastic properties that define their…”
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Sequence similarity in 3D for comparison of protein families by Lima, Igor, Cino, Elio A.

“…Homologous proteins are often compared by pairwise sequence alignment, and structure superposition if the atomic coordinates are available. Unification of…”
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Prediction of Binding Energy of Keap1 Interaction Motifs in the Nrf2 Antioxidant Pathway and Design of Potential High-Affinity Peptides by Karttunen, Mikko, Choy, Wing-Yiu, Cino, Elio A

“…Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor and principal regulator of the antioxidant pathway. The Kelch domain of Kelch-like…”
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Lipid distributions and transleaflet cholesterol migration near heterogeneous surfaces in asymmetric bilayers by Cino, Elio A, Borbuliak, Mariia, Hu, Shangnong, Tieleman, D Peter

“…Specific and nonspecific protein-lipid interactions in cell membranes have important roles in an abundance of biological functions. We have used coarse-grained…”
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Analyzing lipid distributions and curvature in molecular dynamics simulations of complex membranes by Cino, Elio A, Ramirez-Echemendia, Daniel P, Hu, Shangnong, Tieleman, D Peter

“…We describe methods to analyze lipid distributions and curvature in membranes with complex lipid mixtures and embedded membrane proteins. We discuss issues…”
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Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels by Maltarollo, Vinicius Gonçalves, Shevchenko, Ekaterina, Lima, Igor Daniel de Miranda, Cino, Elio A., Ferreira, Glaucio Monteiro, Poso, Antti, Kronenberger, Thales

“…The enzyme enoyl-ACP reductase (FabI) is the limiting step of the membrane’s fatty acid biosynthesis in bacteria and a druggable target for novel antibacterial…”
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Water Leakage Pathway Leads to Internal Hydration of the p53 Core Domain by Lima, Igor D. M., Pedrote, Murilo M., Marques, Mayra A., Sousa, Gileno dos S. de, Silva, Jerson L., de Oliveira, Guilherme A. P., Cino, Elio A.

“…The gene encoding the p53 tumor suppressor protein is the most frequently mutated oncogene in cancer patients; yet, generalized strategies for rescuing the…”
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Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations by Cino, Elio A, Choy, Wing-Yiu, Karttunen, Mikko

“…Intrinsically disordered proteins (IDPs) and regions are highly prevalent in eukaryotic proteomes, and like folded proteins, they perform essential biological…”
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Conformational dynamics of Tetracenomycin aromatase/cyclase regulate polyketide binding and enzyme aggregation propensity by Valadares, Veronica S., Martins, Luan C., Roman, Ernesto A., Valente, Ana Paula, Cino, Elio A., Moraes, Adolfo H.

“…The N-terminal domain of Tetracenomycin aromatase/cyclase (TcmN), an enzyme derived from Streptomyces glaucescens, is involved in polyketide cyclization,…”
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The C-terminal mutation beyond the catalytic site of brown spider phospholipase D significantly impacts its biological activities by Cunha, Laís Cardoso, Barreto, Lucas Passos, Valadares, Veronica Silva, Oliveira, Camila Franco Batista, Vuitika, Larissa, Vilela, Maura Páscoa, Cino, Elio A., Silva, Adolfo Henrique de Moraes, Nagem, Ronaldo A.P., Chávez-Olórtegui, Carlos, Dias-Lopes, Camila, Molina, Franck, Felicori, Liza

“…Loxosceles spider envenomation results in dermonecrosis, principally due to phospholipases D (PLDs) present in the venom. These enzymes have a strongly…”
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