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Škulj S, Kožić M, Barišić A, Vega A, Biarnés X, Piantanida I, Barisic I, Bertoša B. Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Comput Struct Biotechnol J 2024; 23:742-751. [PMID: 38298178 PMCID: PMC10828542 DOI: 10.1016/j.csbj.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.
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Affiliation(s)
- Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Aitor Vega
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10 000 Zagreb, Croatia
| | - Ivan Barisic
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Eko Refugium, Crno Vrelo 2, Slunj 47240, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
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2
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Alagesan K, Nagarajan H, Jeyakanthan J. Repurposing FDA-approved drugs for combating tigecycline resistance in Acinetobacter baumannii: in silico screening against BaeR protein. Mol Divers 2024:10.1007/s11030-024-10988-5. [PMID: 39327354 DOI: 10.1007/s11030-024-10988-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024]
Abstract
Acinetobacter baumannii is becoming a gravely threatening nosocomial infection with a higher mortality rate. The present study targets the BaeR protein that mediates resistance to tigecycline antibiotics. The BaeR protein, along with the aid of BaeS, senses the incoming antibiotics and stimulates the expression of resistance proteins. These resistance proteins efflux the antibiotics and protect the cells from its effect. The main goal of the current study is to determine potential inhibitors from already existing FDA-approved drugs that could mitigate the BaeR protein. A range of in silico approaches, including molecular dynamics, virtual screening, SIFT analysis, ADMET, DFT, MM/GBSA, MMPBSA and per residue interaction analysis, were performed to identify inhibitors against this protein. The screening of FDA-approved compounds against the BaeR protein yielded 620 compounds. These compounds were clustered by SIFT to distinguish related compounds, it resulted in 20 different clusters. The top five clusters that can accommodate the binding site with better interaction and score by fulfilling all criteria were selected. The DFT analysis showed a smaller energy gap among all the compounds, indicating the ability of the compound to form firm interactions. All the compounds showed less binding free energy in both MM/GBSA and MM/PBSA analyses. The compounds were observed to be stable throughout the simulation. The per-residue interaction analysis confirmed that interactions with binding site residues were stable throughout the simulation. As a result of the study, four compounds, namely ZINC000003801919, DB01203, DB11217 and ZINC0000000056652, were identified as efficient candidates to deal with antimicrobial resistance in A. baumannii.
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Affiliation(s)
- Karthika Alagesan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, Tamil Nadu, India.
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3
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Niu H, Li MY, Gao Y, Li JG, Jiang J, Ying YL, Long YT. Direct mapping of tyrosine sulfation states in native peptides by nanopore. Nat Chem Biol 2024:10.1038/s41589-024-01734-x. [PMID: 39322788 DOI: 10.1038/s41589-024-01734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
Abstract
Sulfation is considered the most prevalent post-translational modification (PTM) on tyrosine; however, its importance is frequently undervalued due to difficulties in direct and unambiguous determination from phosphorylation. Here we present a sequence-independent strategy to directly map and quantify the tyrosine sulfation states in universal native peptides using an engineered protein nanopore. Molecular dynamics simulations and nanopore mutations reveal specific interactions between tyrosine sulfation and the engineered nanopore, dominating identification across diverse peptide sequences. We show a nanopore framework to discover tyrosine sulfation in unknown peptide fragments digested from a native protein and determine the sequence of the sulfated fragment based on current blockade enhancement induced by sulfation. Moreover, our method allows direct observation of peptide sulfation in ultra-low abundance, down to 1%, and distinguishes it from isobaric phosphorylation. This sequence-independent strategy suggests the potential of nanopore to explore specific PTMs in real-life samples and at the omics level.
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Affiliation(s)
- Hongyan Niu
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Meng-Yin Li
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
| | - Yan Gao
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Jun-Ge Li
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Jie Jiang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Lun Ying
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Yi-Tao Long
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
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4
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Wang T, Coshic K, Badiee M, McDonald MR, Aksimentiev A, Pollack L, Leung AKL. Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nat Commun 2024; 15:7901. [PMID: 39256374 PMCID: PMC11387394 DOI: 10.1038/s41467-024-51972-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024] Open
Abstract
Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PAR's functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We identify diverse structural ensembles of PAR that fall into distinct subclasses and reveal distinct compaction of two different lengths of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR.
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Affiliation(s)
- Tong Wang
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Kush Coshic
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA
| | - Mohsen Badiee
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Maranda R McDonald
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
- Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA.
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA.
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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5
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da Silva Arouche T, Lobato JCM, Dos Santos Borges R, de Oliveira MS, de Jesus Chaves Neto AM. Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide. J Mol Model 2024; 30:203. [PMID: 38858279 DOI: 10.1007/s00894-024-05996-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024]
Abstract
CONTEXT The Omicron, Kappa, and Delta variants are different strains of the SARS-CoV-2 virus. Graphene oxide quantum dots (GOQDs) represent a burgeoning class of oxygen-enriched, zero-dimensional materials characterized by their sub-20-nm dimensions. Exhibiting pronounced quantum confinement and edge effects, GOQDs manifest exceptional physical-chemical attributes. This study delves into the potential of graphene oxide quantum dots, elucidating their inherent properties pertinent to the surface structures of SARS-CoV-2, employing an integrated computational approach for the repositioning of inhibitory agents. METHODS Following rigorous adjustment tests, a spectrum of divergent bonding conformations emerged, with particular emphasis placed on identifying the conformation exhibiting optimal adjustment scores and interactions. The investigation employed molecular docking simulations integrating affinity energy evaluations, electrostatic potential clouds, molecular dynamics encompassing average square root calculations, and the computation of Gibbs-free energy. These values quantify the strength of interaction between GOQDs and SARS-CoV-2 spike protein variants. The receptor structures were optimized using the CHARM-GUI server employing force field AMBERFF14SB. The algorithm embedded in CHARMM offers an efficient interpolation scheme and automatic step size selection, enhancing the efficiency of the optimization process. The 3D structures of the ligands are constructed and optimized with density functional theory (DFT) method based on the most stable conformer of each binder. Autodock Vina Software (ADV) was utilized, where essential parameters were specified. Electrostatic potential maps (MEPs) provide a visual depiction of molecules' charge distributions and related properties. After this, molecular dynamics simulations employing the CHARM36 force field in Gromacs 2022.2 were conducted to investigate GOs' interactions with surface macromolecules of SARS-CoV-2 in an explicit aqueous environment. Furthermore, our investigation suggests that lower values indicate stronger binding. Notably, GO-E consistently showed the most negative values across interactions with different variants, suggesting a higher affinity compared to other GOQDs (GO-A to GO-D).
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Affiliation(s)
- Tiago da Silva Arouche
- Laboratory of Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil
| | - Julio Cesar Mendes Lobato
- Laboratory of Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil
- Graduate Program in Natural Resources Engineering of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
| | - Rosivaldo Dos Santos Borges
- Universidade Federal do Pará, Departamento de Farmácia/Laboratório de Química Farmacêutica, Belem, PA, 66075-110, Brazil
| | | | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computing of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil.
- Graduate Program in Natural Resources Engineering of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil.
- Graduate Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil.
- Mestrado Nacional Profissional em Ensino de Física, Federal University of Pará, C. P.479, Belém, PA, 66075-110, Brazil.
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Gómez-Castro CZ, Quintanar L, Vela A. An N-terminal acidic β-sheet domain is responsible for the metal-accumulation properties of amyloid-β protofibrils: a molecular dynamics study. J Biol Inorg Chem 2024; 29:407-425. [PMID: 38811408 PMCID: PMC11186886 DOI: 10.1007/s00775-024-02061-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/10/2024] [Indexed: 05/31/2024]
Abstract
The influence of metal ions on the structure of amyloid- β (Aβ) protofibril models was studied through molecular dynamics to explore the molecular mechanisms underlying metal-induced Aβ aggregation relevant in Alzheimer's disease (AD). The models included 36-, 48-, and 188-mers of the Aβ42 sequence and two disease-modifying variants. Primary structural effects were observed at the N-terminal domain, as it became susceptible to the presence of cations. Specially when β-sheets predominate, this motif orients N-terminal acidic residues toward one single face of the β-sheet, resulting in the formation of an acidic region that attracts cations from the media and promotes the folding of the N-terminal region, with implications in amyloid aggregation. The molecular phenotype of the protofibril models based on Aβ variants shows that the AD-causative D7N mutation promotes the formation of N-terminal β-sheets and accumulates more Zn2+, in contrast to the non-amyloidogenic rodent sequence that hinders the β-sheets and is more selective for Na+ over Zn2+ cations. It is proposed that forming an acidic β-sheet domain and accumulating cations is a plausible molecular mechanism connecting the elevated affinity and concentration of metals in Aβ fibrils to their high content of β-sheet structure at the N-terminal sequence.
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Affiliation(s)
- Carlos Z Gómez-Castro
- Conahcyt-Universidad Autónoma del Estado de Hidalgo, Km 4.5 Carr. Pachuca-Tulancingo, Mineral de La Reforma, 42184, Hidalgo, Mexico.
| | - Liliana Quintanar
- Department of Chemistry, Cinvestav, Av. Instituto Politécnico Nacional 2508, CDMX, San Pedro Zacatenco, 07360, Gustavo A. Madero, Mexico.
| | - Alberto Vela
- Department of Chemistry, Cinvestav, Av. Instituto Politécnico Nacional 2508, CDMX, San Pedro Zacatenco, 07360, Gustavo A. Madero, Mexico.
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7
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Coshic K, Maffeo C, Winogradoff D, Aksimentiev A. The structure and physical properties of a packaged bacteriophage particle. Nature 2024; 627:905-914. [PMID: 38448589 PMCID: PMC11196859 DOI: 10.1038/s41586-024-07150-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.
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Affiliation(s)
- Kush Coshic
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher Maffeo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Winogradoff
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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8
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Wang T, Coshic K, Badiee M, Aksimentiev A, Pollack L, Leung AKL. Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564012. [PMID: 37961637 PMCID: PMC10634823 DOI: 10.1101/2023.10.25.564012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Poly(ADP-ribose) (PAR), as part of a post-translational modification, serves as a flexible scaffold for noncovalent protein binding. Such binding is influenced by PAR chain length through a mechanism yet to be elucidated. Structural insights have been elusive, partly due to the difficulties associated with synthesizing PAR chains of defined lengths. Here, we employ an integrated approach combining molecular dynamics (MD) simulations with small-angle X-ray scattering (SAXS) experiments, enabling us to identify highly heterogeneous ensembles of PAR conformers at two different, physiologically relevant lengths: PAR 15 and PAR 22 . Our findings reveal that numerous factors including backbone conformation, base stacking, and chain length contribute to determining the structural ensembles. We also observe length-dependent compaction of PAR upon the addition of small amounts of Mg 2+ ions, with the 22-mer exhibiting ADP-ribose bundles formed through local intramolecular coil-to-globule transitions. This study illuminates how such bundling could be instrumental in deciphering the length-dependent action of PAR. GRAPHICAL ABSTRACT
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9
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Zazeri G, Povinelli APR, Pavan NM, Jones AM, Ximenes VF. Solvent-Induced Lag Phase during the Formation of Lysozyme Amyloid Fibrils Triggered by Sodium Dodecyl Sulfate: Biophysical Experimental and In Silico Study of Solvent Effects. Molecules 2023; 28:6891. [PMID: 37836734 PMCID: PMC10574774 DOI: 10.3390/molecules28196891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Amyloid aggregates arise from either the partial or complete loss of the native protein structure or the inability of proteins to attain their native conformation. These aggregates have been linked to several diseases, including Alzheimer's, Parkinson's, and lysozyme amyloidosis. A comprehensive dataset was recently reported, demonstrating the critical role of the protein's surrounding environment in amyloid formation. In this study, we investigated the formation of lysozyme amyloid fibrils induced by sodium dodecyl sulfate (SDS) and the effect of solvents in the medium. Experimental data obtained through fluorescence spectroscopy revealed a notable lag phase in amyloid formation when acetone solution was present. This finding suggested that the presence of acetone in the reaction medium created an unfavorable microenvironment for amyloid fibril formation and impeded the organization of the denatured protein into the fibril form. The in silico data provided insights into the molecular mechanism of the interaction between acetone molecules and the lysozyme protofibril, once acetone presented the best experimental results. It was observed that the lysozyme protofibril became highly unstable in the presence of acetone, leading to the complete loss of its β-sheet conformation and resulting in an open structure. Furthermore, the solvation layer of the protofibril in acetone solution was significantly reduced compared to that in other solvents, resulting in fewer hydrogen bonds. Consequently, the presence of acetone facilitated the exposure of the hydrophobic portion of the protofibril, precluding the amyloid fibril formation. In summary, our study underscores the pivotal role the surrounding environment plays in influencing amyloid formation.
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Affiliation(s)
- Gabriel Zazeri
- Federal Institute of Education, Science and Technology of Mato Grosso (IFMT), Campo Novo do Parecis 78360-000, Brazil;
| | - Ana Paula Ribeiro Povinelli
- Federal Institute of Education, Science and Technology of Mato Grosso (IFMT), Campo Novo do Parecis 78360-000, Brazil;
| | - Nathália Mariana Pavan
- Department of Chemistry, Faculty of Sciences, São Paulo State University (UNESP), Bauru 17033-360, Brazil;
| | - Alan M. Jones
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Valdecir Farias Ximenes
- Department of Chemistry, Faculty of Sciences, São Paulo State University (UNESP), Bauru 17033-360, Brazil;
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10
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Kreiter J, Škulj S, Brkljača Z, Bardakji S, Vazdar M, Pohl EE. FA Sliding as the Mechanism for the ANT1-Mediated Fatty Acid Anion Transport in Lipid Bilayers. Int J Mol Sci 2023; 24:13701. [PMID: 37762012 PMCID: PMC10531397 DOI: 10.3390/ijms241813701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Mitochondrial adenine nucleotide translocase (ANT) exchanges ADP for ATP to maintain energy production in the cell. Its protonophoric function in the presence of long-chain fatty acids (FA) is also recognized. Our previous results imply that proton/FA transport can be best described with the FA cycling model, in which protonated FA transports the proton to the mitochondrial matrix. The mechanism by which ANT1 transports FA anions back to the intermembrane space remains unclear. Using a combined approach involving measurements of the current through the planar lipid bilayers reconstituted with ANT1, site-directed mutagenesis and molecular dynamics simulations, we show that the FA anion is first attracted by positively charged arginines or lysines on the matrix side of ANT1 before moving along the positively charged protein-lipid interface and binding to R79, where it is protonated. We show that R79 is also critical for the competitive binding of ANT1 substrates (ADP and ATP) and inhibitors (carboxyatractyloside and bongkrekic acid). The binding sites are well conserved in mitochondrial SLC25 members, suggesting a general mechanism for transporting FA anions across the inner mitochondrial membrane.
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Affiliation(s)
- Jürgen Kreiter
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Sanja Škulj
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, 10000 Zagreb, Croatia;
| | - Sarah Bardakji
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
| | - Mario Vazdar
- Department of Mathematics, Informatics, and Cybernetics, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Elena E. Pohl
- Institute of Physiology, Pathophysiology, and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (S.Š.); (S.B.)
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11
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Jiang J, Li MY, Wu XY, Ying YL, Han HX, Long YT. Protein nanopore reveals the renin-angiotensin system crosstalk with single-amino-acid resolution. Nat Chem 2023; 15:578-586. [PMID: 36805037 DOI: 10.1038/s41557-023-01139-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/13/2023] [Indexed: 02/22/2023]
Abstract
The discovery of crosstalk effects on the renin-angiotensin system (RAS) is limited by the lack of approaches to quantitatively monitor, in real time, multiple components with subtle differences and short half-lives. Here we report a nanopore framework to quantitatively determine the effect of the hidden crosstalk between angiotensin-converting enzyme (ACE) and angiotensin-converting enzyme 2 (ACE2) on RAS. By developing an engineered aerolysin nanopore capable of single-amino-acid resolution, we show that the ACE can be selectively inhibited by ACE2 to prevent cleavage of angiotensin I, even when the concentration of ACE is more than 30-fold higher than that of ACE2. We also show that the activity of ACE2 for cleaving angiotensin peptides is clearly suppressed by the spike protein of SARS-CoV-2. This leads to the relaxation of ACE and the increased probability of accumulation of the principal effector angiotensin II. The spike protein of the SARS-CoV-2 Delta variant is demonstrated to have a much greater impact on the crosstalk than the wild type.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Huan-Xing Han
- Department of Pharmacy, Shanghai Changzheng Hospital, Shanghai, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
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12
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Rosales-Hernández MC, Bello M, Toledano JV, Feregrino BCE, Correa Basurto J, Fragoso Morales LG, Torres-Ramos MA. Molecular dynamics simulations depict structural motions of the whole human aryl hydrocarbon receptor influencing its binding of ligands and HSP90. J Biomol Struct Dyn 2023; 41:13138-13153. [PMID: 36705144 DOI: 10.1080/07391102.2023.2171132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/15/2023] [Indexed: 01/28/2023]
Abstract
The aryl hydrocarbon receptor (AhR) has broad biological functions when its ligands activate it; the non-binding interactions with AhR have not been fully elucidated due to the absence of a complete tridimensional (3D) structure. Therefore, utilization of the whole 3D structure from Homo sapiens AhR by in silico studies will allow us to better study and analyze the binding mode of its full and partial agonists, and antagonists, as well as its interaction with the HSP90 chaperone. The 3D AhR structure was obtained from I-TASSER and subjected to molecular dynamics (MD) simulations to obtain different structural conformations and determine the most populated AhR conformer by clustering analyses. The AhR-3D structures selected from MD simulations and those from clustering analyses were used to achieve docking studies with some of its ligands and protein-protein docking with HSP90. Once the AhR-3D structure was built, its Ramachandran maps and energy showed a well-qualified 3D model. MD simulations showed that the per-Arnt-Sim homology (PAS) PAS A, PAS B, and Q domains underwent conformational changes, identifying the conformation when agonists were binding also, and HSP90 was binding near the PAS A, PAS B, and Q domains. However, when antagonists are binding, HSP90 does not bind near the PAS A, PAS B, and Q domains. These studies show that the complex agonist-AhR-HSP90 can be formed, but this complex is not formed when an antagonist is binding. Knowing the conformations when the ligands bind to AHR and the behavior of HSP90 allows for an understanding of its activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Jazziel Velazquez Toledano
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Barbara Citlali Escudero Feregrino
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
- Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Mexico City, México
| | - José Correa Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Leticia Guadalupe Fragoso Morales
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
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13
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Joshi H, Li CY, Aksimentiev A. All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores. Methods Mol Biol 2023; 2639:113-128. [PMID: 37166714 DOI: 10.1007/978-1-0716-3028-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.
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Affiliation(s)
- Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Chen-Yu Li
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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14
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4-Dimethylamino-beta-nitrostyrene, a fluorescent solvatochromic probe to estimate the apparent dielectric constant in serum albumin: Experimental and molecular dynamics studies. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Chen LY. Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183975. [PMID: 35654150 DOI: 10.1016/j.bbamem.2022.183975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37 °C.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, The University of Texas at San Antonio, San Antonio, TX 78249, USA.
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16
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Povinelli APR, Zazeri G, Jones AM, Cornélio ML. A Computational–Experimental Investigation of the Molecular Mechanism of Interleukin-6-Piperine Interaction. Int J Mol Sci 2022; 23:ijms23147994. [PMID: 35887341 PMCID: PMC9323498 DOI: 10.3390/ijms23147994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we elucidate the biophysical aspects of the interaction of an important protein, Interleukin-6 (IL6), which is involved in cytokine storm syndrome, with a natural product with anti-inflammatory activity, piperine. Despite the role of piperine in the inhibition of the transcriptional protein NF-κB pathway responsible for activation of IL6 gene expression, there are no studies to the best of our knowledge regarding the characterisation of the molecular interaction of the IL6-piperine complex. In this context, the characterisation was performed with spectroscopic experiments aided by molecular modelling. Fluorescence spectroscopy alongside van’t Hoff analyses showed that the complexation event is a spontaneous process driven by non-specific interactions. Circular dichroism aided by molecular dynamics revealed that piperine caused local α-helix reduction. Molecular docking and molecular dynamics disclosed the microenvironment of interaction as non-polar amino acid residues. Although piperine has three available hydrogen bond acceptors, only one hydrogen-bond was formed during our simulation experiments, reinforcing the major role of non-specific interactions that we observed experimentally. Root mean square deviation (RMSD) and hydrodynamic radii revealed that the IL6-piperine complex was stable during 800 ns of simulation. Taken together, these results can support ongoing IL6 drug discovery efforts.
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Affiliation(s)
- Ana Paula Ribeiro Povinelli
- Federal Institute of Education, Science and Technology of Mato Grosso, Campo Novo do Parecis 78360-000, Brazil;
| | - Gabriel Zazeri
- Federal Institute of Education, Science and Technology of Mato Grosso, Campo Novo do Parecis 78360-000, Brazil;
- Correspondence: (G.Z.); (M.L.C.)
| | - Alan M. Jones
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Marinônio Lopes Cornélio
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
- Correspondence: (G.Z.); (M.L.C.)
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17
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Vázquez-Durán A, Téllez-Isaías G, Hernández-Rodríguez M, Ruvalcaba RM, Martínez J, Nicolás-Vázquez MI, Aceves-Hernández JM, Méndez-Albores A. The Ability of Chlorophyll to Trap Carcinogen Aflatoxin B 1: A Theoretical Approach. Int J Mol Sci 2022; 23:6068. [PMID: 35682746 PMCID: PMC9181093 DOI: 10.3390/ijms23116068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
The coordination of one and two aflatoxin B1 (AFB1, a potent carcinogen) molecules with chlorophyll a (chl a) was studied at a theoretical level. Calculations were performed using the M06-2X method in conjunction with the 6-311G(d,p) basis set, in both gas and water phases. The molecular electrostatic potential map shows the chemical activity of various sites of the AFB1 and chl a molecules. The energy difference between molecular orbitals of AFB1 and chl a allowed for the establishment of an intermolecular interaction. A charge transfer from AFB1 to the central cation of chl a was shown. The energies of the optimized structures for chl a show two configurations, unfolded and folded, with a difference of 15.41 kcal/mol. Chl a appeared axially coordinated to the plane (α-down or β-up) of the porphyrin moiety, either with the oxygen atom of the ketonic group, or with the oxygen atom of the lactone moiety of AFB1. The complexes of maximum stability were chl a 1-α-E-AFB1 and chl a 2-β-E-AFB1, at -36.4 and -39.2 kcal/mol, respectively. Additionally, with two AFB1 molecules were chl a 1-D-2AFB1 and chl a 2-E-2AFB1, at -60.0 and -64.8 kcal/mol, respectively. Finally, biosorbents containing chlorophyll could improve AFB1 adsorption.
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Affiliation(s)
- Alma Vázquez-Durán
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de Mexico 54714, Mexico; (A.V.-D.); (J.M.A.-H.); (A.M.-A.)
| | | | - Maricarmen Hernández-Rodríguez
- Laboratorio de Cultivo Celular, Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico;
| | - René Miranda Ruvalcaba
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de Mexico 54740, Mexico;
| | - Joel Martínez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosi 78210, Mexico
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de Mexico 54740, Mexico;
| | - Juan Manuel Aceves-Hernández
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de Mexico 54714, Mexico; (A.V.-D.); (J.M.A.-H.); (A.M.-A.)
| | - Abraham Méndez-Albores
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de Mexico 54714, Mexico; (A.V.-D.); (J.M.A.-H.); (A.M.-A.)
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18
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Maffeo C, Chou HY, Aksimentiev A. Single-molecule biophysics experiments in silico: Toward a physical model of a replisome. iScience 2022; 25:104264. [PMID: 35521518 PMCID: PMC9062759 DOI: 10.1016/j.isci.2022.104264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments outright with computational mimics. Here, we offer a blueprint for performing single-molecule studies in silico using a DNA-binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic single-molecule experiments. We apply the model to recapitulate, in silico, force-extension characterization of protein binding to single-stranded DNA and protein and DNA replacement assays, providing a detailed portrait of the underlying mechanics. Finally, we use the model to simulate the trombone loop of a replication fork, a large complex of proteins and DNA. Coarse-grained model derived from all-atom simulation recapitulates experiments Model reproduces the elastic response to force and exchange dynamics Model reveals structure of intermediate states usually inaccessible to experiment Model applied to viral replisome with trombone loop containing tens of SSB proteins
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
| | - Han-Yi Chou
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
- Corresponding author
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19
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O’Connor S, Le Bihan YV, Westwood IM, Liu M, Mak OW, Zazeri G, Povinelli APR, Jones AM, van Montfort R, Reynisson J, Collins I. Discovery and Characterization of a Cryptic Secondary Binding Site in the Molecular Chaperone HSP70. Molecules 2022; 27:817. [PMID: 35164081 PMCID: PMC8839746 DOI: 10.3390/molecules27030817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/23/2022] Open
Abstract
Heat Shock Protein 70s (HSP70s) are key molecular chaperones that are overexpressed in many cancers and often associated with metastasis and poor prognosis. It has proven difficult to develop ATP-competitive, drug-like small molecule inhibitors of HSP70s due to the flexible and hydrophilic nature of the HSP70 ATP-binding site and its high affinity for endogenous nucleotides. The aim of this study was to explore the potential for the inhibition of HSP70 through alternative binding sites using fragment-based approaches. A surface plasmon resonance (SPR) fragment screen designed to detect secondary binding sites in HSP70 led to the identification by X-ray crystallography of a cryptic binding site in the nucleotide-binding domain (NBD) of HSP70 adjacent to the ATP-binding site. Fragment binding was confirmed and characterized as ATP-competitive using SPR and ligand-observed NMR methods. Molecular dynamics simulations were applied to understand the interactions with the protein upon ligand binding, and local secondary structure changes consistent with interconversion between the observed crystal structures with and without the cryptic pocket were detected. A virtual high-throughput screen (vHTS) against the cryptic pocket was conducted, and five compounds with diverse chemical scaffolds were confirmed to bind to HSP70 with micromolar affinity by SPR. These results identified and characterized a new targetable site on HSP70. While targeting HSP70 remains challenging, the new site may provide opportunities to develop allosteric ATP-competitive inhibitors with differentiated physicochemical properties from current series.
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Affiliation(s)
- Suzanne O’Connor
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Isaac M. Westwood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Oi Wei Mak
- School of Pharmacy and Bioengineering, Keele University, Keele ST5 5BG, UK; (O.W.M.); (J.R.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gabriel Zazeri
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
| | - Ana P. R. Povinelli
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
| | - Alan M. Jones
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
| | - Rob van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Keele ST5 5BG, UK; (O.W.M.); (J.R.)
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
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20
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Škulj S, Barišić A, Mutter N, Spadiut O, Barišić I, Bertoša B. Effect of N-glycosylation on horseradish peroxidase structural and dynamical properties. Comput Struct Biotechnol J 2022; 20:3096-3105. [PMID: 35782731 PMCID: PMC9233188 DOI: 10.1016/j.csbj.2022.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022] Open
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21
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Unravelling the Interaction of Piperlongumine with the Nucleotide-Binding Domain of HSP70: A Spectroscopic and In Silico Study. Pharmaceuticals (Basel) 2021; 14:ph14121298. [PMID: 34959698 PMCID: PMC8703466 DOI: 10.3390/ph14121298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Piperlongumine (PPL) is an alkaloid extracted from several pepper species that exhibits anti-inflammatory and anti-carcinogenic properties. Nevertheless, the molecular mode of action of PPL that confers such powerful pharmacological properties remains unknown. From this perspective, spectroscopic methods aided by computational modeling were employed to characterize the interaction between PPL and nucleotide-binding domain of heat shock protein 70 (NBD/HSP70), which is involved in the pathogenesis of several diseases. Steady-state fluorescence spectroscopy along with time-resolved fluorescence revealed the complex formation based on a static quenching mechanism. Van't Hoff analyses showed that the binding of PPL toward NBD is driven by equivalent contributions of entropic and enthalpic factors. Furthermore, IDF and Scatchard methods applied to fluorescence intensities determined two cooperative binding sites with Kb of (6.3 ± 0.2) × 104 M-1. Circular dichroism determined the thermal stability of the NBD domain and showed that PPL caused minor changes in the protein secondary structure. Computational simulations elucidated the microenvironment of these interactions, showing that the binding sites are composed mainly of polar amino acids and the predominant interaction of PPL with NBD is Van der Waals in nature.
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22
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Setayesh-Mehr Z, Poorsargol M. HL-7 and HL-10 Peptides Stimulate Insulin Secretion in the INS-1 Insulinoma Cell Line through Incretin-Dependent Pathway and Increasing the Glucose Uptake in L6 Myoblast. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10249-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Li MY, Ying YL, Yu J, Liu SC, Wang YQ, Li S, Long YT. Revisiting the Origin of Nanopore Current Blockage for Volume Difference Sensing at the Atomic Level. JACS AU 2021; 1:967-976. [PMID: 34467343 PMCID: PMC8395674 DOI: 10.1021/jacsau.1c00109] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 05/21/2023]
Abstract
Changes in the nanopore ionic current during entry of a target molecule underlie the sensing capability and dominate the intensity and extent of applications of the nanopore approach. The volume exclusion model has been proposed and corrected to describe the nanopore current blockage. However, increasing evidence shows nonconformity with this model, suggesting that the ionic current within a nanopore should be entirely reconsidered. Here, we revisit the origin of nanopore current blockage from a theoretical perspective and propose that the noncovalent interactions between a nanopore and a target molecule affect the conductance of the solution inside the nanopore, leading to enhanced current blockage. Moreover, by considering the example of an aerolysin nanopore discriminating the cytosine DNA and methylcytosine DNA that differ by a single methyl group, we completely demonstrate, by nanopore experiments and molecular dynamics simulations, the essential nature of this noncovalent interaction for discrimination. Our conductance model suggests multiplicative effects of both volume exclusion and noncovalent interaction on the current blockage and provides a new strategy to achieve volume difference sensing at the atomic level with highly specific current events, which would promote the nanopore protein sequencing and its applications in real-life systems.
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Affiliation(s)
- Meng-Yin Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
- Chemistry
and Biomedicine Innovation Center, Nanjing
University, Nanjing 210023, P.R. China
| | - Yi-Lun Ying
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
- Chemistry
and Biomedicine Innovation Center, Nanjing
University, Nanjing 210023, P.R. China
| | - Jie Yu
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Shao-Chuang Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
| | - Ya-Qian Wang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Shuang Li
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Yi-Tao Long
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
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24
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Jung J, Kasahara K, Kobayashi C, Oshima H, Mori T, Sugita Y. Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems. J Chem Theory Comput 2021; 17:5312-5321. [PMID: 34278793 DOI: 10.1021/acs.jctc.1c00185] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, molecular dynamics (MD) simulations with larger time steps have been performed with the hydrogen-mass-repartitioning (HMR) scheme, where the mass of each hydrogen atom is increased to reduce high-frequency motion while the mass of a non-hydrogen atom bonded to a hydrogen atom is decreased to keep the total molecular mass unchanged. Here, we optimize the scaling factors in HMR and combine them with previously developed accurate temperature/pressure evaluations. The heterogeneous HMR scaling factors are useful to avoid the structural instability of amino acid residues having a five- or six-membered ring in MD simulations with larger time steps. It also reproduces kinetic properties, namely translational and rotational diffusions, if the HMR scaling factors are applied to only solute molecules. The integration scheme is tested for biological systems that include soluble/membrane proteins and lipid bilayers for about 200 μs MD simulations in total and give consistent results in MD simulations with both a small time step of 2.0 fs and a large, multiple time step integration with time steps of 3.5 fs (for fast motions) and 7.0 fs (for slower motions). We also confirm that the multiple time step integration scheme used in this study provides more accurate energy conservations than the RESPA/C1 and is comparable to the RESPA/C2 in NAMD. In summary, the current integration scheme combining the optimized HMR with accurate temperature/pressure evaluations can provide stable and reliable MD trajectories with a larger time step, which are computationally more than 2-fold efficient compared to the conventional methods.
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Affiliation(s)
- Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kento Kasahara
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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25
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Díaz-Hernández M, Javier-Reyna R, Sotto-Ortega I, García-Rivera G, Montaño S, Betanzos A, Zanatta D, Orozco E. Protein Sumoylation Is Crucial for Phagocytosis in Entamoeba histolytica Trophozoites. Int J Mol Sci 2021; 22:ijms22115709. [PMID: 34071922 PMCID: PMC8198320 DOI: 10.3390/ijms22115709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 01/12/2023] Open
Abstract
Posttranslational modifications provide Entamoeba histolytica proteins the timing and signaling to intervene during different processes, such as phagocytosis. However, SUMOylation has not been studied in E. histolytica yet. Here, we characterized the E. histolytica SUMO gene, its product (EhSUMO), and the relevance of SUMOylation in phagocytosis. Our results indicated that EhSUMO has an extended N-terminus that differentiates SUMO from ubiquitin. It also presents the GG residues at the C-terminus and the ΨKXE/D binding motif, both involved in target protein contact. Additionally, the E. histolytica genome possesses the enzymes belonging to the SUMOylation-deSUMOylation machinery. Confocal microscopy assays disclosed a remarkable EhSUMO membrane activity with convoluted and changing structures in trophozoites during erythrophagocytosis. SUMOylated proteins appeared in pseudopodia, phagocytic channels, and around the adhered and ingested erythrocytes. Docking analysis predicted interaction of EhSUMO with EhADH (an ALIX family protein), and immunoprecipitation and immunofluorescence assays revealed that the association increased during phagocytosis; whereas the EhVps32 (a protein of the ESCRT-III complex)-EhSUMO interaction appeared stronger since basal conditions. In EhSUMO knocked-down trophozoites, the bizarre membranous structures disappeared, and EhSUMO interaction with EhADH and EhVps32 diminished. Our results evidenced the presence of a SUMO gene in E. histolytica and the SUMOylation relevance during phagocytosis. This is supported by bioinformatics screening of many other proteins of E. histolytica involved in phagocytosis, which present putative SUMOylation sites and the ΨKXE/D binding motif.
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Affiliation(s)
- Mitzi Díaz-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Rosario Javier-Reyna
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Izaid Sotto-Ortega
- Bacteriología y Laboratorio Clínico, Universidad de Santander, 200004 Valledupar, Colombia;
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Sarita Montaño
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Sinaloa 80030, Mexico;
| | - Abigail Betanzos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
- Consejo Nacional de Ciencia y Tecnología (Conacyt), Mexico City 03940, Mexico
| | - Dxinegueela Zanatta
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
- Correspondence: ; Tel.: +52-55-5747-5642
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26
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Hernandes-Alejandro M, Montaño S, Harrington CR, Wischik CM, Salas-Casas A, Cortes-Reynosa P, Pérez Salazar E, Cazares-Apatiga J, Apatiga-Perez R, Ontiveros Torres MÁ, Perry G, Pacheco-Herrero M, Luna-Muñoz J. Analysis of the Relationship Between Metalloprotease-9 and Tau Protein in Alzheimer's Disease. J Alzheimers Dis 2021; 76:553-569. [PMID: 32538846 DOI: 10.3233/jad-200146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Neurofibrillary tangles (NFTs) and amyloid plaques are the neuropathological hallmarks in brains with Alzheimer's disease (AD). Post-translational modifications of tau, such as phosphorylation and truncation, have been proposed as initiators in the assembly of the abnormal paired helical filaments that constitute the NFTs. Neurons and NFTs are sites of matrix metalloproteinases (MMPs). OBJECTIVE The aim of this study was to analyze the relationship of MMP-9 and tau protein in brain samples with AD. METHODS This study was performed on brain tissue samples from patients with early, moderate, and late AD. MMPs and tau levels were analyzed by western blot and gelatin-substrate zymography. Immunofluorescence techniques and confocal microscopy were used to analyze the presence of both proteins in NFTs. Further, molecular dynamics simulations (MDS) and protein-protein docking were conducted to predict interaction between MMP-9 and tau protein. RESULTS MMP-9 expression was greatest in moderate and late AD, whereas MMP-2 expression was only increased in late-stage AD. Interestingly, confocal microscopy revealed NFTs in which there was co-localization of MMP-9 and tau protein. MDS and protein-protein docking predictions indicate that a high-affinity complex can be formed between MMP-9 and full-length tau protein. CONCLUSION These observations provide preliminary evidence of an interaction between these two proteins. Post-translational modifications of tau protein, such as C-terminal truncation or phosphorylation of amino acid residues in the MMP-9 recognition site and conformational changes in the protein, such as folding of the N-terminal sequence over the three-repeat domain, could preclude the interaction between MMP-9 and tau protein during stages of NFT development.
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Affiliation(s)
- Mario Hernandes-Alejandro
- Departamento de Bioingeniería, Unidad Profesional Interdisciplinaria de Biotecnología del Instituto Politécnico Nacional (UPIBI-IPN), Gustavo A. Madero, México
| | - Sarita Montaño
- Laboratorio de Modelado Molecular y Bioinformática de la Facultad de Ciencias-Químico Biológicas de la Universidad Autónoma de Sinaloa, México
| | - Charles R Harrington
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Claude M Wischik
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Andrés Salas-Casas
- Instituto de Ciencias de la Salud, Área Académica de Gerontología Universidad Autónoma del Estado de Hidalgo, México
| | - Pedro Cortes-Reynosa
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN (Instituto Politécnico Nacional), Gustavo A. Madero, México
| | - Eduardo Pérez Salazar
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN (Instituto Politécnico Nacional), Gustavo A. Madero, México
| | - Javier Cazares-Apatiga
- Laboratorio de Biología Molecular y Bioseguridad Nivel 3, Centro Médico Naval, CDMX, México
| | - Ricardo Apatiga-Perez
- Escuela Nacional de Ciencias Biológicas, Depto. Fisiología, Instituto Politécnico Nacional, CDMX, Mexico.,National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores, Cuautitlán campo 1, UNAM, Estado de México, México
| | | | - George Perry
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Mar Pacheco-Herrero
- School of Medicine, Faculty of Health Sciences, Pontificia Universidad Catolica Madre y Maestra, Dominican Republic
| | - José Luna-Muñoz
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores, Cuautitlán campo 1, UNAM, Estado de México, México
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27
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Schlick T, Portillo-Ledesma S. Biomolecular modeling thrives in the age of technology. NATURE COMPUTATIONAL SCIENCE 2021; 1:321-331. [PMID: 34423314 PMCID: PMC8378674 DOI: 10.1038/s43588-021-00060-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
Abstract
The biomolecular modeling field has flourished since its early days in the 1970s due to the rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase in size and timespan of biomolecular simulations has outpaced Moore's law. Here, we discuss the role of knowledge-based versus physics-based methods and hardware versus software advances in propelling the field forward. This rapid adaptation and outreach suggests a bright future for modeling, where theory, experimentation and simulation define three pillars needed to address future scientific and biomedical challenges.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
- New York University–East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China
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28
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Hübner K, Joshi H, Aksimentiev A, Stefani FD, Tinnefeld P, Acuna GP. Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures. ACS NANO 2021; 15:5109-5117. [PMID: 33660975 DOI: 10.1021/acsnano.0c10259] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores' binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise double-stranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores' probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.
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Affiliation(s)
- Kristina Hübner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH-1700, Switzerland
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29
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Patel S, Srivastav AK, Gupta SK, Kumar U, Mahapatra SK, Gajjar PN, Banerjee I. Carbon nanotubes for rapid capturing of SARS-COV-2 virus: revealing a mechanistic aspect of binding based on computational studies. RSC Adv 2021; 11:5785-5800. [PMID: 35423109 PMCID: PMC8694767 DOI: 10.1039/d0ra08888a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
We investigate the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus. Two essential components of the SARS-CoV-2 structure i.e.6LU7 (main protease of SARS-CoV-2) and 6LZG (spike receptor-binding domain complexed with its receptor ACE2) were used for computational studies. MWCNTs of different morphologies (zigzag, armchair and chiral) were synthesized through a thermal chemical vapour deposition process as a function of pyrolysis temperature. A direct correlation between radius to volume ratio of the synthesized MWCNTs and the binding energies for all three (zigzag, armchair and chiral) conformations were observed in our computational studies. Our result suggests that MWCNTs interact with the active sites of the main protease along with the host angiotensin-converting enzyme2 (ACE2) receptors. Furthermore, it is also observed that MWCNTs have significant binding affinities towards SARS-CoV-2. However, the highest free binding energy of -87.09 kcal mol-1 with 6LZG were shown by the armchair MWCNTs with SARS-CoV-2 through the simulated molecular dynamic trajectories, which could alter the SARS-CoV-2 structure with higher accuracy. The radial distribution function also confirms the density variation as a function of distance from a reference particle of MWCNTs for the study of interparticle interactions of the MWCNT and SARS-CoV-2. Due to these interesting attributes, such MWCNTs could find potential application in personal protective equipment (PPE) and diagnostic kits.
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Affiliation(s)
- Shivkumar Patel
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
| | | | - Sanjeev K Gupta
- Computational Materials and Nanoscience Group, Department of Physics, St. Xavier's College Ahmedabad 380009 India
| | - Umesh Kumar
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
| | - S K Mahapatra
- Department of Physics, Central University of Punjab Bathinda 151001 India
| | - P N Gajjar
- Department of Physics, University School of Sciences, Gujarat University Ahmedabad 380009 India
| | - I Banerjee
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
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30
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Detailed Characterization of the Cooperative Binding of Piperine with Heat Shock Protein 70 by Molecular Biophysical Approaches. Biomedicines 2020; 8:biomedicines8120629. [PMID: 33353024 PMCID: PMC7766160 DOI: 10.3390/biomedicines8120629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
In this work, for the first time, details of the complex formed by heat shock protein 70 (HSP70) independent nucleotide binding domain (NBD) and piperine were characterized through experimental and computational molecular biophysical methods. Fluorescence spectroscopy results revealed positive cooperativity between the two binding sites. Circular dichroism identified secondary conformational changes. Molecular dynamics along with molecular mechanics Poisson Boltzmann surface area (MM/PBSA) reinforced the positive cooperativity, showing that the affinity of piperine for NBD increased when piperine occupied both binding sites instead of one. The spontaneity of the complexation was demonstrated through the Gibbs free energy (∆G < 0 kJ/mol) for different temperatures obtained experimentally by van’t Hoff analysis and computationally by umbrella sampling with the potential of mean force profile. Furthermore, the mean forces which drove the complexation were disclosed by van’t Hoff and MM/PBSA as being the non-specific interactions. In conclusion, the work revealed characteristics of NBD and piperine interaction, which may support further drug discover studies.
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31
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Choudhary A, Joshi H, Chou HY, Sarthak K, Wilson J, Maffeo C, Aksimentiev A. High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System. ACS NANO 2020; 14:15566-15576. [PMID: 33174731 PMCID: PMC8848087 DOI: 10.1021/acsnano.0c06191] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing-an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores-could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion-flossing-of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.
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Affiliation(s)
- Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Han-Yi Chou
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kumar Sarthak
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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32
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Yang SC, Li B, Zhu YL, Laaksonen A, Wang YL. The ENUF method-Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application. J Comput Chem 2020; 41:2316-2335. [PMID: 32808686 DOI: 10.1002/jcc.26395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 11/12/2022]
Abstract
Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between charged particles constitute a prominent factor in determining structures and states of model systems. How to efficiently calculate electrostatic interactions in simulation systems subjected to partial or full periodic boundary conditions has been a grand challenging task. In the past decades, a large variety of computational schemes has been proposed, among which the Ewald summation method is the most reliable route to accurately deal with electrostatic interactions between charged particles in simulation systems. In addition, extensive efforts have been done to improve computational efficiencies of the Ewald summation based methods. Representative examples are approaches based on cutoffs, reaction fields, multi-poles, multi-grids, and particle-mesh schemes. We sketched an ENUF method, an abbreviation for the Ewald summation method based on the nonuniform fast Fourier transform technique, and have implemented this method in particle-based simulation packages to calculate electrostatic energies and forces at micro- and mesoscopic levels. Extensive computational studies of conformational properties of polyelectrolytes, dendrimer-membrane complexes, and ionic fluids demonstrated that the ENUF method and its derivatives conserve both energy and momentum to floating point accuracy, and exhibit a computational complexity of O N log N with optimal physical parameters. These ENUF based methods are attractive alternatives in molecular simulations where high accuracy and efficiency of simulation methods are needed to accelerate calculations of electrostatic interactions at extended spatiotemporal scales.
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Affiliation(s)
- Sheng-Chun Yang
- School of Computer Science, Northeast Electric Power University, Jilin, China
| | - Bin Li
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai, China
| | - You-Liang Zhu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, Iasi, Romania.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
| | - Yong-Lei Wang
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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33
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Zazeri G, Povinelli APR, de Freitas Lima M, Cornélio ML. The Cytokine IL-1β and Piperine Complex Surveyed by Experimental and Computational Molecular Biophysics. Biomolecules 2020; 10:biom10091337. [PMID: 32962126 PMCID: PMC7563551 DOI: 10.3390/biom10091337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/16/2023] Open
Abstract
The bioactive piperine, a compound found in some pepper species, has been widely studied because of its therapeutic properties that include the inhibition of an important inflammation pathway triggered by interleukin-1 beta (IL-1β). However, investigation into the molecular interactions between IL-1β and piperine is not reported in the literature. Here, we present for the first time the characterisation of the complex formed by IL-1β and piperine through experimental and computational molecular biophysical analyses. Fluorescence spectroscopy unveiled the presence of one binding site for piperine with an affinity constant of 14.3 × 104 M−1 at 298 K. The thermodynamic analysis indicated that the interaction with IL-1β was spontaneous (∆G = −25 kJ/mol) and, when split into enthalpic and entropic contributions, the latter was more significant. Circular dichroism spectroscopy showed that piperine did not affect IL-1β secondary structure (~2%) and therefore its stability. The set of experimental data parameterized the computational biophysical approach. Through molecular docking, the binding site micro-environment was revealed to be composed mostly by non-polar amino acids. Furthermore, molecular dynamics, along with umbrella sampling, are in agreement with the thermodynamic parameters obtained by fluorescence assays and showed that large protein movements are not present in IL-1β, corroborating the circular dichroism data.
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Affiliation(s)
- Gabriel Zazeri
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto CEP 15054-000, Brazil; (G.Z.); (A.P.R.P.)
| | - Ana Paula Ribeiro Povinelli
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto CEP 15054-000, Brazil; (G.Z.); (A.P.R.P.)
| | - Marcelo de Freitas Lima
- Departamento de Química, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto CEP 15054-000, Brazil;
| | - Marinônio Lopes Cornélio
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto CEP 15054-000, Brazil; (G.Z.); (A.P.R.P.)
- Correspondence:
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Shankla M, Aksimentiev A. Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS 2 Nanopore. ACS APPLIED MATERIALS & INTERFACES 2020; 12:26624-26634. [PMID: 32393017 PMCID: PMC7292782 DOI: 10.1021/acsami.0c04523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.
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Affiliation(s)
- Manish Shankla
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
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35
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Zhu J, Qi R, Liu Y, Zhao L, Han W. Mechanistic Insights into the Effect of Ligands on Structural Stability and Selectivity of Sulfotransferase 2A1 (SULT2A1). ACS OMEGA 2019; 4:22021-22034. [PMID: 31891082 PMCID: PMC6933797 DOI: 10.1021/acsomega.9b03136] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/14/2019] [Indexed: 05/04/2023]
Abstract
Cytosolic sulfotransferases (SULTs) acting as phase II metabolic enzymes can be used in the sulfonation of small molecules by transferring a sulfonate group from the unique co-factor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the substrates. In the present study, molecular dynamics (MD) simulations and ensemble docking study were employed to theoretically characterize the mechanism for the effect of co-factor (PAP) and ligands (LCA, raloxifene, α-hydroxytamoxifen, ouabain, and 3'-phosphoadenylyl sulfate) on structural stability and selectivity of SULT2A1 from the perspective of the dynamic behavior of SULT2A1 structures. Structural stability and network analyses indicated that the cooperation between PAP and LCA may enhance the thermal stability and compact communication in enzymes. During the MD simulations, the obviously rigid region and inward displacement were detected in the active-site cap (loop16) of the conformation containing PAP, which may be responsible for the significant changes in substrate accessibility and catalytic activity. The smaller substrates such as LCA could bind stably to the active pocket in the presence of PAP. However, the substrates or inhibitors with a large spatial structure needed to bind to the open conformation (without PAP) prior to PAPS binding.
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Jun H, Wang X, Bricker WP, Bathe M. Automated sequence design of 2D wireframe DNA origami with honeycomb edges. Nat Commun 2019; 10:5419. [PMID: 31780654 PMCID: PMC6882874 DOI: 10.1038/s41467-019-13457-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials. Wireframe DNA origami is a powerful approach to creating 2D and 3D geometries. Here the authors introduce an automated computational design approach that programs structures with high structural fidelity.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Uba AI, Yelekçi K. Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10. J Biomol Struct Dyn 2019; 38:4397-4406. [PMID: 31701819 DOI: 10.1080/07391102.2019.1691658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of Danio rerio (zebrafish) HDAC10 (zHDAC10) (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) as a template. Here, in continuation with our study, both hHDAC10 and zHDAC10, and their respective complexes with trichostatin A (TSA), quisinostat, and the native ligand (in 5TD7), 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol (PDB ID; FKS) were submitted to 100 ns-long unrestrained molecular dynamics (MD) simulations. Comparative analyses of the MD trajectories revealed that zHDAC10 and its complexes displayed higher stability than hHDAC10 and its corresponding complexes over time. Nonetheless, docking of active and inactive set molecules revealed that more reliable conformations of hHDAC10 could be obtained at an extended time period. This study may shed more light on the reliability of hHDAC10 modeled structure for use in selective inhibitor design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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Gómez-Castro CZ, Rodriguez JA, Cruz-Borbolla J, Quintanar-Guzman A, Sanchez-Ortega I, Santos EM. A theoretical and experimental approach to evaluate zein-calcium interaction in nixtamalization process. Food Chem 2019; 297:124995. [PMID: 31253267 DOI: 10.1016/j.foodchem.2019.124995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/24/2019] [Accepted: 06/10/2019] [Indexed: 11/27/2022]
Abstract
The possible interactions between α-zein and Ca2+ in nixtamalization process were analyzed from a multidisciplinary approach, considering the effect of these interactions on the thermal properties of the nixtamalized flour. SDS-PAGE under reducing and non-reducing conditions did not reveal differences between patterns of zeins from nixtamalized and control samples. However, analysis from affinity capillary electrophoresis indicated an increment in protein volume when calcium is added to zein extracted from nixtamalized flour. In addition, the binding constant for the zein-calcium interaction was calculated indicating a higher affinity for calcium by zein from nixtamalized samples. Molecular dynamics simulations indicated that the interaction α-zein-Ca2+ through C-ter was more favorable than Glu48. However, in excess of Ca2+ ions, each site could bind one calcium atom at the same time, confirming that aggregation of α-zein through calcium bridges is possible, expanding the technological applications of this protein.
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Affiliation(s)
- Carlos Z Gómez-Castro
- CONACYT Research Fellow, Universidad Autónoma del Estado de Hidalgo, Ciudad del Conocimiento, Carretera Pachuca-Tulancingo, Km 4.5, CP. 42184 Mineral de la Reforma, Hidalgo, Mexico
| | - Jose A Rodriguez
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química, Ciudad del Conocimiento, Crta Pachuca-Tulancingo, Km 4.5 s/n, CP. 42184 Mineral de la Reforma, Hidalgo, Mexico
| | - Julian Cruz-Borbolla
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química, Ciudad del Conocimiento, Crta Pachuca-Tulancingo, Km 4.5 s/n, CP. 42184 Mineral de la Reforma, Hidalgo, Mexico
| | | | - Irais Sanchez-Ortega
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química, Ciudad del Conocimiento, Crta Pachuca-Tulancingo, Km 4.5 s/n, CP. 42184 Mineral de la Reforma, Hidalgo, Mexico
| | - Eva M Santos
- Universidad Autónoma del Estado de Hidalgo, Área Académica de Química, Ciudad del Conocimiento, Crta Pachuca-Tulancingo, Km 4.5 s/n, CP. 42184 Mineral de la Reforma, Hidalgo, Mexico.
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Javier-Reyna R, Montaño S, García-Rivera G, Rodríguez MA, González-Robles A, Orozco E. EhRabB mobilises the EhCPADH complex through the actin cytoskeleton during phagocytosis of Entamoeba histolytica. Cell Microbiol 2019; 21:e13071. [PMID: 31219662 DOI: 10.1111/cmi.13071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/15/2019] [Accepted: 06/11/2019] [Indexed: 12/30/2022]
Abstract
Movement and phagocytosis are clue events in colonisation and invasion of tissues by Entamoeba histolytica, the protozoan causative of human amoebiasis. During phagocytosis, EhRab proteins interact with other functional molecules, conducting them to the precise cellular site. The gene encoding EhrabB is located in the complementary chain of the DNA fragment containing Ehcp112 and Ehadh genes, which encode for the proteins of the EhCPADH complex, involved in phagocytosis. This particular genetic organisation suggests that the three corresponding proteins may be functionally related. Here, we studied the relationship of EhRabB with EhCPADH and actin during phagocytosis. First, we obtained the EhRabB 3D structure to carry out docking analysis to predict the interaction sites involved in the EhRabB protein and the EhCPADH complex contact. By confocal microscopy, transmission electron microscopy, and immunoprecipitation assays, we revealed the interaction among these proteins when they move through different vesicles formed during phagocytosis. The role of the actin cytoskeleton in this event was also confirmed using Latrunculin A to interfere with actin polymerisation. This affected the movement of EhRabB and EhCPADH, as well as the rate of phagocytosis. Mutant trophozoites, silenced in EhrabB gene, evidenced the interaction of this molecule with EhCPADH and strengthened the role of actin during erythrophagocytosis.
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Affiliation(s)
- Rosario Javier-Reyna
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN, Mexico City, Mexico
| | - Sarita Montaño
- Laboratorio de Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa (FCQB-UAS), Culiacán, Sinaloa, México
| | | | | | | | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN, Mexico City, Mexico
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Giussani L, Tabacchi G, Coluccia S, Fois E. Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels. Int J Mol Sci 2019; 20:E2965. [PMID: 31216631 PMCID: PMC6627703 DOI: 10.3390/ijms20122965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 02/01/2023] Open
Abstract
Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.
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Affiliation(s)
- Lara Giussani
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Gloria Tabacchi
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Salvatore Coluccia
- Dipartimento di Chimica, Turin University, Via P. Giuria 7, I-10125 Turin, Italy.
| | - Ettore Fois
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
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41
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Bonome EL, Cecconi F, Chinappi M. Translocation intermediates of ubiquitin through an α-hemolysin nanopore: implications for detection of post-translational modifications. NANOSCALE 2019; 11:9920-9930. [PMID: 31069350 DOI: 10.1039/c8nr10492a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopore based sensors constitute a promising approach to single molecule protein characterization being able, in principle, to detect sequences, structural elements and folding states of proteins and polypeptide chains. In narrow nanopores, one of the open issues concerns the coupling between unfolding and translocation. Here, we studied the ubiquitin translocation in an α-hemolysin nanopore, the most widely used pore for nanopore sensing, via all-atom molecular dynamics simulations. We completely characterize the co-translocational unfolding pathway finding that robust translocation intermediates are associated with the rearrangement of secondary structural elements, as also confirmed by coarse grained simulations. An interesting recurrent pattern is the clogging of the α-hemolysin constriction by an N-terminal β-hairpin. This region of ubiquitin is the target of several post-translational modifications. We propose a strategy to detect post-translational modifications at the N-terminal using the α-hemolysin nanopore based on the comparison of the co-translocational unfolding signals associated with modified and unmodified proteins.
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Affiliation(s)
- Emma Letizia Bonome
- Dipartimento di Ingegneria Meccanica e Aerospaziale Sapienza Università di Roma, Roma, 00185, Italy
| | - Fabio Cecconi
- CNR-Istituto dei Sistemi Complessi UoS Sapienza, Via dei Taurini 19, Roma, 00185, Italy
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Roma, 00133, Italy.
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42
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Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M. Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. ACS NANO 2019; 13:2083-2093. [PMID: 30605605 PMCID: PMC6679942 DOI: 10.1021/acsnano.8b08671] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. In order to test its generality, we apply TALOS to design an in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tyson R. Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kaiming Zhang
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - William P. Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shanshan Li
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Wah Chiu
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Author
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Montaño S, Constantino-Jonapa LA, Sixto-López Y, Hernández-Ramírez VI, Hernández-Ceruelos A, Romero-Quezada LC, Ruvalcaba-Ledezma JC, Talamás-Rohana P, López-Contreras L. Vorinostat, a possible alternative to metronidazole for the treatment of amebiasis caused by Entamoeba histolytica. J Biomol Struct Dyn 2019; 38:597-603. [PMID: 30744531 DOI: 10.1080/07391102.2019.1578693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AbbreviationsSAHAsuberoylanilide hydroxamic acidEhHDACHistone Deacetylase from Entamoeba histolyticaRgRadius of gyrationRMSDroot-mean-square deviationRMSFroot-mean-square fluctuationMDSmolecular dynamics simulationVMDVisual Molecular DynamicsNAMDNanoscale Molecular DynamicsPBCperiodic boundary conditionsPMEParticle Mesh Ewald3Dthree-dimensionalCαalpha carbonFDAFood and Drug AdministrationnsnanosecondsGPU CUDAGraphics Processing Unit Compute Unified Device ArchitectureCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Montaño
- Laboratorio de Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa (FCQB-UAS), Blvd. de las Américas y Josefa Ortiz de Domínguez s/n. Ciudad Universitaria, Culiacán Sinaloa, México
| | - L A Constantino-Jonapa
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV -IPN), Mexico City, México
| | - Y Sixto-López
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, CDMX, México
| | - V I Hernández-Ramírez
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV -IPN), Mexico City, México
| | - A Hernández-Ceruelos
- Área Académica de Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda La Concepción S/N Carretera Pachuca-Actopan, San Agustín Tlaxiaca, Hidalgo, México
| | - L C Romero-Quezada
- Área Académica de Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda La Concepción S/N Carretera Pachuca-Actopan, San Agustín Tlaxiaca, Hidalgo, México
| | - J C Ruvalcaba-Ledezma
- Área Académica de Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda La Concepción S/N Carretera Pachuca-Actopan, San Agustín Tlaxiaca, Hidalgo, México
| | - P Talamás-Rohana
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV -IPN), Mexico City, México
| | - L López-Contreras
- Área Académica de Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda La Concepción S/N Carretera Pachuca-Actopan, San Agustín Tlaxiaca, Hidalgo, México
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Evaluation of the Antimicrobial Activity of Cationic Peptides Loaded in Surface-Modified Nanoliposomes against Foodborne Bacteria. Int J Mol Sci 2019; 20:ijms20030680. [PMID: 30764495 PMCID: PMC6386929 DOI: 10.3390/ijms20030680] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 01/03/2023] Open
Abstract
Bacteria are a common group of foodborne pathogens presenting public health issues with a large economic burden for the food industry. Our work focused on a solution to this problem by evaluating antibiotic activity against two bacteria (Listeria monocytogenes and Escherichia coli) of relevance in the field of foodstuffs. We used two approaches: (i) structural modification of the antimicrobial peptides and (ii) nano-vehiculisation of the modified peptides into polymer-coated liposomes. To achieve this, two antimicrobial peptides, herein named ‘peptide +2′ and ‘peptide +5′ were synthesised using the solid phase method. The physicochemical characterisation of the peptides was carried out using measurements of surface tension and dynamic light scattering. Additionally, nanoliposomes were elaborated by the ethanol injection method and coated with a cationic polymer (Eudragit E-100) through the layer-by-layer process. Liposome characterisation, in terms of size, polydispersity and zeta potential, was undertaken using dynamic light scattering. The results show that the degree of hydrophilic modification in the peptide leads to different characteristics of amphipathicity and subsequently to different physicochemical behaviour. On the other hand, antibacterial activity against both bacteria was slightly altered after modifying peptide sequence. Nonetheless, after the encapsulation of the peptides into polymer-coated nano-liposomes, the antibacterial activity increased approximately 2000-fold against that of L. monocytogenes.
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45
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Martínez-Archundia M, Correa-Basurto J, Montaño S, Rosas-Trigueros JL. Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis. J Biomol Struct Dyn 2019; 37:4685-4700. [DOI: 10.1080/07391102.2018.1564700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sarita Montaño
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacan, Sinaloa, Mexico
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Cómputo, Instituto Politécnico Nacional, Mexico City, Mexico
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46
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Correa-Basurto AM, Romero-Castro A, Correa-Basurto J, Hernández-Rodríguez M, Soriano-Ursúa MA, García-Machorro J, Tolentino-López LE, Rosales-Hernández MC, Mendieta-Wejebe JE. Pharmacokinetics and tissue distribution of N-(2-hydroxyphenyl)-2-propylpentanamide in Wistar Rats and its binding properties to human serum albumin. J Pharm Biomed Anal 2019; 162:130-139. [PMID: 30236821 DOI: 10.1016/j.jpba.2018.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 02/07/2023]
Abstract
N-(2-hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) is a novel valproic acid derivative that has shown anti-proliferative activity against epitheloid cervix carcinoma (HeLa), rhabdomyosarcoma (A204), and several breast cancer cell lines. The aim of this research was to evaluate the pharmacokinetic profile and tissue distribution of HO-AAVPA in Wistar rats, as well as its human serum albumin binding potential by experimental and in silico methods. A single dose of HO-AAVPA was given to male rats by intravenous, intragastric or intraperitoneal routes at doses of 25, 100, and 100 mg/kg, respectively. Then, blood samples were drawn at predetermined intervals of time, and the HO-AAVPA concentration in the plasma was quantified with a validated HPLC method. The elimination half-life (t1/2) was approximately 222 min, and the systemic clearance (CL) and apparent volume of distribution (Vd) were 2.20 mL/min/kg and 0.70 L/kg, respectively. The absolute oral bioavailability of HO-AAVPA was 33.8%, and the binding rate of HO-AAVPA with rat plasma proteins was between 66.2% and 83.0%. Additionally, in silico, UV and Raman spectroscopy data showed weak interactions between the test compound and human serum albumin. Thus, the results that were obtained demonstrated that despite its low oral bioavailability, the potential anticancer agent HO-AAVPA exhibits acceptable pharmacokinetic properties that would allow it to reach its site of action and exert its pharmacological effect in Wistar Rats, and it has a convenient profile for future assays to evaluate its human applications.
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Affiliation(s)
- Ana María Correa-Basurto
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Aurelio Romero-Castro
- División de Ciencias de la Salud, Universidad de Quintana Roo, Av. Erik Paolo Martínez s/n, esquina Av. 4 de marzo, Colonia Magisterial, Chetumal, Quintana Roo 77039, Mexico
| | - José Correa-Basurto
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico; Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico.
| | - Maricarmen Hernández-Rodríguez
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Marvin Antonio Soriano-Ursúa
- Laboratorio de Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Jazmin García-Machorro
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Luis Esteban Tolentino-López
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico; Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Jessica Elena Mendieta-Wejebe
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico.
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47
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Bernardo-García N, Sánchez-Murcia PA, Espaillat A, Martínez-Caballero S, Cava F, Hermoso JA, Gago F. Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Org Biomol Chem 2019; 17:4350-4358. [DOI: 10.1039/c9ob00223e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The commonly used Tris buffer acts as a surrogate substrate and deformylates pyridoxal phosphate in a bacterial alanine racemase at subzero temperatures.
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Affiliation(s)
- Noelia Bernardo-García
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | | | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | - Federico Gago
- Department of Biomedical Sciences
- “Unidad Asociada IQM-CSIC”
- University of Alcalá
- Madrid
- Spain
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48
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Ghosh S, Chatterjee A, Bhattacharya S. Accelerated Construction of Kinetic Network Model of Biomolecules Using Steered Molecular Dynamics. J Chem Theory Comput 2018; 14:5393-5405. [PMID: 30212629 DOI: 10.1021/acs.jctc.8b00398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new class of rare event acceleration techniques based on steered molecular dynamics (SMD) simulations is introduced. A stretching force applied on a biomolecule causes it to access large end-to-end distances. Under these conditions the biomolecule undergoes rapid conformational changes that are rare at zero-force conditions. A theory describing kinetics of a biomolecule at various stretching forces is presented. Using the theory, a master-Markov state model (master-MSM) is constructed from rates frequently accessed over a small range of force conditions. The master-MSM is shown to be applicable over a wide range of force conditions. We demonstrate application of the theory to three different biomolecular systems, namely, deca-alanine, TBA (thrombin binding aptamer), and a RNA hairpin. The master-MSM is used to estimate the kinetics at zero-force conditions, i.e., on the unbiased free-energy landscape, resulting inasmuch as 2-6 orders-of-magnitude speed-up over standard molecular dynamics.
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Affiliation(s)
- Susmita Ghosh
- Department of Physics , Indian Institute of Technology Guwahati , Guwahati , India 781039
| | - Abhijit Chatterjee
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai , India 400076
| | - Swati Bhattacharya
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai , India 400076
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49
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Manjari SR, Banavali NK. Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching. J Chem Inf Model 2018; 58:453-463. [PMID: 29357231 DOI: 10.1021/acs.jcim.7b00699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A strategy named "restrained geometries and topology switching" (RGATS) is presented to obtain detailed trajectories for complex biochemical reactions using molecular mechanics (MM) methods. It enables prediction of realistic dynamical pathways for chemical reactions, especially for accurately characterizing the structural adjustments of highly complex environments to any proximal biochemical reaction. It can be used to generate reactive conformations, model stepwise or concerted reactions in complex environments, and probe the influence of changes in the environment. Its ability to take reactively nonoptimal conformations and generate favorable starting conformations for a biochemical reaction is illustrated for a proton transfer between two model compounds. Its ability to study concerted reactions in explicit solvent is illustrated using proton transfers between an ammonium ion and two conserved histidines in an ammonia transporter channel embedded in a lipid membrane. Its ability to characterize the changes induced by subtle differences in the active site environment is illustrated using nucleotide addition by a DNA polymerase in the presence of two versus three Mg2+ ions. RGATS can be employed within any MM program and requires no additional software implementation. This allows the full assortment of computational methods implemented in all available MM programs to be used to tackle virtually any question about biochemical reactions that is answerable without using a quantum mechanical (QM) model. It can also be applied to generate reasonable starting structures for more detailed and expensive QM or QM/MM methods. In particular, this strategy enables rapid prediction of reactant, intermediary, or product state structures in any macromolecular context, with the only requirement being that the structure in any one of these states is either known or can be accurately modeled.
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Affiliation(s)
- Swati R Manjari
- Laboratory of Computational and Structural Biology, Division of Genetics, NYS Department of Health , CMS 2008, Biggs Laboratory, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, United States
| | - Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, NYS Department of Health , CMS 2008, Biggs Laboratory, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, United States.,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , Albany, New York 12222, United States
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50
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Yang HJ, Hwang KS, Lee CJ. Stochastic Optimization of a Natural Gas Liquefaction Process Considering Seawater Temperature Variation Based on Particle Swarm Optimization. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b04546] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hye Jin Yang
- Department
of Polymer Science and Chemical Engineering, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Kyu Suk Hwang
- Department
of Polymer Science and Chemical Engineering, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Chang Jun Lee
- Department
of Safety Engineering, Pukyong National University, 45, Yongso-ro, Nam-gu, Busan 48513, Republic of Korea
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