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Das A, Thapa P, Santiago U, Shanmugam N, Banasiak K, Dązbrowska K, Nolte H, Szulc NA, Gathungu RM, Cysewski D, Krüeger M, Dadlez M, Nowotny M, Camacho CJ, Hoppe T, Pokrzywa W. Author Correction: A heterotypic assembly mechanism regulates CHIP E3 ligase activity. EMBO J 2024; 43:1110-1111. [PMID: 38388749 PMCID: PMC10943065 DOI: 10.1038/s44318-024-00042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Affiliation(s)
- Aniruddha Das
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Pankaj Thapa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Ulises Santiago
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nilesh Shanmugam
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Katarzyna Banasiak
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | | | - Hendrik Nolte
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Natalia A Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | | | | | - Marcus Krüeger
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931, Cologne, Germany
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931, Cologne, Germany
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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Vergara S, Zhou X, Santiago U, Conway JF, Sluis-Cremer N, Calero G. Structures of kinetic intermediate states of HIV-1 reverse transcriptase DNA synthesis. bioRxiv 2023:2023.12.18.572243. [PMID: 38187617 PMCID: PMC10769260 DOI: 10.1101/2023.12.18.572243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Reverse transcription of the retroviral single-stranded RNA into double-stranded DNA is an integral step during HIV-1 replication, and reverse transcriptase (RT) is a primary target for antiviral therapy. Despite a wealth of structural information on RT, we lack critical insight into the intermediate kinetic states of DNA synthesis. Using catalytically active substrates, and a novel blot/diffusion cryo-electron microscopy approach, we captured 11 structures that define the substrate binding, reactant, transition and product states of dATP addition by RT at 1.9 to 2.4 Å resolution in the active site. Initial dATP binding to RT-template/primer complex involves a single Mg 2+ (site B), and promotes partial closure of the active site pocket by a large conformational change in the β3-β4 loop in the Fingers domain, and formation of a negatively charged pocket where a second "drifting" Mg 2+ can bind (site A). During the transition state, the α-phosphate oxygen from a previously unobserved dATP conformer aligns with the site A Mg 2+ and the primer 3'-OH for nucleophilic attack. In the product state, we captured two substrate conformations in the active site: 1) dATP that had yet to be incorporated into the nascent DNA, and 2) an incorporated dAMP with the pyrophosphate leaving group coordinated by metal B and stabilized through H- bonds in the active site of RT. This study provides insights into a fundamental chemical reaction that impacts polymerase fidelity, nucleoside inhibitor drug design, and mechanisms of drug resistance.
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Gomez K, Santiago U, Nelson TS, Allen HN, Calderon-Rivera A, Hestehave S, Rodríguez Palma EJ, Zhou Y, Duran P, Loya-Lopez S, Zhu E, Kumar U, Shields R, Koseli E, McKiver B, Giuvelis D, Zuo W, Inyang KE, Dorame A, Chefdeville A, Ran D, Perez-Miller S, Lu Y, Liu X, Handoko, Arora PS, Patek M, Moutal A, Khanna M, Hu H, Laumet G, King T, Wang J, Damaj MI, Korczeniewska OA, Camacho CJ, Khanna R. A peptidomimetic modulator of the Ca V2.2 N-type calcium channel for chronic pain. Proc Natl Acad Sci U S A 2023; 120:e2305215120. [PMID: 37972067 PMCID: PMC10666126 DOI: 10.1073/pnas.2305215120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
Transmembrane Cav2.2 (N-type) voltage-gated calcium channels are genetically and pharmacologically validated, clinically relevant pain targets. Clinical block of Cav2.2 (e.g., with Prialt/Ziconotide) or indirect modulation [e.g., with gabapentinoids such as Gabapentin (GBP)] mitigates chronic pain but is encumbered by side effects and abuse liability. The cytosolic auxiliary subunit collapsin response mediator protein 2 (CRMP2) targets Cav2.2 to the sensory neuron membrane and regulates their function via an intrinsically disordered motif. A CRMP2-derived peptide (CBD3) uncouples the Cav2.2-CRMP2 interaction to inhibit calcium influx, transmitter release, and pain. We developed and applied a molecular dynamics approach to identify the A1R2 dipeptide in CBD3 as the anchoring Cav2.2 motif and designed pharmacophore models to screen 27 million compounds on the open-access server ZincPharmer. Of 200 curated hits, 77 compounds were assessed using depolarization-evoked calcium influx in rat dorsal root ganglion neurons. Nine small molecules were tested electrophysiologically, while one (CBD3063) was also evaluated biochemically and behaviorally. CBD3063 uncoupled Cav2.2 from CRMP2, reduced membrane Cav2.2 expression and Ca2+ currents, decreased neurotransmission, reduced fiber photometry-based calcium responses in response to mechanical stimulation, and reversed neuropathic and inflammatory pain across sexes in two different species without changes in sensory, sedative, depressive, and cognitive behaviors. CBD3063 is a selective, first-in-class, CRMP2-based peptidomimetic small molecule, which allosterically regulates Cav2.2 to achieve analgesia and pain relief without negative side effect profiles. In summary, CBD3063 could potentially be a more effective alternative to GBP for pain relief.
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Affiliation(s)
- Kimberly Gomez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Ulises Santiago
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15261
| | - Tyler S. Nelson
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Heather N. Allen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Aida Calderon-Rivera
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Sara Hestehave
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Erick J. Rodríguez Palma
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Yuan Zhou
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ85724
| | - Paz Duran
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Santiago Loya-Lopez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Elaine Zhu
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY10016
- Interdisciplinary Pain Research Program, New York University Langone Health, New York, NY10016
| | - Upasana Kumar
- Department of Diagnostic Sciences, Center for Orofacial Pain and Temporomandibular Disorders, Rutgers School of Dental Medicine, Newark, NJ07101
| | - Rory Shields
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ07101
| | - Eda Koseli
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, VA23298
| | - Bryan McKiver
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, VA23298
| | - Denise Giuvelis
- Department of Biomedical Sciences, College of Osteopathic Medicine, Center for Excellence in the Neurosciences, University of New England, Biddeford, ME04005
| | - Wanhong Zuo
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ07103
| | | | - Angie Dorame
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ85724
| | - Aude Chefdeville
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ85724
| | - Dongzhi Ran
- Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing400016, China
| | - Samantha Perez-Miller
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Yi Lu
- Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing400016, China
| | - Xia Liu
- Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing400016, China
| | - Handoko
- Department of Chemistry, New York University, New York, NY10003
| | | | - Marcel Patek
- Bright Rock Path Limited Liability Company, Tucson, AZ85724
| | - Aubin Moutal
- Department of Pharmacology and Physiology, School of Medicine, St. Louis University, St. Louis, MO63104
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
| | - Huijuan Hu
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ07103
| | - Geoffroy Laumet
- Department of Physiology, Michigan State University, East Lansing, MI48824
| | - Tamara King
- Department of Biomedical Sciences, College of Osteopathic Medicine, Center for Excellence in the Neurosciences, University of New England, Biddeford, ME04005
| | - Jing Wang
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY10016
- Interdisciplinary Pain Research Program, New York University Langone Health, New York, NY10016
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY10010
| | - M. Imad Damaj
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, VA23298
| | - Olga A. Korczeniewska
- Department of Diagnostic Sciences, Center for Orofacial Pain and Temporomandibular Disorders, Rutgers School of Dental Medicine, Newark, NJ07101
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ07101
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15261
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- New York University Pain Research Center, New York, NY10010
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY10010
- Chemical, and Biomolecular Engineering Department, Tandon School of Engineering, New York University, New York City, NY11201
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Fancher AT, Hua Y, Close DA, Xu W, McDermott LA, Strock CJ, Santiago U, Camacho CJ, Johnston PA. Characterization of allosteric modulators that disrupt androgen receptor co-activator protein-protein interactions to alter transactivation-Drug leads for metastatic castration resistant prostate cancer. SLAS Discov 2023:S2472-5552(23)00053-9. [PMID: 37549772 DOI: 10.1016/j.slasd.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/06/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Three series of compounds were prioritized from a high content screening campaign that identified molecules that blocked dihydrotestosterone (DHT) induced formation of Androgen Receptor (AR) protein-protein interactions (PPIs) with the Transcriptional Intermediary Factor 2 (TIF2) coactivator and also disrupted preformed AR-TIF2 PPI complexes; the hydrobenzo-oxazepins (S1), thiadiazol-5-piperidine-carboxamides (S2), and phenyl-methyl-indoles (S3). Compounds from these series inhibited AR PPIs with TIF2 and SRC-1, another p160 coactivator, in mammalian 2-hybrid assays and blocked transcriptional activation in reporter assays driven by full length AR or AR-V7 splice variants. Compounds inhibited the growth of five prostate cancer cell lines, with many exhibiting differential cytotoxicity towards AR positive cell lines. Representative compounds from the 3 series substantially reduced both endogenous and DHT-enhanced expression and secretion of the prostate specific antigen (PSA) cancer biomarker in the C4-2 castration resistant prostate cancer (CRPC) cell line. The comparatively weak activities of series compounds in the H3-DHT and/or TIF2 box 3 LXXLL-peptide binding assays to the recombinant ligand binding domain of AR suggest that direct antagonism at the orthosteric ligand binding site or AF-2 surface respectively are unlikely mechanisms of action. Cellular enhanced thermal stability assays (CETSA) indicated that compounds engaged AR and reduced the maximum efficacy and right shifted the EC50 of DHT-enhanced AR thermal stabilization consistent with the effects of negative allosteric modulators. Molecular docking of potent representative hits from each series to AR structures suggest that S1-1 and S2-6 engage a novel binding pocket (BP-1) adjacent to the orthosteric ligand binding site, while S3-11 occupies the AR binding function 3 (BF-3) allosteric pocket. Hit binding poses indicate spaces and residues adjacent to the BP-1 and BF-3 pockets that will be exploited in future medicinal chemistry optimization studies. Small molecule allosteric modulators that prevent/disrupt AR PPIs with coactivators like TIF2 to alter transcriptional activation in the presence of orthosteric agonists might evade the resistance mechanisms to existing prostate cancer drugs and provide novel starting points for medicinal chemistry lead optimization and future development into therapies for metastatic CRPC.
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Affiliation(s)
- Ashley T Fancher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Nucleus Global, 2 Ravinia Drive, Suite 605, Atlanta, GA 30346, USA
| | - Yun Hua
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David A Close
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lee A McDermott
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; PsychoGenics Inc, 215 College Road, Paramus, NJ 07652, USA
| | | | - Ulises Santiago
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA 15232, USA.
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Gomez K, Santiago U, Calderon-Rivera A, Duran P, Loya-Lopez S, Ran D, Perez-Miller S, Handoko H, Arora PS, Patek M, King TD, Hu H, Camacho CJ, Khanna R. A Selective Peptidomimetic Modulator Of Cav2.2 (N-Type) Voltage-Gated Calcium Channels For Chronic Pain. The Journal of Pain 2023. [DOI: 10.1016/j.jpain.2023.02.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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6
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Asberry AM, Cai X, Deng X, Santiago U, Liu S, Sims HS, Liang W, Xu X, Wan J, Jiang W, Camacho CJ, Dai M, Hu CD. Discovery and Biological Characterization of PRMT5:MEP50 Protein-Protein Interaction Inhibitors. J Med Chem 2022; 65:13793-13812. [PMID: 36206451 DOI: 10.1021/acs.jmedchem.2c01000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein arginine methyltransferase 5 (PRMT5) is a master epigenetic regulator and an extensively validated therapeutic target in multiple cancers. Notably, PRMT5 is the only PRMT that requires an obligate cofactor, methylosome protein 50 (MEP50), to function. We developed compound 17, a novel small-molecule PRMT5:MEP50 protein-protein interaction (PPI) inhibitor, after initial virtual screen hit identification and analogue refinement. Molecular docking indicated that compound 17 targets PRMT5:MEP50 PPI by displacing the MEP50 W54 burial into a hydrophobic pocket of the PRMT5 TIM barrel. In vitro analysis indicates IC50 < 500 nM for prostate and lung cancer cells with selective, specific inhibition of PRMT5:MEP50 substrate methylation and target gene expression, and RNA-seq analysis suggests that compound 17 may dysregulate TGF-β signaling. Compound 17 provides a proof of concept in targeting PRMT5:MEP50 PPI, as opposed to catalytic targeting, as a novel mechanism of action and supports further preclinical development of inhibitors in this class.
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Affiliation(s)
- Andrew M Asberry
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xinpei Cai
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xuehong Deng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ulises Santiago
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.,The Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana 46202, United States
| | - Hunter S Sims
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Weida Liang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xueyong Xu
- Department of Biological Sciences, Purdue University, 240 S Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.,The Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana 46202, United States.,The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, 240 S Martin Jischke Drive, West Lafayette, Indiana 47907, United States.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Chang-Deng Hu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Das A, Thapa P, Santiago U, Shanmugam N, Banasiak K, Dąbrowska K, Nolte H, Szulc NA, Gathungu RM, Cysewski D, Krüger M, Dadlez M, Nowotny M, Camacho CJ, Hoppe T, Pokrzywa W. A heterotypic assembly mechanism regulates CHIP E3 ligase activity. EMBO J 2022; 41:e109566. [PMID: 35762422 PMCID: PMC9340540 DOI: 10.15252/embj.2021109566] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
CHIP (C-terminus of Hsc70-interacting protein) and its worm ortholog CHN-1 are E3 ubiquitin ligases that link the chaperone system with the ubiquitin-proteasome system (UPS). CHN-1 can cooperate with UFD-2, another E3 ligase, to accelerate ubiquitin chain formation; however, the basis for the high processivity of this E3s set has remained obscure. Here, we studied the molecular mechanism and function of the CHN-1-UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. However, HSP70/HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding, thereby promoting a shift to the autoinhibited CHN-1 state by acting on a conserved residue in its U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitylate and regulate S-adenosylhomocysteinase (AHCY-1), a key enzyme in the S-adenosylmethionine (SAM) regeneration cycle, which is essential for SAM-dependent methylation. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation.
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Affiliation(s)
- Aniruddha Das
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Pankaj Thapa
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Ulises Santiago
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPAUSA
| | - Nilesh Shanmugam
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Katarzyna Banasiak
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | | | - Hendrik Nolte
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Present address:
Max‐Planck‐Institute for Biology of AgeingCologneGermany
| | - Natalia A Szulc
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | | | | | - Marcus Krüger
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Center for Molecular Medicine (CMMC), Faculty of MedicineUniversity Hospital of CologneCologneGermany
| | - Michał Dadlez
- Institute of Biochemistry and BiophysicsPASWarsawPoland
| | - Marcin Nowotny
- Laboratory of Protein StructureInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Carlos J Camacho
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPAUSA
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Center for Molecular Medicine (CMMC), Faculty of MedicineUniversity Hospital of CologneCologneGermany
| | - Wojciech Pokrzywa
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
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8
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Shen Z, Xiang Y, Vergara S, Chen A, Xiao Z, Santiago U, Jin C, Sang Z, Luo J, Chen K, Schneidman-Duhovny D, Camacho C, Calero G, Hu B, Shi Y. A resource of high-quality and versatile nanobodies for drug delivery. iScience 2021; 24:103014. [PMID: 34522857 PMCID: PMC8426283 DOI: 10.1016/j.isci.2021.103014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/09/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
Therapeutic and diagnostic efficacies of small biomolecules and chemical compounds are hampered by suboptimal pharmacokinetics. Here, we developed a repertoire of robust and high-affinity antihuman serum albumin nanobodies (NbHSA) that can be readily fused to small biologics for half-life extension. We characterized the thermostability, binding kinetics, and cross-species reactivity of NbHSAs, mapped their epitopes, and structurally resolved a tetrameric HSA-Nb complex. We parallelly determined the half-lives of a cohort of selected NbHSAs in an HSA mouse model by quantitative proteomics. Compared to short-lived control nanobodies, the half-lives of NbHSAs were drastically prolonged by 771-fold. NbHSAs have distinct and diverse pharmacokinetics, positively correlating with their albumin binding affinities at the endosomal pH. We then generated stable and highly bioactive NbHSA-cytokine fusion constructs “Duraleukin” and demonstrated Duraleukin's high preclinical efficacy for cancer treatment in a melanoma model. This high-quality and versatile Nb toolkit will help tailor drug half-life to specific medical needs. We provide a resource of high-affinity and versatile albumin nanobodies for drug delivery We systematically map albumin nanobody epitopes by hybrid structural approaches We parallelly measure the pharmacokinetics of nanobodies in a humanized mouse model We develop nanobody-cytokine conjugates “Duraleukin” for cancer immunotherapy
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Affiliation(s)
- Zhuolun Shen
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Apeng Chen
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA.,Pediatric Neurosurgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Zhengyun Xiao
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ulises Santiago
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Changzhong Jin
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.,University of Pittsburgh-Carnegie Mellon University Joint Program for Computational Biology, Pittsburgh, PA, USA
| | - Jiadi Luo
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kong Chen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, University of Jerusalem, Tambaram, Israel
| | - Carlos Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA.,Pediatric Neurosurgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Molecular and Cellular Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.,University of Pittsburgh-Carnegie Mellon University Joint Program for Computational Biology, Pittsburgh, PA, USA
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9
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Chen A, Jiang Y, Li Z, Wu L, Santiago U, Zou H, Cai C, Sharma V, Guan Y, McCarl LH, Ma J, Wu YL, Michel J, Shi Y, Konnikova L, Amankulor NM, Zinn PO, Kohanbash G, Agnihotri S, Lu S, Lu X, Sun D, Gittes GK, Wang Q, Xiao X, Yimlamai D, Pollack IF, Camacho CJ, Hu B. Chitinase-3-like 1 protein complexes modulate macrophage-mediated immune suppression in glioblastoma. J Clin Invest 2021; 131:e147552. [PMID: 34228644 DOI: 10.1172/jci147552] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Apeng Chen
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yinan Jiang
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Zhengwei Li
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Lingxiang Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | | | - Han Zou
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chunhui Cai
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vaibhav Sharma
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yongchang Guan
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Neurosurgery, The Fourth Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lauren H McCarl
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jie Ma
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yijen L Wu
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Developmental Biology and
| | - Joshua Michel
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Liza Konnikova
- Section of Neonatal, Perinatal Medicine, Department of Pediatrics and Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nduka M Amankulor
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pascal O Zinn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gary Kohanbash
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Songjian Lu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dandan Sun
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - George K Gittes
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Xiangwei Xiao
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dean Yimlamai
- Section of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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10
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Chen A, Jiang Y, Li Z, Zou H, Santiago U, Xiao X, Camacho C, Pollack I, Hu B. TAMI-50. CHITINASE-3-LIKE-1 PROTEIN BINDING COMPLEXES REGULATE IMMUNE SUPPRESSION IN GLIOBLASTOMA. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Glioblastoma (GBM), the most common and lethal brain tumor, remains incurable despite intensive multimodal treatment. While immunotherapies have been highly effective in some types of cancer, the disappointing results from clinical trials for GBM immunotherapy represent continued challenges. GBM is highly immunosuppressive and resistant to immunotherapy because of glioma cells escaping from immune surveillance by reprograming the tumor microenvironment (TME). However, understanding the mechanisms of immune evasion by GBM remains elusive. Here, we found that Chitinase-3-like-1 (CHI3L1) is highly expressed in GBM and associated with a poor clinical outcome. CHI3L1, also known as human homolog YKL-40, plays a role in tissue remodeling, inflammation and cancer. Interestingly, we found that genetic knockdown (KD) of Chi3l1 in syngeneic immunocompetent mouse GBM models resulted in increased tumor-infiltrating lymphocytes, tumor size reduction, and improved animal survival. Surprisingly, the parallel loss-of-function experiment revealed that Chi3l1 KD did not repress tumor progression in the orthotopic immunodeficient mice with deficient T and B cells. These results suggest the predominant role of CHI3L1 in regulating the GBM immune TME, rather than in tumor cells per se. Mechanistically, we discovered that Galectin-3 (Gal-3) and Galectin-3 binding protein (Gal-3BP) interact competitively with the same binding motif on CHI3L1, leading to selective migration of protumor M2-like versus antitumor M1-like bone marrow-derived macrophages (BMDMs) and resident microglia (MG). Transcriptomic analysis revealed that pro-inflammatory signature and T cell mediated immunity and cytotoxicity signaling are significantly enriched in tumor associated macrophages/microglia (TAMs) composed of BMDMs and MG, which were isolated from tumors with Chi3l1 KD versus wild type. In vitro validations suggest that CHI3L1-Gal-3, but not CHI3L1-Gal-3BP protein binding complex, activates PI3K/AKT/mTOR signaling to control the TAM switch of immune suppression and immune stimulation. Together, these results shed light on molecular mechanism of GBM immune evasion and potential new immunotherapeutic strategies for GBM treatment.
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Affiliation(s)
- Apeng Chen
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yinan Jiang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhengwei Li
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Han Zou
- Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | | | - Xiangwei Xiao
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Ian Pollack
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Baoli Hu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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11
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Abstract
Cell surface receptor engagement is a critical aspect of viral infection. At low pH, binding of SARS-CoV and its ACE2 receptor has a tight interaction that catalyzes the fusion of the spike and endosomal membranes followed by genome release. Largely overlooked has been the role of neutral pH in the respiratory tract, where we find that SARS-CoV stabilizes a transition state that enhances the off-rate from its receptor. An alternative pH-switch is found in CoV-2-like coronaviruses of tropical pangolins, but with a reversed phenotype where the tight interaction with ACE2 is at neutral pH. We show that a single point mutation in pangolin-CoV, unique to CoV-2, that deletes the last His residue in their receptor binding domain perpetuates this tight interaction independent of pH. This tight bond, not present in previous respiratory syndromes, implies that CoV-2 stays bound to the highly expressed ACE2 receptors in the nasal cavity about 100 times longer than CoV. This finding supports the unfamiliar pathology of CoV-2, observed virus retention in upper respiratory tract 1 , longer incubation times and extended periods of shedding. Implications to combat pandemics that, like SARS-CoV-2, export evolutionarily successful strains via higher transmission rates due to retention in nasal epithelium and their evolutionary origin are discussed.
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12
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Macchione MA, Mendoza-Cruz R, Bazán-Diaz L, Velázquez-Salazar JJ, Santiago U, Arellano-Jiménez MJ, Perez JF, José-Yacamán M, Samaniego-Benitez JE. Electron microscopy study of the carbon-induced 2H–3R–1T phase transition of MoS 2. NEW J CHEM 2020. [DOI: 10.1039/c9nj03850g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phase transition of molybdenum disulfide (MoS2) was carried out in a pure monocrystal using a combination milling and heating process.
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Affiliation(s)
- Micaela A. Macchione
- Universidad Nacional de Córdoba
- Facultad De Ciencias Químicas
- Córdoba
- Argentina
- CONICET-Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC)
| | - Rubén Mendoza-Cruz
- Instituto de Investigaciones en Materiales
- Universidad Nacional Autónoma de México
- México City
- Mexico
| | - Lourdes Bazán-Diaz
- Instituto de Investigaciones en Materiales
- Universidad Nacional Autónoma de México
- México City
- Mexico
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13
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Ortega E, Santiago U, Giuliani JG, Monton C, Ponce A. In-situ magnetization/heating electron holography to study the magnetic ordering in arrays of nickel metallic nanowires. AIP Adv 2018; 8:056813. [PMID: 29375931 PMCID: PMC5760265 DOI: 10.1063/1.5007671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Magnetic nanostructures of different size, shape, and composition possess a great potential to improve current technologies like data storage and electromagnetic sensing. In thin ferromagnetic nanowires, their magnetization behavior is dominated by the competition between magnetocrystalline anisotropy (related to the crystalline structure) and shape anisotropy. In this way electron diffraction methods like precession electron diffraction (PED) can be used to link the magnetic behavior observed by Electron Holography (EH) with its crystallinity. Using off-axis electron holography under Lorentz conditions, we can experimentally determine the magnetization distribution over neighboring nanostructures and their diamagnetic matrix. In the case of a single row of nickel nanowires within the alumina template, the thin TEM samples showed a dominant antiferromagnetic arrangement demonstrating long-range magnetostatic interactions playing a major role.
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Affiliation(s)
- Eduardo Ortega
- Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, 78249, United States
| | - Ulises Santiago
- Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, 78249, United States
| | - Jason G Giuliani
- Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, 78249, United States
| | - Carlos Monton
- Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, 78249, United States
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14
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Parajuli P, Mendoza-Cruz R, Santiago U, Ponce A, Yacamán MJ. The Evolution of Growth, Crystal Orientation, and Grain Boundaries Disorientation Distribution in Gold Thin Films. Crystal Research and Technology 2018. [DOI: 10.1002/crat.201800038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prakash Parajuli
- Department of Physics and Astronomy; University of Texas at San Antonio; One UTSA Circle San Antonio Texas 78249 USA
| | - Rubén Mendoza-Cruz
- Department of Physics and Astronomy; University of Texas at San Antonio; One UTSA Circle San Antonio Texas 78249 USA
| | - Ulises Santiago
- Department of Physics and Astronomy; University of Texas at San Antonio; One UTSA Circle San Antonio Texas 78249 USA
| | - Arturo Ponce
- Department of Physics and Astronomy; University of Texas at San Antonio; One UTSA Circle San Antonio Texas 78249 USA
| | - Miguel José Yacamán
- Department of Physics and Astronomy; University of Texas at San Antonio; One UTSA Circle San Antonio Texas 78249 USA
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15
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Benítez A, Santiago U, Sanchez JE, Ponce A. Design of a cathodoluminescence image generator using a Raspberry Pi coupled to a scanning electron microscope. Rev Sci Instrum 2018; 89:013702. [PMID: 29390658 PMCID: PMC5771752 DOI: 10.1063/1.4986044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
In this work, an innovative cathodoluminescence (CL) system is coupled to a scanning electron microscope and synchronized with a Raspberry Pi computer integrated with an innovative processing signal. The post-processing signal is based on a Python algorithm that correlates the CL and secondary electron (SE) images with a precise dwell time correction. For CL imaging, the emission signal is collected through an optical fiber and transduced to an electrical signal via a photomultiplier tube (PMT). CL Images are registered in a panchromatic mode and can be filtered using a monochromator connected between the optical fiber and the PMT to produce monochromatic CL images. The designed system has been employed to study ZnO samples prepared by electrical arc discharge and microwave methods. CL images are compared with SE images and chemical elemental mapping images to correlate the emission regions of the sample.
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Affiliation(s)
- Alfredo Benítez
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
| | - Ulises Santiago
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
| | - John E Sanchez
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
| | - Arturo Ponce
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
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16
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Vergara S, Lukes DA, Martynowycz MW, Santiago U, Plascencia-Villa G, Weiss SC, de la Cruz MJ, Black DM, Alvarez MM, Lopez-Lozano X, Barnes CO, Lin G, Weissker HC, Whetten RL, Gonen T, Jose-Yacaman M, Calero G. MicroED Structure of Au 146(p-MBA) 57 at Subatomic Resolution Reveals a Twinned FCC Cluster. J Phys Chem Lett 2017; 8:5523-5530. [PMID: 29072840 PMCID: PMC5769702 DOI: 10.1021/acs.jpclett.7b02621] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.
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Affiliation(s)
- Sandra Vergara
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Dylan A. Lukes
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ulises Santiago
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - German Plascencia-Villa
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - David M. Black
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Marcos M. Alvarez
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Xochitl Lopez-Lozano
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | | | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Robert L. Whetten
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Miguel Jose-Yacaman
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
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17
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Ortega E, Cantu-Valle J, Plascencia-Villa G, Vergara S, Mendoza-Santoyo F, Londono-Calderon A, Santiago U, Ponce A. Morphology visualization of irregular shape bacteria by electron holography and tomography. Microsc Res Tech 2017; 80:1249-1255. [PMID: 28799676 DOI: 10.1002/jemt.22923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 11/08/2022]
Abstract
In the current work, irregular morphology of Staphylococcus aureus bacteria has been visualized by phase retrieval employing off-axis electron holography (EH) and 3D reconstruction electron tomography using high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM). Bacteria interacting with gold nanoparticles (AuNP) acquired a shrunken or irregular shape due to air dehydration processing. STEM imaging shows the attachment of AuNP on the surface of cells and suggests an irregular 3D morphology of the specimen. The phase reconstruction demonstrates that off-axis electron holography can reveal with a single hologram the morphology of the specimen and the distribution of the functionalized AuNPs. In addition, EH reduces significantly the acquisition time and the cumulative radiation damage (in three orders of magnitude) over biological samples in comparison with multiple tilted electron expositions intrinsic to electron tomography, as well as the processing time and the reconstruction artifacts that may arise during tomogram reconstruction.
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Affiliation(s)
- Eduardo Ortega
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
| | - Jesús Cantu-Valle
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
| | - Germán Plascencia-Villa
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
| | - Sandra Vergara
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
| | - Fernando Mendoza-Santoyo
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
| | - Alejandra Londono-Calderon
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
| | | | - Arturo Ponce
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249
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18
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Londoño-Calderon A, Ponce A, Santiago U, Mejia S, José-Yacamán M. Controlling the Number of Atoms on Catalytic Metallic Clusters. Studies in Surface Science and Catalysis 2017. [DOI: 10.1016/b978-0-12-805090-3.00006-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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19
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Ortega E, Ponce A, Santiago U, Alducin D, Benitez-Lara A, Plascencia-Villa G, José-Yacamán M. Structural damage reduction in protected gold clusters by electron diffraction methods. Adv Struct Chem Imaging 2016; 2:12. [PMID: 27738593 PMCID: PMC5037159 DOI: 10.1186/s40679-016-0026-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/15/2016] [Indexed: 11/12/2022]
Abstract
The present work explores electron diffraction methods for studying the structure of metallic clusters stabilized with thiol groups, which are susceptible to structural damage caused by electron beam irradiation. There is a compromise between the electron dose used and the size of the clusters since they have small interaction volume with electrons and as a consequence weak reflections in the diffraction patterns. The common approach of recording individual clusters using nanobeam diffraction has the problem of an increased current density. Dosage can be reduced with the use of a smaller condenser aperture and a higher condenser lens excitation, but even with those set ups collection times tend to be high. For that reason, the methods reported herein collects in a faster way diffraction patterns through the scanning across the clusters under nanobeam diffraction mode. In this way, we are able to collect a map of diffraction patterns, in areas with dispersed clusters, with short exposure times (milliseconds) using a high sensitive CMOS camera. When these maps are compared with their theoretical counterparts, oscillations of the clusters can be observed. The stability of the patterns acquired demonstrates that our methods provide a systematic and precise way to unveil the structure of atomic clusters without extensive detrimental damage of their crystallinity.
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Affiliation(s)
- Eduardo Ortega
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Arturo Ponce
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Ulises Santiago
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Diego Alducin
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Alfredo Benitez-Lara
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Germán Plascencia-Villa
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Miguel José-Yacamán
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
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20
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Sanchez JE, Santiago U, Benitez A, Yacamán MJ, González FJ, Ponce A. Structural analysis of the epitaxial interface Ag/ZnO in hierarchical nanoantennas. Appl Phys Lett 2016; 109:153104. [PMID: 27795571 PMCID: PMC5065564 DOI: 10.1063/1.4964719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
Detectors, photo-emitter, and other high order radiation devices work under the principle of directionality to enhance the power of emission/transmission in a particular direction. In order to understand such directionality, it is important to study their coupling mechanism of their active elements. In this work, we present a crystalline orientation analysis of ZnO nanorods grown epitaxially on the pentagonal faces of silver nanowires. The analysis of the crystalline orientation at the metal-semiconductor interface (ZnO/Ag) is performed with precession electron diffraction under assisted scanning mode. In addition, high resolution X-ray diffraction on a Bragg-Brentano configuration has been used to identify the crystalline phases of the arrangement between ZnO rods and silver nanowires. The work presented herein provides a fundamental knowledge to understand the metal-semiconductor behavior related to the receiving/transmitting mechanisms of ZnO/Ag nanoantennas.
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Affiliation(s)
- John Eder Sanchez
- Department of Physics and Astronomy, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, USA
| | - Ulises Santiago
- Department of Physics and Astronomy, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, USA
| | - Alfredo Benitez
- Department of Physics and Astronomy, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, USA
| | - Miguel José Yacamán
- Department of Physics and Astronomy, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, USA
| | - Francisco Javier González
- Universidad Autónoma de San Luis Potosí , LANCYTT, Sierra Leona 550, San Luis Potosí, SLP 78210, Mexico
| | - Arturo Ponce
- Department of Physics and Astronomy, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, USA
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21
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Mannix AJ, Zhou XF, Kiraly B, Wood JD, Alducin D, Myers BD, Liu X, Fisher BL, Santiago U, Guest JR, Yacaman MJ, Ponce A, Oganov AR, Hersam MC, Guisinger NP. Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs. Science 2016; 350:1513-6. [PMID: 26680195 DOI: 10.1126/science.aad1080] [Citation(s) in RCA: 864] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.
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Affiliation(s)
- Andrew J Mannix
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, IL 60439, USA. Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Xiang-Feng Zhou
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794, USA. School of Physics, Nankai University, Tianjin 300071, China
| | - Brian Kiraly
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, IL 60439, USA. Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Joshua D Wood
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Diego Alducin
- Department of Physics, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Benjamin D Myers
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA. NUANCE Center, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Xiaolong Liu
- Applied Physics Graduate Program, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Brandon L Fisher
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, IL 60439, USA
| | - Ulises Santiago
- Department of Physics, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Jeffrey R Guest
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, IL 60439, USA
| | - Miguel Jose Yacaman
- Department of Physics, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Arturo Ponce
- Department of Physics, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, 5 Nobel Street, Moscow 143026, Russia. Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny City, Moscow Region, 141700, Russia. Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Mark C Hersam
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA. Applied Physics Graduate Program, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA. Department of Chemistry, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA.
| | - Nathan P Guisinger
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building 440, Argonne, IL 60439, USA.
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Ponce A, Veron M, Ruiz-Zepeda F, Sanchez JE, Santiago U, Mendoza-Santoyo F, Velazquez-Salazar J, Jose-Yacaman M. Crystal orientation mapping on metallic nanoparticles by electron diffraction methods. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315094401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Miramontes O, Bonafé F, Santiago U, Larios-Rodriguez E, Velázquez-Salazar JJ, Mariscal MM, Yacaman MJ. Ultra-small rhenium clusters supported on graphene. Phys Chem Chem Phys 2015; 17:7898-906. [PMID: 25721176 PMCID: PMC4365820 DOI: 10.1039/c4cp05660d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption of very small rhenium clusters (2-13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional theory calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones.
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Affiliation(s)
| | - Franco Bonafé
- INFIQC, CONICET. Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba Argentina
| | - Ulises Santiago
- Department of Physics and Astronomy, University of Texas at San Antonio
| | - Eduardo Larios-Rodriguez
- Departamento de Ingeniería Química y Metalurgia, Universidad de Sonora, Rosales y Luis Encinas S/N, Hermosillo, Sonora, C.P. 83000 México
| | | | - Marcelo M. Mariscal
- INFIQC, CONICET. Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba Argentina
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Casillas G, Santiago U, Barrón H, Alducin D, Ponce A, José-Yacamán M. Elasticity of MoS 2 Sheets by Mechanical Deformation Observed by in Situ Electron Microscopy. J Phys Chem C Nanomater Interfaces 2015; 119:710-715. [PMID: 25598860 PMCID: PMC4291041 DOI: 10.1021/jp5093459] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/05/2014] [Indexed: 06/01/2023]
Abstract
MoS2 has been the focus of extensive research due to its potential applications. More recently, the mechanical properties of MoS2 layers have raised interest due to applications in flexible electronics. In this article, we show in situ transmission electron microcsopy (TEM) observation of the mechanical response of a few layers of MoS2 to an external load. We used a scanning tunneling microscope (STM) tip mounted on a TEM stage to induce deformation on nanosheets of MoS2 containing few layers. The results confirm the outstanding mechanical properties on the MoS2. The layers can be bent close to 180°. However, when the tip is retrieved the initial structure is recovered. Evidence indicates that there is a significant bond reconstruction during the bending with an outstanding capability to recover the initial bond structure. The results show that flexibility of three layers of MoS2 remains the same as a single layer while increasing the bending modulus by 3 orders of magnitude. Our findings are consistent with theoretical calculations and confirm the great potential of MoS2 for applications.
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Ruiz-Zepeda F, Casallas-Moreno YL, Cantu-Valle J, Alducin D, Santiago U, José-Yacaman M, López-López M, Ponce A. Precession electron diffraction-assisted crystal phase mapping of metastable c-GaN films grown on (001) GaAs. Microsc Res Tech 2014; 77:980-5. [DOI: 10.1002/jemt.22424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/05/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Francisco Ruiz-Zepeda
- Department of Physics and Astronomy; University of Texas at San Antonio; San Antonio Texas 78254
| | - Yenny L. Casallas-Moreno
- Physics Department; Centro de Investigación y de Estudios Avanzados del IPN; Apartado Postal 14-740 México, D. F. 07000 México
| | - Jesus Cantu-Valle
- Department of Physics and Astronomy; University of Texas at San Antonio; San Antonio Texas 78254
| | - Diego Alducin
- Department of Physics and Astronomy; University of Texas at San Antonio; San Antonio Texas 78254
| | - Ulises Santiago
- Department of Physics and Astronomy; University of Texas at San Antonio; San Antonio Texas 78254
| | - Miguel José-Yacaman
- Department of Physics and Astronomy; University of Texas at San Antonio; San Antonio Texas 78254
| | - Máximo López-López
- Physics Department; Centro de Investigación y de Estudios Avanzados del IPN; Apartado Postal 14-740 México, D. F. 07000 México
| | - Arturo Ponce
- Department of Physics and Astronomy; University of Texas at San Antonio; San Antonio Texas 78254
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Tlahuice-Flores A, Santiago U, Bahena D, Vinogradova E, Conroy CV, Ahuja T, Bach SBH, Ponce A, Wang G, José-Yacamán M, Whetten RL. Structure of the thiolated Au130 cluster. J Phys Chem A 2013. [PMID: 24004091 DOI: 10.1021/jp407150t] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The structure of the recently discovered Au130-thiolate and -dithiolate clusters is explored in a combined experiment-theory approach. Rapid electron diffraction in scanning/transmission electron microscopy (STEM) enables atomic-resolution imaging of the gold core and the comparison with density functional theory (DFT)-optimized realistic structure models. The results are consistent with a 105-atom truncated-decahedral core protected by 25 short staple motifs, incorporating disulfide bridges linking the dithiolate ligands. The optimized structure also accounts, via time-dependent DFT (TD-DFT) simulation, for the distinctive optical absorption spectrum, and rationalizes the special stability underlying the selective formation of the Au130 cluster in high yield. The structure is distinct from, yet shares some features with, each of the known Au102 and Au144/Au146 systems.
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Affiliation(s)
- Alfredo Tlahuice-Flores
- Department of Physics and Astronomy and ‡Department of Chemistry, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, United States
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Tlahuice-Flores A, Santiago U, Bahena D, Vinogradova E, Conroy CV, Ahuja T, Bach SBH, Ponce A, Wang G, José-Yacamán M, Whetten RL. Structure of the Thiolated Au130 Cluster. J Phys Chem A 2013; 117:10470-6. [DOI: 10.1021/jp406665m] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | | | | | - Cecil V. Conroy
- Department
of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States
| | - Tarushee Ahuja
- Department
of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States
| | | | | | - Gangli Wang
- Department
of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States
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Cantu-Valle J, Ruiz-Zepeda F, Voelkl E, Kawasaki M, Santiago U, José-Yacaman M, Ponce A. Determination of the surface morphology of gold-decahedra nanoparticles using an off-axis electron holography dual-lens imaging system. Micron 2013; 54-55:82-6. [PMID: 24055122 DOI: 10.1016/j.micron.2013.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/27/2013] [Accepted: 07/29/2013] [Indexed: 11/18/2022]
Abstract
The purpose of this paper is to show surface irregularities in gold decahedra nanoparticles extracted by using off-axis electron holography in a JEOL ARM 200F microscope. Electron holography has been used in a dual-lens system within the objective lenses: main objective lens and objective minilens. Parameters such as biprism voltage, fringe spacing (σ), fringe width (W) and optimum fringe contrast have been calibrated. The reliability of the transmission electron microscope performance with these parameters was carried out through a plug-in in the Digital-Micrograph software, which considers the mean inner potential within the particle leading a precise determination of the morphological surface of decahedral nanoparticles obtained from the reconstructed unwrapped phase and image processing. We have also shown that electron holography has the capability to extract information from nanoparticle shape that is currently impossible to obtain with any other electron microscopy technique.
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Affiliation(s)
- J Cantu-Valle
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
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Khanal S, Casillas G, Bhattarai N, Velázquez-Salazar JJ, Santiago U, Ponce A, Mejía-Rosales S, José-Yacamán M. CuS2-passivated Au-core, Au3Cu-shell nanoparticles analyzed by atomistic-resolution Cs-corrected STEM. Langmuir 2013; 29:9231-9. [PMID: 23802756 PMCID: PMC3805048 DOI: 10.1021/la401598e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Au-core, Au3Cu-alloyed shell nanoparticles passivated with CuS2 were fabricated by the polyol method, and characterized by Cs-corrected scanning transmission electron microscopy. The analysis of the high-resolution micrographs reveals that these nanoparticles have decahedral structure with shell periodicity, and that each of the particles is composed by Au core and Au3Cu alloyed shell surrounded by CuS2 surface layer. X-ray diffraction measurements and results from numerical simulations confirm these findings. From the atomic resolution micrographs, we identified edge dislocations at the twin boundaries of the particles, as well as evidence of the diffusion of Cu atoms into the Au region, and the reordering of the lattice on the surface, close to the vertices of the particle. These defects will impact the atomic and electronic structures, thereby changing the physical and chemical properties of the nanoparticles. On the other hand, we show for the first time the formation of an ordered superlattice of Au3Cu and a self-capping layer made using one of the alloy metals. This has significant consequences on the physical mechanism that form multicomponent nanoparticles.
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Affiliation(s)
- Subarna Khanal
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
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Bahena D, Bhattarai N, Santiago U, Tlahuice A, Ponce A, Bach SBH, Yoon B, Whetten RL, Landman U, Jose-Yacaman M. STEM Electron Diffraction and High Resolution Images Used in the Determination of the Crystal Structure of Au 144(SR) 60 Cluster. J Phys Chem Lett 2013; 4:975-981. [PMID: 23687562 PMCID: PMC3655783 DOI: 10.1021/jz400111d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Determination of the total structure of molecular nanocrystals is an outstanding experimental challenge that has been met, in only a few cases, by single-crystal X-ray diffraction. Described here is an alternative approach that is of most general applicability and does not require the fabrication of a single crystal. The method is based on rapid, time-resolved nanobeam electron diffraction (NBD) combined with high-angle annular dark field scanning/transmission electron microscopy (HAADF-STEM) images in a probe corrected STEM microscope, operated at reduced voltages. The results are compared with theoretical simulations of images and diffraction patterns obtained from atomistic structural models derived through first-principles density functional theory (DFT) calculations. The method is demonstrated by application to determination of the structure of the Au144(SCH2CH2Ph)60 cluster.
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Affiliation(s)
- Daniel Bahena
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
| | - Nabraj Bhattarai
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
| | - Ulises Santiago
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
| | - Alfredo Tlahuice
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
| | - Arturo Ponce
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
| | - Stephan B. H. Bach
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
| | - Bokwon Yoon
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
| | - Robert L. Whetten
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332
| | - Uzi Landman
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
| | - Miguel Jose-Yacaman
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249
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Santiago U. [Epidemiology of traffic accidents, in Salvador]. Rev Bras Med 1969; 26:415-9. [PMID: 5347019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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