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Böhm ME, Razavi M, Marathe NP, Flach CF, Larsson DGJ. Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities. Microbiome 2020; 8:41. [PMID: 32197644 PMCID: PMC7085159 DOI: 10.1186/s40168-020-00814-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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] [Received: 12/19/2019] [Accepted: 03/02/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics. RESULTS We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now. CONCLUSION To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.
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Affiliation(s)
- Maria-Elisabeth Böhm
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nachiket P. Marathe
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Institute of Marine Research (IMR), Bergen, Norway
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Smith CA, Toth M, Stewart NK, Maltz L, Vakulenko SB. Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2''-phosphotransferases. Acta Crystallogr D Struct Biol 2019; 75:1129-1137. [PMID: 31793906 DOI: 10.1107/s2059798319015079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022]
Abstract
Aminoglycoside phosphotransferases (APHs) are one of three families of aminoglycoside-modifying enzymes that confer high-level resistance to the aminoglycoside antibiotics via enzymatic modification. This has now rendered many clinically important drugs almost obsolete. The APHs specifically phosphorylate hydroxyl groups on the aminoglycosides using a nucleotide triphosphate as the phosphate donor. The APH(2'') family comprises four distinct members, isolated primarily from Enterococcus sp., which vary in their substrate specificities and also in their preference for the phosphate donor (ATP or GTP). The structure of the ternary complex of APH(2'')-IIIa with GDP and kanamycin was solved at 1.34 Å resolution and was compared with substrate-bound structures of APH(2'')-Ia, APH(2'')-IIa and APH(2'')-IVa. In contrast to the case for APH(2'')-Ia, where it was proposed that the enzyme-mediated hydrolysis of GTP is regulated by conformational changes in its N-terminal domain upon GTP binding, APH(2'')-IIa, APH(2'')-IIIa and APH(2'')-IVa show no such regulatory mechanism, primarily owing to structural differences in the N-terminal domains of these enzymes.
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Affiliation(s)
- Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Nichole K Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Lauren Maltz
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sergei B Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Szymanek-Majchrzak K, Mlynarczyk A, Kawecki D, Pacholczyk M, Durlik M, Deborska-Materkowska D, Paczek L, Mlynarczyk G. Resistance to Aminoglycosides of Methicillin-Resistant Strains of Staphylococcus aureus, Originating in the Surgical and Transplantation Wards of the Warsaw Clinical Center-A Retrospective Analysis. Transplant Proc 2018; 50:2170-2175. [PMID: 30177131 DOI: 10.1016/j.transproceed.2018.02.158] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/06/2018] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Aminoglycoside resistance (AR) is common in health care-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). AR is most often associated with the production of antibiotic modifying enzymes: bidomain AAC(6')-Ie/APH(2″)-Ia acetyltransferase and phosphotransferase, ANT(4')-Ia nucleotidyltransferase, and APH(3″)-IIIa phosphotransferase. AIM Determination of aminoglycoside sensitivity, presence of genes encoding enzymes, and molecular typing of HA-MRSA strains derived from patients hospitalized in surgical and transplantation wards. MATERIALS AND METHODS Fifty-four HA-MRSA strains, isolated from various materials from patients in the surgical and transplantation wards of Warsaw's clinical hospital, hospitalized between 1991 and 2007. The MIC values of gentamicin-GEN/tobramycin-TOB/amikacin-AK/netilmicin-NET were determined by the E-test (CLSI/EUCAST). Genes mecA/aacA-aphD/aadD/aph(3″)-IIIa were detected using PCR. SCCmec types were determined according to the Oliveira method and the sequence type (ST)/clonal complex (CC) by the MLST method. RESULTS Of the isolates tested, 36 (66.7%) showed resistance to at least one aminoglycoside: TOB (57.4%), GEN (53.7%), AK (55.6%), NET (24.1%). The aacA-aphD gene was present in 29 MRSA-GEN-R (most often in combination with aadD, 15/29 or aph(3″)-IIIa, 10/29); the aacA-aphD gene was the only determinant of resistance in 1 isolate. The AR variants mainly belonged to the CC8 clonal complex (ST239/247/241/254/8) and most frequently contained SCCmec type III (3A) cassettes. CONCLUSIONS Resistance to at least one aminoglycoside was present in 66.7% of HA-MRSA and in more than 22% to all of them. The presence of the aacA-aphD gene was sufficient to express the resistance phenotype to GEN/TOB/AK/NET. Resistant isolates were closely related to each other.
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Affiliation(s)
- K Szymanek-Majchrzak
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland.
| | - A Mlynarczyk
- Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland
| | - D Kawecki
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - M Pacholczyk
- Department of General and Transplantation Surgery, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - M Durlik
- Department of Transplant Medicine and Nephrology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - D Deborska-Materkowska
- Department of Transplant Medicine and Nephrology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - L Paczek
- Department of Immunology, Transplantology and Internal Diseases, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - G Mlynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland
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Ramirez MS, Tolmasky ME. Amikacin: Uses, Resistance, and Prospects for Inhibition. Molecules 2017; 22:E2267. [PMID: 29257114 DOI: 10.3390/molecules22122267] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022] Open
Abstract
Aminoglycosides are a group of antibiotics used since the 1940s to primarily treat a broad spectrum of bacterial infections. The primary resistance mechanism against these antibiotics is enzymatic modification by aminoglycoside-modifying enzymes that are divided into acetyl-transferases, phosphotransferases, and nucleotidyltransferases. To overcome this problem, new semisynthetic aminoglycosides were developed in the 70s. The most widely used semisynthetic aminoglycoside is amikacin, which is refractory to most aminoglycoside modifying enzymes. Amikacin was synthesized by acylation with the l-(-)-γ-amino-α-hydroxybutyryl side chain at the C-1 amino group of the deoxystreptamine moiety of kanamycin A. The main amikacin resistance mechanism found in the clinics is acetylation by the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib], an enzyme coded for by a gene found in integrons, transposons, plasmids, and chromosomes of Gram-negative bacteria. Numerous efforts are focused on finding strategies to neutralize the action of AAC(6')-Ib and extend the useful life of amikacin. Small molecules as well as complexes ionophore-Zn+2 or Cu+2 were found to inhibit the acetylation reaction and induced phenotypic conversion to susceptibility in bacteria harboring the aac(6')-Ib gene. A new semisynthetic aminoglycoside, plazomicin, is in advance stage of development and will contribute to renewed interest in this kind of antibiotics.
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Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics famous for their antibacterial activity against Gram-positive and Gram-negative bacteria, as well as mycobacteria. In the United States, the most prescribed AGs, including amikacin (AMK), gentamicin (GEN), and tobramycin (TOB), are vital components of the treatment for resistant bacterial infections. Arbekacin (ABK), a semisynthetic AG, is widely used for the treatment of resistant Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus in Asia. However, the rapid emergence and development of bacterial resistance are limiting the clinical application of AG antibiotics. Of all bacterial resistance mechanisms against AGs, the acquisition of AG-modifying enzymes (AMEs) by bacteria is the most common. It was previously reported that a variant of a bifunctional AME, the 6'-N-AG acetyltransferase-Ie/2″-O-AG phosphotransferase-Ia [AAC(6')-Ie/APH(2″)-Ia], containing a D80G point mutation and a truncation after amino acid 240 modified ABK and AMK at a new position, the 4‴-amine, therefore displaying a change in regiospecificity. In this study, we aimed to verify the altered regiospecificity of this bifunctional enzyme by mutation and truncation for the potential of derivatizing AGs with chemoenzymatic reactions. With the three variant enzymes in this study that contained either mutation only (D80G), truncation only (1-240), or mutation and truncation (D80G-1-240), we characterized their activity by profiling their substrate promiscuity, determined their kinetics parameters, and performed mass spectrometry to determine how and where ABK and AMK were acetylated by these enzymes. We found that the three mutant enzymes possessed distinct acetylation regiospecificity compared to that of the bifunctional AAC(6')-Ie/APH(2″)-Ia enzyme and the functional AAC(6')-Ie domain [AAC(6')/APH(2″)-1-194].
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Affiliation(s)
- Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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Salah Ud-Din AIM, Tikhomirova A, Roujeinikova A. Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT). Int J Mol Sci 2016; 17:E1018. [PMID: 27367672 PMCID: PMC4964394 DOI: 10.3390/ijms17071018] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
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Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Alexandra Tikhomirova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
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Caldwell SJ, Huang Y, Berghuis AM. Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2″)-Ia. Structure 2016; 24:935-45. [PMID: 27161980 DOI: 10.1016/j.str.2016.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/14/2016] [Accepted: 04/04/2016] [Indexed: 11/28/2022]
Abstract
APH(2″)-Ia is a widely disseminated resistance factor frequently found in clinical isolates of Staphylococcus aureus and pathogenic enterococci, where it is constitutively expressed. APH(2″)-Ia confers high-level resistance to gentamicin and related aminoglycosides through phosphorylation of the antibiotic using guanosine triphosphate (GTP) as phosphate donor. We have determined crystal structures of the APH(2″)-Ia in complex with GTP analogs, guanosine diphosphate, and aminoglycosides. These structures collectively demonstrate that aminoglycoside binding to the GTP-bound kinase drives conformational changes that bring distant regions of the protein into contact. These changes in turn drive a switch of the triphosphate cofactor from an inactive, stabilized conformation to a catalytically competent active conformation. This switch has not been previously reported for antibiotic kinases or for the structurally related eukaryotic protein kinases. This catalytic triphosphate switch presents a means by which the enzyme can curtail wasteful hydrolysis of GTP in the absence of aminoglycosides, providing an evolutionary advantage to this enzyme.
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Affiliation(s)
- Shane J Caldwell
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Yue Huang
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
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Abstract
Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.
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Affiliation(s)
- Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. ; Tel: 859-218-1686
| | - Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI, USA. ; Tel: 608-363-2273
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Ortego L, Gonzalo-Asensio J, Laguna A, Villacampa MD, Gimeno MC. (Aminophosphane)gold(I) and silver(I) complexes as antibacterial agents. J Inorg Biochem 2015; 146:19-27. [DOI: 10.1016/j.jinorgbio.2015.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 12/20/2022]
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Smith CA, Toth M, Weiss TM, Frase H, Vakulenko SB. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis. Acta Crystallogr D Biol Crystallogr 2014; 70:2754-64. [PMID: 25286858 PMCID: PMC4188014 DOI: 10.1107/s1399004714017635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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] [Received: 06/06/2014] [Accepted: 07/31/2014] [Indexed: 11/11/2022]
Abstract
Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and enterococcal pathogens is primarily conferred by the bifunctional enzyme AAC(6')-Ie-APH(2'')-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6')-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2'')-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2'')-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6')-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6')-Ie enzyme is joined to APH(2'')-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2'')-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6')-Ie-APH(2'')-Ia enzyme.
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Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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