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Judge A, Hu L, Sankaran B, Van Riper J, Venkataram Prasad BV, Palzkill T. Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M β-lactamase. Commun Biol 2023; 6:35. [PMID: 36635385 PMCID: PMC9837174 DOI: 10.1038/s42003-023-04422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
CTX-M β-lactamases are prevalent antibiotic resistance enzymes and are notable for their ability to rapidly hydrolyze the extended-spectrum cephalosporin, cefotaxime. We hypothesized that the active site sequence requirements of CTX-M-mediated hydrolysis differ between classes of β-lactam antibiotics. Accordingly, we use codon randomization, antibiotic selection, and deep sequencing to determine the CTX-M active-site residues required for hydrolysis of cefotaxime and the penicillin, ampicillin. The study reveals positions required for hydrolysis of all β-lactams, as well as residues controlling substrate specificity. Further, CTX-M enzymes poorly hydrolyze the extended-spectrum cephalosporin, ceftazidime. We further show that the sequence requirements for ceftazidime hydrolysis follow those of cefotaxime, with the exception that key active-site omega loop residues are not required, and may be detrimental, for ceftazidime hydrolysis. These results provide insights into cephalosporin hydrolysis and demonstrate that changes to the active-site omega loop are likely required for the evolution of CTX-M-mediated ceftazidime resistance.
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Affiliation(s)
- Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Justin Van Riper
- Graduate Program in Chemical, Physical, and Structural Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
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Penicillanic Acid Sulfones Inactivate the Extended-Spectrum β-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of β-Lactamase Inhibition. mBio 2022; 13:e0179321. [PMID: 35612361 PMCID: PMC9239225 DOI: 10.1128/mbio.01793-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
β-Lactamases hydrolyze β-lactam antibiotics and are major determinants of antibiotic resistance in Gram-negative pathogens. Enmetazobactam (formerly AAI101) and tazobactam are penicillanic acid sulfone (PAS) β-lactamase inhibitors that differ by an additional methyl group on the triazole ring of enmetazobactam, rendering it zwitterionic. In this study, ultrahigh-resolution X-ray crystal structures and mass spectrometry revealed the mechanism of PAS inhibition of CTX-M-15, an extended-spectrum β-lactamase (ESBL) globally disseminated among Enterobacterales. CTX-M-15 crystals grown in the presence of enmetazobactam or tazobactam revealed loss of the Ser70 hydroxyl group and formation of a lysinoalanine cross-link between Lys73 and Ser70, two residues critical for catalysis. Moreover, the residue at position 70 undergoes epimerization, resulting in formation of a d-amino acid. Cocrystallization of enmetazobactam or tazobactam with CTX-M-15 with a Glu166Gln mutant revealed the same cross-link, indicating that this modification is not dependent on Glu166-catalyzed deacylation of the PAS-acylenzyme. A cocrystal structure of enmetazobactam with CTX-M-15 with a Lys73Ala mutation indicates that epimerization can occur without cross-link formation and positions the Ser70 Cβ closer to Lys73, likely facilitating formation of the Ser70-Lys73 cross-link. A crystal structure of a tazobactam-derived imine intermediate covalently linked to Ser70, obtained after 30 min of exposure of CTX-M-15 crystals to tazobactam, supports formation of an initial acylenzyme by PAS inhibitors on reaction with CTX-M-15. These data rationalize earlier results showing CTX-M-15 deactivation by PAS inhibitors to involve loss of protein mass, and they identify a distinct mechanism of β-lactamase inhibition by these agents.
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Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition. Antimicrob Agents Chemother 2020; 64:AAC.00398-20. [PMID: 32778546 DOI: 10.1128/aac.00398-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
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Lewandowski EM, Szczupak Ł, Kowalczyk A, Mendoza G, Arruebo M, Jacobs LMC, Stączek P, Chen Y, Kowalski K. Metallocenyl 7‐ACA Conjugates: Antibacterial Activity Studies and Atomic‐Resolution X‐ray Crystal Structure with CTX‐M β‐Lactamase. Chembiochem 2020; 21:2187-2195. [DOI: 10.1002/cbic.202000054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/13/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Eric M. Lewandowski
- Department of Molecular Medicine University of South Florida, >Morsani College of Medicine 12901 Bruce B. Downs Boulevard Tampa FL 33612 US
| | - Łukasz Szczupak
- Department of Organic Chemistry, Faculty of Chemistry University of Łódź Tamka 12 91-403 Łódź Poland
| | - Aleksandra Kowalczyk
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection University of Łódź Banacha 12/16 90-237 Łódź Poland
| | - Gracia Mendoza
- Department of Chemical Engineering Aragon Health Research Institute (IIS Aragón) University of Zaragoza Campus Río Ebro-Edificio I+D, c/ Poeta Mariano Esquillor s/n 5018 Zaragoza Spain
| | - Manuel Arruebo
- Department of Chemical Engineering Aragon Health Research Institute (IIS Aragón) University of Zaragoza Campus Río Ebro-Edificio I+D, c/ Poeta Mariano Esquillor s/n 5018 Zaragoza Spain
- Networking Research Center on Bioengineering Biomaterials and Nanomedicine CIBER-BBN 28029 Madrid Spain
| | - Lian M. C. Jacobs
- Department of Molecular Medicine University of South Florida, >Morsani College of Medicine 12901 Bruce B. Downs Boulevard Tampa FL 33612 US
| | - Paweł Stączek
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection University of Łódź Banacha 12/16 90-237 Łódź Poland
| | - Yu Chen
- Department of Molecular Medicine University of South Florida, >Morsani College of Medicine 12901 Bruce B. Downs Boulevard Tampa FL 33612 US
| | - Konrad Kowalski
- Department of Organic Chemistry, Faculty of Chemistry University of Łódź Tamka 12 91-403 Łódź Poland
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Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc Natl Acad Sci U S A 2020; 117:5818-5825. [PMID: 32123084 DOI: 10.1073/pnas.1922203117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The acyl-enzyme intermediate is a central milestone in the hydrolysis reaction catalyzed by these enzymes. However, the protonation states of the catalytic residues in this complex have never been fully analyzed experimentally due to inherent difficulties. To help unravel the ambiguity surrounding class A β-lactamase catalysis, we have used ultrahigh-resolution X-ray crystallography and the recently approved β-lactamase inhibitor avibactam to trap the acyl-enzyme complex of class A β-lactamase CTX-M-14 at varying pHs. A 0.83-Å-resolution CTX-M-14 complex structure at pH 7.9 revealed a neutral state for both Lys73 and Glu166. Furthermore, the avibactam hydroxylamine-O-sulfonate group conformation varied according to pH, and this conformational switch appeared to correspond to a change in the Lys73 protonation state at low pH. In conjunction with computational analyses, our structures suggest that Lys73 has a perturbed acid dissociation constant (pKa) compared with acyl-enzyme complexes with β-lactams, hindering its function to deprotonate Glu166 and the initiation of the deacylation reaction. Further NMR analysis demonstrated Lys73 pKa to be ∼5.2 to 5.6. Together with previous ultrahigh-resolution crystal structures, these findings enable us to follow the proton transfer process of the entire acylation reaction and reveal the critical role of Lys73. They also shed light on the stability and reversibility of the avibactam carbamoyl acyl-enzyme complex, highlighting the effect of substrate functional groups in influencing the protonation states of catalytic residues and subsequently the progression of the reaction.
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Langan PS, Sullivan B, Weiss KL, Coates L. Probing the role of the conserved residue Glu166 in a class A β-lactamase using neutron and X-ray protein crystallography. Acta Crystallogr D Struct Biol 2020; 76:118-123. [PMID: 32038042 PMCID: PMC7008513 DOI: 10.1107/s2059798319016334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
The amino-acid sequence of the Toho-1 β-lactamase contains several conserved residues in the active site, including Ser70, Lys73, Ser130 and Glu166, some of which coordinate a catalytic water molecule. This catalytic water molecule is essential in the acylation and deacylation parts of the reaction mechanism through which Toho-1 inactivates specific antibiotics and provides resistance to its expressing bacterial strains. To investigate the function of Glu166 in the acylation part of the catalytic mechanism, neutron and X-ray crystallographic studies were performed on a Glu166Gln mutant. The structure of this class A β-lactamase mutant provides several insights into its previously reported reduced drug-binding kinetic rates. A joint refinement of both X-ray and neutron diffraction data was used to study the effects of the Glu166Gln mutation on the active site of Toho-1. This structure reveals that while the Glu166Gln mutation has a somewhat limited impact on the positions of the conserved amino acids within the active site, it displaces the catalytic water molecule from the active site. These subtle changes offer a structural explanation for the previously observed decreases in the binding of non-β-lactam inhibitors such as the recently developed diazobicyclooctane inhibitor avibactam.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Szczupak Ł, Kowalczyk A, Trzybiński D, Woźniak K, Mendoza G, Arruebo M, Steverding D, Stączek P, Kowalski K. Organometallic ciprofloxacin conjugates with dual action: synthesis, characterization, and antimicrobial and cytotoxicity studies. Dalton Trans 2020; 49:1403-1415. [DOI: 10.1039/c9dt03948a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Organometallic ciprofloxacin conjugates were synthesized and two mechanisms of antimicrobial activity were demonstrated. The first mechanism involves the inhibition of type IIA topoisomerases and the second involves ROS generation in bacterial cells.
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Affiliation(s)
- Łukasz Szczupak
- Faculty of Chemistry
- Department of Organic Chemistry
- University of Łódź
- 91-403 Łódź
- Poland
| | - Aleksandra Kowalczyk
- Department of Microbial Genetics
- Faculty of Biology and Environmental Protection
- University of Łódź
- 90-237 Łódź
- Poland
| | - Damian Trzybiński
- Faculty of Chemistry
- Biological and Chemical Research Centre
- University of Warsaw
- 02-089 Warszawa
- Poland
| | - Krzysztof Woźniak
- Faculty of Chemistry
- Biological and Chemical Research Centre
- University of Warsaw
- 02-089 Warszawa
- Poland
| | - Gracia Mendoza
- Department of Chemical Engineering
- University of Zaragoza
- 5018 Zaragoza
- Spain
- Aragon Health Research Institute (IIS Aragón)
| | - Manuel Arruebo
- Department of Chemical Engineering
- University of Zaragoza
- 5018 Zaragoza
- Spain
- Aragon Health Research Institute (IIS Aragón)
| | - Dietmar Steverding
- Bob Champion Research & Education Building
- Norwich Medical School
- University of East Anglia
- Norwich NR4 7UQ
- UK
| | - Paweł Stączek
- Department of Microbial Genetics
- Faculty of Biology and Environmental Protection
- University of Łódź
- 90-237 Łódź
- Poland
| | - Konrad Kowalski
- Faculty of Chemistry
- Department of Organic Chemistry
- University of Łódź
- 91-403 Łódź
- Poland
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Tassoni R, Blok A, Pannu NS, Ubbink M. New Conformations of Acylation Adducts of Inhibitors of β-Lactamase from Mycobacterium tuberculosis. Biochemistry 2019; 58:997-1009. [PMID: 30632739 PMCID: PMC6383187 DOI: 10.1021/acs.biochem.8b01085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Mycobacterium tuberculosis (Mtb), the main causative
agent of tuberculosis (TB), is naturally resistant to β-lactam
antibiotics due to the production of the extended spectrum β-lactamase
BlaC. β-Lactam/β-lactamase inhibitor combination therapies
can circumvent the BlaC-mediated resistance of Mtb and are promising
treatment options against TB. However, still little is known of the
exact mechanism of BlaC inhibition by the β-lactamase inhibitors
currently approved for clinical use, clavulanic acid, sulbactam, tazobactam,
and avibactam. Here, we present the X-ray diffraction crystal structures
of the acyl-enzyme adducts of wild-type BlaC with the four inhibitors.
The +70 Da adduct derived from clavulanate and the trans-enamine acylation adducts of sulbactam and tazobactam are reported.
BlaC in complex with avibactam revealed two inhibitor conformations.
Preacylation binding could not be observed because inhibitor binding
was not detected in BlaC variants carrying a substitution of the active
site serine 70 to either alanine or cysteine, by crystallography,
ITC or NMR. These results suggest that the catalytic serine 70 is
necessary not only for enzyme acylation but also for increasing BlaC
affinity for inhibitors in the preacylation state. The structure of
BlaC with the serine to cysteine mutation showed a covalent linkage
of the cysteine 70 Sγ atom to the nearby amino group of lysine
73. The differences of adduct conformations between BlaC and other
β-lactamases are discussed.
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Affiliation(s)
- Raffaella Tassoni
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
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Azam M, Al-Resayes SI, Wabaidur SM, Altaf M, Chaurasia B, Alam M, Shukla SN, Gaur P, Albaqami NTM, Islam MS, Park S. Synthesis, Structural Characterization and Antimicrobial Activity of Cu(II) and Fe(III) Complexes Incorporating Azo-Azomethine Ligand. Molecules 2018; 23:molecules23040813. [PMID: 29614828 PMCID: PMC6017743 DOI: 10.3390/molecules23040813] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/16/2022] Open
Abstract
We are reporting a novel azo-azomethine ligand, HL and its complexes with Cu(II) and Fe(III) ions. The ligand and its complexes are characterized by various physico-chemical techniques using C,H,N analyses, FT-IR, 1H-NMR, ESI-MS and UV-Vis studies. TGA analyses reveal complexes are sufficiently stable and undergo two-step degradation processes. The redox behavior of the complexes was evaluated by cyclic voltammetry. Furthermore, the ligand and its complexes were tested for antimicrobial activity against bacterial and fungal strains by determining inhibition zone, minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). The complexes showed moderate antimicrobial activity when tested against Gram +ve and Gram −ve bacterial strains. To obtain insights into the structure of ligand, DFT studies are recorded. The results obtained are quite close to the experimental results. In addition, the energy gap, chemical hardness, softness, electronegativity, electrophilic index and chemical potential were calculated using HOMO, LUMO energy value of ligand.
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Affiliation(s)
- Mohammad Azam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (S.I.A.-R.); (S.M.W.); (M.A.); (N.T.M.A.); (M.S.I.)
- Correspondence: ; Tel./Fax: +966-11-467-5982
| | - Saud I. Al-Resayes
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (S.I.A.-R.); (S.M.W.); (M.A.); (N.T.M.A.); (M.S.I.)
| | - Saikh Mohammad Wabaidur
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (S.I.A.-R.); (S.M.W.); (M.A.); (N.T.M.A.); (M.S.I.)
| | - Mohammad Altaf
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (S.I.A.-R.); (S.M.W.); (M.A.); (N.T.M.A.); (M.S.I.)
| | - Bhaskar Chaurasia
- Coordination Chemistry Research Laboratory, Department of Chemistry, Govt. Science College, Jabalpur 482001, India; (B.C.); (S.N.S.); (P.G.)
| | - Mahboob Alam
- Division of Chemistry and Biotechnology, Dongguk University, 123 Dongdae-ro, Gyeongju 780-714, Korea;
| | - Satyendra Nath Shukla
- Coordination Chemistry Research Laboratory, Department of Chemistry, Govt. Science College, Jabalpur 482001, India; (B.C.); (S.N.S.); (P.G.)
| | - Pratiksha Gaur
- Coordination Chemistry Research Laboratory, Department of Chemistry, Govt. Science College, Jabalpur 482001, India; (B.C.); (S.N.S.); (P.G.)
| | - Nader Talmas M. Albaqami
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (S.I.A.-R.); (S.M.W.); (M.A.); (N.T.M.A.); (M.S.I.)
| | - Mohammad Shahidul Islam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (S.I.A.-R.); (S.M.W.); (M.A.); (N.T.M.A.); (M.S.I.)
| | - Soonheum Park
- Department of Advanced Materials Chemistry, Dongguk University, 123 Dongdae-ro, Gyeongju 780-714, Korea;
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Langan PS, Vandavasi VG, Cooper CJ, Weiss KL, Ginell SL, Parks JM, Coates L. Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04114] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan L. Ginell
- Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jerry M. Parks
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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