1
|
Delcourte L, Berbon M, Rodriguez M, Subban K, Lends A, Grélard A, Morvan E, Habenstein B, Saupe SJ, Delhaes L, Aimanianda V, Daskalov A, Loquet A. Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme. Methods 2024; 230:59-67. [PMID: 39047926 DOI: 10.1016/j.ymeth.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Most bacterial, plant and fungal cells possess at their surface a protective layer called the cell wall, conferring strength, plasticity and rigidity to withstand the osmotic pressure. This molecular barrier is crucial for pathogenic microorganisms, as it protects the cell from the local environment and often constitutes the first structural component encountered in the host-pathogen interaction. In pathogenic molds and yeasts, the cell wall constitutes the main target for the development of clinically-relevant antifungal drugs. In the past decade, solid-state NMR has emerged as a powerful analytical technique to investigate the molecular organization of microbial cell walls in the context of intact cells. 13C NMR chemical shift is an exquisite source of information to identify the polysaccharides present in the cell wall, and two-dimensional 13C-13C correlation experiments provide an efficient tool to rapidly access the polysaccharide composition in whole cells. Here we investigate the use of the adiabatic DREAM (for dipolar recoupling enhancement through amplitude modulation) recoupling scheme to improve solid-state NMR analysis of polysaccharides in intact cells. We demonstrate the advantages of two-dimensional 13C-13C experiments using the DREAM recoupling scheme. We report the spectral editing of polysaccharide signals by varying the radio-frequency carrier position. We provide practical considerations for the implementation of DREAM experiments to characterize polysaccharides in whole cells. We demonstrate the approach on intact fungal cells of Neurospora crassa and Aspergillus fumigatus, a model and a pathogenic filamentous fungus, respectively. The approach could be envisioned to efficiently reduce the spectral crowding of more complex cell surfaces, such as cell wall and peptidoglycan in bacteria.
Collapse
Affiliation(s)
- Loic Delcourte
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Marion Rodriguez
- CNR des Aspergilloses Chroniques, Mycology-Parasitology Department, CHU Bordeaux, Bordeaux 33000, France
| | - Kamalraj Subban
- ImmunoConcEpT, CNRS, UMR 5164, University of Bordeaux, Bordeaux, France
| | - Alons Lends
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Axelle Grélard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- Univ. Bordeaux, CNRS, Inserm, IECB, UAR3033, US01, Pessac, France
| | - Birgit Habenstein
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sven J Saupe
- CNRS, Université de Bordeaux, IBGC, UMR 5095, Bordeaux, France
| | - Laurence Delhaes
- CNR des Aspergilloses Chroniques, Mycology-Parasitology Department, CHU Bordeaux, Bordeaux 33000, France; Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, Bordeaux 33000, France
| | - Vishukumar Aimanianda
- Institut Pasteur, Université Paris Cité, Immunobiology of Aspergillus, Mycology Department, Paris, France
| | - Asen Daskalov
- ImmunoConcEpT, CNRS, UMR 5164, University of Bordeaux, Bordeaux, France; State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Antoine Loquet
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France.
| |
Collapse
|
2
|
Byeon CH, Hansen KH, DePas W, Akbey Ü. High-resolution 2D solid-state NMR provides insights into nontuberculous mycobacteria. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 134:101970. [PMID: 39312837 DOI: 10.1016/j.ssnmr.2024.101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024]
Abstract
We present a high-resolution magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize nontuberculous mycobacteria (NTM). We studied two different NTM strains, Mycobacterium smegmatis, a model, non-pathogenic strain, and Mycobacterium abscessus, an emerging and important human pathogen. Hydrated NTM samples were studied at natural abundance without isotope-labelling, as whole-cells versus cell envelope isolates, and native versus fixed sample preparations. We utilized 1D13C and 2D 1H-13C ssNMR spectra and peak deconvolution to identify NTM cell-wall chemical sites. More than ∼100 distinct 13C signals were identified in the ssNMR spectra. We provide tentative assignments for ∼30 polysaccharides by using well resolved 1H/13C chemical shifts from the 2D INEPT-based 1H-13C ssNMR spectrum. The signals originating from both the flexible and rigid fractions of the whole-cell bacteria samples were selectively analyzed by utilizing either CP or INEPT based 13C ssNMR spectra. CP buildup curves provide insights into the dynamical similarity of the cell-wall components for NTM strains. Signals from peptidoglycan, arabinogalactan and mycolic acid were identified. The majority of the 13C signals were not affected by fixation of the whole cell samples. The isolated cell envelope NMR spectrum overlap with the whole-cell spectrum to a large extent, where the latter has more signals. As an orthogonal way of characterizing these bacteria, electron microscopy (EM) was used to provide spatial information. ssNMR and EM data suggest that the M. abscessus cell-wall is composed of a smaller peptidoglycan layer which is more flexible compared to M. smegmatis, which may be related to its higher pathogenicity. Here in this work, we used high-resolution 2D ssNMR first time to characterize NTM strains and identify chemical sites. These results will aid the development of structure-based approaches to combat NTM infections.
Collapse
Affiliation(s)
| | | | - William DePas
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15261, United States
| | - Ümit Akbey
- Department of Structural Biology, United States.
| |
Collapse
|
3
|
Vallet A, Ayala I, Perrone B, Hassan A, Simorre JP, Bougault C, Schanda P. MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107708. [PMID: 38901173 DOI: 10.1016/j.jmr.2024.107708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13C13C and heteronuclear 1H15N, 1H13C and 15N13C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples.
Collapse
Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71, avenue des martyrs, Grenoble, 38000, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71, avenue des martyrs, Grenoble, 38000, France
| | | | - Alia Hassan
- Bruker Biospin, Fällanden, 8117, Switzerland
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71, avenue des martyrs, Grenoble, 38000, France
| | - Catherine Bougault
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71, avenue des martyrs, Grenoble, 38000, France.
| | - Paul Schanda
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria.
| |
Collapse
|
4
|
Zhao W, Debnath D, Gautam I, Fernando LD, Wang T. Charting the solid-state NMR signals of polysaccharides: A database-driven roadmap. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:298-309. [PMID: 37724740 DOI: 10.1002/mrc.5397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) measurements of intact cell walls and cellular samples often generate spectra that are difficult to interpret due to the presence of many coexisting glycans and the structural polymorphism observed in native conditions. To overcome this analytical challenge, we present a statistical approach for analyzing carbohydrate signals using high-resolution ssNMR data indexed in a carbohydrate database. We generate simulated spectra to demonstrate the chemical shift dispersion and compare this with experimental data to facilitate the identification of important fungal and plant polysaccharides, such as chitin and glucans in fungi and cellulose, hemicellulose, and pectic polymers in plants. We also demonstrate that chemically distinct carbohydrates from different organisms may produce almost identical signals, highlighting the need for high-resolution spectra and validation of resonance assignments. Our study provides a means to differentiate the characteristic signals of major carbohydrates and allows us to summarize currently undetected polysaccharides in plants and fungi, which may inspire future investigations.
Collapse
Affiliation(s)
- Wancheng Zhao
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Debkumar Debnath
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Isha Gautam
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Liyanage D Fernando
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
5
|
Rahman S, Nath S, Mohan U, Das AK. Targeting Staphylococcal Cell-Wall Biosynthesis Protein FemX Through Steered Molecular Dynamics and Drug-Repurposing Approach. ACS OMEGA 2023; 8:29292-29301. [PMID: 37599983 PMCID: PMC10433341 DOI: 10.1021/acsomega.3c02691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023]
Abstract
Staphylococcus aureus-mediated infection is a serious threat in this antimicrobial-resistant world. S. aureus has become a "superbug" by challenging conventional as well as modern treatment strategies. Nowadays, drug repurposing has become a new trend for the discovery of new drug molecules. This study focuses on evaluating FDA-approved drugs that can be repurposed against S. aureus infection. Steered molecular dynamics (SMD) has been performed for Lumacaftor and Olaparib against staphylococcal FemX to understand their binding to the active site. A time-dependent external force or rupture force has been applied to the ligands to calculate the force required to dislocate the ligand from the binding pocket. SMD analysis indicates that Lumacaftor has a high affinity for the substrate binding pocket in comparison to Olaparib. Umbrella sampling exhibits that Lumacaftor possesses a higher free energy barrier to displace it from the ligand-binding site. The bactericidal activity of Lumacaftor and Olaparib has been tested, and it shows that Lumacaftor has moderate activity along with biofilm inhibition potential (MIC value with conc. 128 μg/mL). Pharmacokinetic and toxicology evaluations indicate that Lumacaftor has higher pharmacokinetic potential with lower toxicity. This is the first experimental report where staphylococcal FemX has been targeted for the discovery of new drugs. It is suggested that Lumacaftor may be a potential lead molecule against S. aureus.
Collapse
Affiliation(s)
- Shakilur Rahman
- Department
of Biotechnology, Indian Institute of Technology
Kharagpur, Kharagpur, West Bengal 721302, India
| | - Subham Nath
- National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West Bengal 700054, India
| | - Utpal Mohan
- National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West Bengal 700054, India
| | - Amit Kumar Das
- Department
of Biotechnology, Indian Institute of Technology
Kharagpur, Kharagpur, West Bengal 721302, India
| |
Collapse
|
6
|
Rimal B, Chang J, Liu C, Rashid R, Singh M, Kim SJ. The effects of daptomycin on cell wall biosynthesis in Enterococcal faecalis. Sci Rep 2023; 13:12227. [PMID: 37507537 PMCID: PMC10382475 DOI: 10.1038/s41598-023-39486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
Daptomycin is a cyclic lipodepsipeptide antibiotic reserved for the treatment of serious infections by multidrug-resistant Gram-positive pathogens. Its mode of action is considered to be multifaceted, encompassing the targeting and depolarization of bacterial cell membranes, alongside the inhibition of cell wall biosynthesis. To characterize the daptomycin mode of action, 15N cross-polarization at magic-angle spinning NMR measurements were performed on intact whole cells of Staphylococcus aureus grown in the presence of a sub-inhibitory concentration of daptomycin in a chemically defined media containing L-[ϵ-15N]Lys. Daptomycin-treated cells showed a reduction in the lysyl-ε-amide intensity that was consistent with cell wall thinning. However, the reduced lysyl-ε-amine intensity at 10 ppm indicated that the daptomycin-treated cells did not accumulate in Park's nucleotide, the cytoplasmic peptidoglycan (PG) precursor. Consequently, daptomycin did not inhibit the transglycosylation step of PG biosynthesis. To further elucidate the daptomycin mode of action, the PG composition of daptomycin-susceptible Enterococcus faecalis grown in the presence of daptomycin was analyzed using liquid chromatography-mass spectrometry. Sixty-nine muropeptide ions correspond to PG with varying degrees of modifications including crosslinking, acetylation, alanylation, and 1,6-anhydrous ring formation at MurNAc were quantified. Analysis showed that the cell walls of daptomycin-treated E. faecalis had a significant reduction in PG crosslinking which was accompanied by an increase in lytic transglycosylase activities and a decrease in PG-stem modifications by the carboxypeptidases. The changes in PG composition suggest that daptomycin inhibits cell wall biosynthesis by impeding the incorporation of nascent PG into the cell walls by transpeptidases and maturation by carboxypeptidases. As a result, the newly formed cell walls become highly susceptible to degradation by the autolysins, resulting in thinning of the cell wall.
Collapse
Affiliation(s)
- Binayak Rimal
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - James Chang
- Department of Chemistry One Bear Place #97046, Baylor University, Waco, TX, 76798, USA
| | - Chengyin Liu
- Department of Chemistry, Howard University, Washington, DC, 20059, USA
| | - Raiyan Rashid
- Department of Chemistry, Howard University, Washington, DC, 20059, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO, 63110, USA
| | - Sung Joon Kim
- Department of Chemistry, Howard University, Washington, DC, 20059, USA.
| |
Collapse
|
7
|
Liauw CM, Vaidya M, Slate AJ, Hickey NA, Ryder S, Martínez-Periñán E, McBain AJ, Banks CE, Whitehead KA. Analysis of Cellular Damage Resulting from Exposure of Bacteria to Graphene Oxide and Hybrids Using Fourier Transform Infrared Spectroscopy. Antibiotics (Basel) 2023; 12:antibiotics12040776. [PMID: 37107138 PMCID: PMC10135141 DOI: 10.3390/antibiotics12040776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
With the increase in antimicrobial resistance, there is an urgent need to find new antimicrobials. Four particulate antimicrobial compounds, graphite (G), graphene oxide (GO), silver-graphene oxide (Ag-GO) and zinc oxide-graphene oxide (ZnO-GO) were tested against Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus. The antimicrobial effects on the cellular ultrastructure were determined using Fourier transform infrared spectroscopy (FTIR), and selected FTIR spectral metrics correlated with cell damage and death arising from exposure to the GO hybrids. Ag-GO caused the most severe damage to the cellular ultrastructure, whilst GO caused intermediate damage. Graphite exposure caused unexpectedly high levels of damage to E. coli, whereas ZnO-GO exposure led to relatively low levels of damage. The Gram-negative bacteria demonstrated a stronger correlation between FTIR metrics, indicated by the perturbation index and the minimal bactericidal concentration (MBC). The blue shift of the combined ester carbonyl and amide I band was stronger for the Gram-negative varieties. FTIR metrics tended to provide a better assessment of cell damage based on correlation with cellular imaging and indicated that damage to the lipopolysaccharide, peptidoglycan and phospholipid bilayers had occurred. Further investigations into the cell damage caused by the GO-based materials will allow the development of this type of carbon-based multimode antimicrobials.
Collapse
Affiliation(s)
- Christopher M Liauw
- Microbiology at Interfaces Group, School of Healthcare Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Misha Vaidya
- Microbiology at Interfaces Group, School of Healthcare Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Anthony J Slate
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Niall A Hickey
- Microbiology at Interfaces Group, School of Healthcare Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Steven Ryder
- Microbiology at Interfaces Group, School of Healthcare Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Emiliano Martínez-Periñán
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Andrew J McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Craig E Banks
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| | - Kathryn A Whitehead
- Microbiology at Interfaces Group, School of Healthcare Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK
| |
Collapse
|
8
|
Influence of NaCl and pH on lysostaphin catalytic activity, cell binding, and bacteriolytic activity. Appl Microbiol Biotechnol 2022; 106:6519-6534. [DOI: 10.1007/s00253-022-12173-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2022]
|
9
|
Weidenbacher PAB, Rodriguez-Rivera FP, Sanyal M, Visser JA, Do J, Bertozzi CR, Kim PS. Chemically Modified Bacterial Sacculi as a Vaccine Microparticle Scaffold. ACS Chem Biol 2022; 17:1184-1196. [PMID: 35412807 PMCID: PMC9127789 DOI: 10.1021/acschembio.2c00140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Vaccine scaffolds
and carrier proteins increase the immunogenicity
of subunit vaccines. Here, we developed, characterized, and demonstrated
the efficacy of a novel microparticle vaccine scaffold comprised of
bacterial peptidoglycan (PGN), isolated as an entire sacculi. The
PGN microparticles contain bio-orthogonal chemical handles allowing
for site-specific attachment of immunogens. We first evaluated the
purification, integrity, and immunogenicity of PGN microparticles
derived from a variety of bacterial species. We then optimized PGN
microparticle modification conditions; Staphylococcus
aureus PGN microparticles containing azido-d-alanine yielded robust conjugation to immunogens. We then demonstrated
that this vaccine scaffold elicits comparable immunostimulation to
the conventional carrier protein, keyhole limpet hemocyanin (KLH).
We further modified the S. aureus PGN
microparticle to contain the SARS-CoV-2 receptor-binding domain (RBD)—this
conjugate vaccine elicited neutralizing antibody titers comparable
to those elicited by the KLH-conjugated RBD. Collectively, these findings
suggest that chemically modified bacterial PGN microparticles are
a conjugatable and biodegradable microparticle scaffold capable of
eliciting a robust immune response toward an antigen of interest.
Collapse
Affiliation(s)
- Payton A.-B. Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Frances P. Rodriguez-Rivera
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Joshua A. Visser
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jonathan Do
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Carolyn R. Bertozzi
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter S. Kim
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| |
Collapse
|
10
|
Gao C, Judge PT, Sesti EL, Price LE, Alaniva N, Saliba EP, Albert BJ, Soper NJ, Chen PH, Barnes AB. Four millimeter spherical rotors spinning at 28 kHz with double-saddle coils for cross polarization NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 303:1-6. [PMID: 30978570 DOI: 10.1016/j.jmr.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/07/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Spherical rotors in magic angle spinning (MAS) experiments have significant advantages over traditional cylindrical rotors including simplified spinning implementation, easy sample exchange, more efficient microwave coupling for dynamic nuclear polarization (DNP), and feasibility of downscaling to access higher spinning frequencies. Here, we implement spherical rotors with 4 mm outside diameter (o.d.) and demonstrate spinning >28 kHz using a single aperture for spinning gas. We show a modified stator geometry to improve fiber optic detection, increase NMR filling factor, and improve alignment for sample exchange and microwave irradiation. Higher NMR Rabi frequencies were obtained using smaller radiofrequency (RF) coils on small-diameter spherical rotors, compared to our previous implementation of MAS spheres with an o.d. of 9.5 mm. We report nutation fields of 110 kHz on 13C with 820 W of input power and 100 kHz on 1H with 800 W of input power. Proton decoupling fields of 78 kHz were applied over 20 ms of signal acquisition without any sign of arcing. Compared to our initial demonstration of a split coil for 9.5 mm spheres, this current implementation of a double-saddle coil inductor for 4 mm spheres not only intensifies the RF fields, but also improves RF homogeneity. We achieve an 810°/90° nutation intensity ratio of 0.84 at 300.197 MHz (1H). We also show electromagnetic simulations predicting a nearly 3-fold improvement in electron Rabi frequency of 0.99 MHz (with 4 mm spheres) compared to 0.38 MHz (with 3.2 mm cylinders), with 5 W of incident microwave power. Further improvements in magnetic resonance spin control are expected as RF inductors and microwave coupling are optimized for spherical rotors and scaled down to the micron scale.
Collapse
Affiliation(s)
- Chukun Gao
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Patrick T Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biochemistry, Biophysics & Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Erika L Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lauren E Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brice J Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nathan J Soper
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Pin-Hui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander B Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
11
|
Maya-Martinez R, Alexander JAN, Otten CF, Ayala I, Vollmer D, Gray J, Bougault CM, Burt A, Laguri C, Fonvielle M, Arthur M, Strynadka NCJ, Vollmer W, Simorre JP. Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 From Staphylococcus aureus. Front Microbiol 2019; 9:3223. [PMID: 30713527 PMCID: PMC6346638 DOI: 10.3389/fmicb.2018.03223] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan (PG) is an essential component of the cell envelope, maintaining bacterial cell shape and protecting it from bursting due to turgor pressure. The monoderm bacterium Staphylococcus aureus has a highly cross-linked PG, with ~90% of peptide stems participating in DD-cross-links and up to 15 peptide stems connected with each other. These cross-links are formed in transpeptidation reactions catalyzed by penicillin-binding proteins (PBPs) of classes A and B. Most S. aureus strains have three housekeeping PBPs with this function (PBP1, PBP2, and PBP3) but MRSA strains have acquired a third class B PBP, PBP2a, which is encoded by the mecA gene and required for the expression of high-level resistance to β-lactams. Another housekeeping PBP of S. aureus is PBP4, which belongs to the class C PBPs, and hence would be expected to have PG hydrolase (DD-carboxypeptidase or DD-endopeptidase) activity. However, previous works showed that, unexpectedly, PBP4 has transpeptidase activity that significantly contributes to both the high level of cross-linking in the PG of S. aureus and to the low level of β-lactam resistance in the absence of PBP2a. To gain insights into this unusual activity of PBP4, we studied by NMR spectroscopy its interaction in vitro with different substrates, including intact peptidoglycan, synthetic peptide stems, muropeptides, and long glycan chains with uncross-linked peptide stems. PBP4 showed no affinity for the complex, intact peptidoglycan or the smallest isolated peptide stems. Transpeptidase activity of PBP4 was verified with the disaccharide peptide subunits (muropeptides) in vitro, producing cyclic dimer and multimer products; these assays also showed a designed PBP4(S75C) nucleophile mutant to be inactive. Using this inactive but structurally highly similar variant, liquid-state NMR identified two interaction surfaces in close proximity to the central nucleophile position that can accommodate the potential donor and acceptor stems for the transpeptidation reaction. A PBP4:muropeptide model structure was built from these experimental restraints, which provides new mechanistic insights into mecA independent resistance to β-lactams in S. aureus.
Collapse
Affiliation(s)
| | - J Andrew N Alexander
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Christian F Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Isabel Ayala
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Daniela Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Alister Burt
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Cédric Laguri
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Matthieu Fonvielle
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Université Sorbone-Paris, Paris, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Université Sorbone-Paris, Paris, France
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | |
Collapse
|
12
|
Bougault C, Ayala I, Vollmer W, Simorre JP, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. J Struct Biol 2018; 206:66-72. [PMID: 30031884 DOI: 10.1016/j.jsb.2018.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 12/19/2022]
Abstract
The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling.
Collapse
Affiliation(s)
- Catherine Bougault
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France.
| |
Collapse
|
13
|
Surface proteins and the formation of biofilms by Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:749-756. [PMID: 29229527 DOI: 10.1016/j.bbamem.2017.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus biofilms pose a serious clinical threat as reservoirs for persistent infections. Despite this clinical significance, the composition and mechanism of formation of S. aureus biofilms are unknown. To address these problems, we used solid-state NMR to examine S. aureus (SA113), a strong biofilm-forming strain. We labeled whole cells and cell walls of planktonic cells, young biofilms formed for 12-24h after stationary phase, and more mature biofilms formed for up to 60h after stationary phase. All samples were labeled either by (i) [15N]glycine and l-[1-13C]threonine, or in separate experiments, by (ii) l-[2-13C,15N]leucine. We then measured 13C-15N direct bonds by C{N} rotational-echo double resonance (REDOR). The increase in peptidoglycan stems that have bridges connected to a surface protein was determined directly by a cell-wall double difference (biofilm REDOR difference minus planktonic REDOR difference). This procedure eliminates errors arising from differences in 15N isotopic enrichments and from the routing of 13C label from threonine degradation to glycine. For both planktonic cells and the mature biofilm, 20% of pentaglycyl bridges are not cross-linked and are potential surface-protein attachment sites. None of these sites has a surface protein attached in the planktonic cells, but one-fourth have a surface protein attached in the mature biofilm. Moreover, the leucine-label shows that the concentration of β-strands in leucine-rich regions doubles in the mature biofilm. Thus, a primary event in establishing a S. aureus biofilm is extensive decoration of the cell surface with surface proteins that are linked covalently to the cell wall and promote cell-cell adhesion.
Collapse
|
14
|
Yang H, Singh M, Kim SJ, Schaefer J. Characterization of the tertiary structure of the peptidoglycan of Enterococcus faecalis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2017; 1859:2171-2180. [PMID: 28784459 PMCID: PMC5610627 DOI: 10.1016/j.bbamem.2017.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022]
Abstract
Solid-state NMR spectra of whole cells and isolated cell walls of Enterococcus faecalis grown in media containing combinations of 13C and 15N specific labels in d- and l-alanine and l-lysine (in the presence of an alanine racemase inhibitor alaphosphin) have been used to determine the composition and architecture of the cell-wall peptidoglycan. The compositional variables include the concentrations of (i) peptidoglycan stems without bridges, (ii) d-alanylated wall teichoic acid, (iii) cross-links, and (iv) uncross-linked tripeptide and tetra/pentapeptide stems. Connectivities of l-alanyl carbonyl‑carbon bridge labels to d-[3-13C]alanyl and l-[ε-15N]lysyl stem labels prove that the peptidoglycan of E. faecalis has the same hybrid short-bridge architecture (with a mix of parallel and perpendicular stems) as the FemA mutant of Staphylococcus aureus, in which the cross-linked stems are perpendicular to one another and the cross-linking is close to the ideal 50% value. This is the first determination of the cell-wall chemical and geometrical architecture of whole cells of E. faecalis, a major source of nosocomial infections worldwide.
Collapse
Affiliation(s)
- Hao Yang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
| |
Collapse
|
15
|
Kim SJ, Singh M, Sharif S, Schaefer J. Desleucyl-Oritavancin with a Damaged d-Ala-d-Ala Binding Site Inhibits the Transpeptidation Step of Cell-Wall Biosynthesis in Whole Cells of Staphylococcus aureus. Biochemistry 2017; 56:1529-1535. [PMID: 28221772 PMCID: PMC5508972 DOI: 10.1021/acs.biochem.6b01125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used solid-state nuclear magnetic resonance to characterize the exact nature of the dual mode of action of oritavancin in preventing cell-wall assembly in Staphylococcus aureus. Measurements performed on whole cells labeled selectively in vivo have established that des-N-methylleucyl-N-4-(4-fluorophenyl)benzyl-chloroeremomycin, an Edman degradation product of [19F]oritavancin, which has a damaged d-Ala-d-Ala binding aglycon, is a potent inhibitor of the transpeptidase activity of cell-wall biosynthesis. The desleucyl drug binds to partially cross-linked peptidoglycan by a cleft formed between the drug aglycon and its biphenyl hydrophobic side chain. This type of binding site is present in other oritavancin-like glycopeptides, which suggests that for these drugs a similar transpeptidase inhibition occurs.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, 101 Bagby Ave., Waco, TX 76798
| | - Manmilan Singh
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Shasad Sharif
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Jacob Schaefer
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| |
Collapse
|
16
|
O'Connor RD, Singh M, Chang J, Kim SJ, VanNieuwenhze M, Schaefer J. Dual Mode of Action for Plusbacin A 3 in Staphylococcus aureus. J Phys Chem B 2017; 121:1499-1505. [PMID: 28135800 PMCID: PMC5555578 DOI: 10.1021/acs.jpcb.6b11039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used C{F}, N{F}, and N{P} rotational-echo double resonance NMR to determine the location and conformation of 19F and 15N double-labeled plusbacin A3 and of double-labeled deslipo-plusbacin A3, each bound to the cell walls of whole cells of Staphyloccocus aureus grown in media containing [1-13C]glycine. The 31P is primarily in wall teichoic acid. Approximately 25% of plusbacin headgroups (the cyclic depsipeptide backbone) are in a closed conformation (N-F separation of 6 Å), while 75% are in a more open conformation (N-F separation of 12 Å). The closed headgroups have no contact with wall teichoic acid, whereas the open headgroups have a strong contact. This places the closed headgroups in hydrophobic regions of the cell wall and the open headgroups in hydrophilic regions. None of the plusbacin tails have contact with the 31P of either wall teichoic acid or the cell membrane and thus are in hydrophobic regions of the cell wall. In addition, both heads and tails of plusbacin A3 have contact with the glycyl 13C incorporated in cell-wall peptidoglycan pentaglycyl bridges and with 13C-labeled purines near the membrane surface. We interpret these results in terms of a dual mode of action for plusbacin A3: first, disruption of the peptidoglycan layer nearest to the membrane surface by closed-conformation plusbacin A3 leading to an inhibition of chain extension by transglycosylation; second, thinning and disruption of the membrane (possibly including disruption of ATP-binding cassette transporters embedded in the membrane) by open-conformation plusbacin A3, thereby leading to release of ATP to the hydrophilic regions of the cell wall and subsequent binding by plusbacin A3.
Collapse
Affiliation(s)
- Robert D. O'Connor
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - James Chang
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| |
Collapse
|
17
|
In-Cell Solid-State NMR: An Emerging Technique for the Study of Biological Membranes. Biophys J 2016; 109:2461-2466. [PMID: 26682804 DOI: 10.1016/j.bpj.2015.10.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/20/2015] [Accepted: 10/30/2015] [Indexed: 11/22/2022] Open
Abstract
Biological molecular processes are often studied in model systems, which simplifies their inherent complexity but may cause investigators to lose sight of the effects of the molecular environment. Information obtained in this way must therefore be validated by experiments in the cell. NMR has been used to study biological cells since the early days of its development. The first NMR structural studies of a protein inside a cell (by solution-state NMR) and of a membrane protein (by solid-state NMR) were published in 2001 and 2011, respectively. More recently, dynamic nuclear polarization, which has been used to enhance the signal in solid-state NMR, has also been applied to the study of frozen cells. Much progress has been made in the past 5 years, and in this review we take stock of this new technique, which is particularly appropriate for the study of biological membranes.
Collapse
|
18
|
Solid-state NMR characterization of amphomycin effects on peptidoglycan and wall teichoic acid biosyntheses in Staphylococcus aureus. Sci Rep 2016; 6:31757. [PMID: 27538449 PMCID: PMC4990924 DOI: 10.1038/srep31757] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 07/27/2016] [Indexed: 11/09/2022] Open
Abstract
Amphomycin and MX-2401 are cyclic lipopeptides exhibiting bactericidal activities against Gram-positive pathogens. Amphomycin and MX-2401 share structural similarities with daptomycin, but unlike daptomycin they do not target bacterial membrane. In this study, we investigate in vivo modes of action for amphomycin and MX-2401 in intact whole cells of Staphylococcus aureus by measuring the changes of peptidoglycan and wall teichoic acid compositions using solid-state NMR. S. aureus were grown in a defined media containing isotope labels [1-13C]glycine and L-[ε-15N]lysin, L-[1-13C]lysine and D-[15N]alanine, or D-[1-13C]alanine and [15N]glycine, to selectively 13C-15N pair label peptidoglycan bridge-link, stem-link, and cross-link, respectively. 13C{15N} and 15N{13C} rotational-echo double resonance NMR measurements determined that cyclic lipopeptide-treated S. aureus exhibited thinning of the cell wall, accumulation of Park’s nucleotide, inhibition of glycine utilization for purine biosynthesis, reduction of ester-linked D-Ala in teichoic acids, and reduction of peptidoglycan cross-linking. Whole cell NMR analysis also revealed that S. aureus, in presence of amphomycin and MX-2401, maintained the incorporation of D-Ala during peptidoglycan biosynthesis while the incorporation of D-Ala into teichoic acids was inhibited. These effects are consistent with amphomycin’s dual inhibition of both peptidoglycan and wall teichoic acid biosyntheses in S. aureus.
Collapse
|
19
|
Romaniuk JAH, Cegelski L. Bacterial cell wall composition and the influence of antibiotics by cell-wall and whole-cell NMR. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0024. [PMID: 26370936 DOI: 10.1098/rstb.2015.0024] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The ability to characterize bacterial cell-wall composition and structure is crucial to understanding the function of the bacterial cell wall, determining drug modes of action and developing new-generation therapeutics. Solid-state NMR has emerged as a powerful tool to quantify chemical composition and to map cell-wall architecture in bacteria and plants, even in the context of unperturbed intact whole cells. In this review, we discuss solid-state NMR approaches to define peptidoglycan composition and to characterize the modes of action of old and new antibiotics, focusing on examples in Staphylococcus aureus. We provide perspectives regarding the selected NMR strategies as we describe the exciting and still-developing cell-wall and whole-cell NMR toolkit. We also discuss specific discoveries regarding the modes of action of vancomycin analogues, including oritavancin, and briefly address the reconsideration of the killing action of β-lactam antibiotics. In such chemical genetics approaches, there is still much to be learned from perturbations enacted by cell-wall assembly inhibitors, and solid-state NMR approaches are poised to address questions of cell-wall composition and assembly in S. aureus and other organisms.
Collapse
Affiliation(s)
- Joseph A H Romaniuk
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, CA 94305, USA
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, CA 94305, USA
| |
Collapse
|
20
|
Chang J, Zhou H, Preobrazhenskaya M, Tao P, Kim SJ. The Carboxyl Terminus of Eremomycin Facilitates Binding to the Non-d-Ala-d-Ala Segment of the Peptidoglycan Pentapeptide Stem. Biochemistry 2016; 55:3383-91. [PMID: 27243469 PMCID: PMC6020039 DOI: 10.1021/acs.biochem.6b00188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycopeptide antibiotics inhibit cell wall biosynthesis in Gram-positive bacteria by targeting the peptidoglycan (PG) pentapeptide stem structure (l-Ala-d-iso-Gln-l-Lys-d-Ala-d-Ala). Structures of the glycopeptide complexed with a PG stem mimic have shown that the d-Ala-d-Ala segment is the primary drug binding site; however, biochemical evidence suggests that the glycopeptide-PG interaction involves more than d-Ala-d-Ala binding. Interactions of the glycopeptide with the non-d-Ala-d-Ala segment of the PG stem were investigated using solid-state nuclear magnetic resonance (NMR). LCTA-1421, a double (15)N-enriched eremomycin derivative with a C-terminal [(15)N]amide and [(15)N]Asn amide, was complexed with whole cells of Staphylococcus aureus grown in a defined medium containing l-[3-(13)C]Ala and d-[1-(13)C]Ala in the presence of alanine racemase inhibitor alaphosphin. (13)C{(15)N} and (15)N{(13)C} rotational-echo double-resonance (REDOR) NMR measurements determined the (13)C-(15)N internuclear distances between the [(15)N]Asn amide of LCTA-1421 and the (13)C atoms of the bound d-[1-(13)C]Ala-d-[1-(13)C]Ala to be 5.1 and 4.8 Å, respectively. These measurements also determined the distance from the C-terminal [(15)N]amide of LCTA-1421 to the l-[3-(13)C]Ala of PG to be 3.5 Å. The measured REDOR distance constraints position the C-terminus of the glycopeptide in the proximity of the l-Ala of the PG, suggesting that the C-terminus of the glycopeptide interacts near the l-Ala segment of the PG stem. In vivo REDOR measurements provided structural insight into how C-terminally modified glycopeptide antibiotics operate.
Collapse
Affiliation(s)
- James Chang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706
| | - Hongyu Zhou
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 7 5275, USA
| | | | - Peng Tao
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 7 5275, USA
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706
| |
Collapse
|
21
|
Nygaard R, Romaniuk JAH, Rice DM, Cegelski L. Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. Biophys J 2016; 108:1380-1389. [PMID: 25809251 DOI: 10.1016/j.bpj.2015.01.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/13/2015] [Indexed: 01/28/2023] Open
Abstract
Gram-positive bacteria surround themselves with a thick cell wall that is essential to cell survival and is a major target of antibiotics. Quantifying alterations in cell-wall composition are crucial to evaluating drug modes of action, particularly important for human pathogens that are now resistant to multiple antibiotics such as Staphylococcus aureus. Macromolecular and whole-cell NMR spectroscopy allowed us to observe the full panel of carbon and nitrogen pools in S. aureus cell walls and intact whole cells. We discovered that one-dimensional (13)C and (15)N NMR spectra, together with spectroscopic selections based on dipolar couplings as well as two-dimensional spin-diffusion measurements, revealed the dramatic compositional differences between intact cells and cell walls and allowed the identification of cell-wall signatures in whole-cell samples. Furthermore, the whole-cell NMR approach exhibited the sensitivity to detect distinct compositional changes due to treatment with the antibiotics fosfomycin (a cell-wall biosynthesis inhibitor) and chloramphenicol (a protein synthesis inhibitor). Whole cells treated with fosfomycin exhibited decreased peptidoglycan contributions while those treated with chloramphenicol contained a higher percentage of peptidoglycan as cytoplasmic protein content was reduced. Thus, general antibiotic modes of action can be identified by profiling the total carbon pools in intact whole cells.
Collapse
Affiliation(s)
- Rie Nygaard
- Department of Chemistry, Stanford University, Stanford, California
| | | | - David M Rice
- Department of Chemistry, Stanford University, Stanford, California
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, California.
| |
Collapse
|
22
|
Rice DM, Romaniuk JAH, Cegelski L. Frequency-selective REDOR and spin-diffusion relays in uniformly labeled whole cells. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 72:132-9. [PMID: 26493462 PMCID: PMC4674448 DOI: 10.1016/j.ssnmr.2015.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 06/05/2023]
Abstract
Solid-state NMR is a powerful and non-perturbative method to measure and define chemical composition and architecture in bacterial cell walls, even in the context of whole cells. Most NMR studies on whole cells have used selectively labeled samples. Here, we introduce an NMR sequence relay using frequency-selective REDOR (fsREDOR) and spin diffusion elements to probe a unique amine contribution in uniformly (13)C- and (15)N-labeled Staphylococcus aureus whole cells that we attribute to the d-alanine of teichoic acid. In addition to the primary peptidoglycan structural scaffold, cell walls can contain significant amounts of teichoic acid that contribute to cell-wall function. When incorporated into teichoic acid, d-alanine is present as an ester, connected via its carbonyl to a ribitol carbon, and thus has a free amine. Teichoic acid d-Ala is removed during cell-wall isolations and can only be detected in the context of whole cells. The sequence presented here begins with fsREDOR and a chemical shift evolution period for 2D data acquisition, followed by DARR spin diffusion and then an additional fsREDOR period. fsREDOR elements were used for (13)C observation to avoid complications from (13)C-(13)C couplings due to uniform labeling and for (15)N dephasing to achieve selectivity in the nitrogens serving as dephasers. The results show that the selected amine nitrogen of interest is near to teichoic acid ribitol carbons and also the methyl group carbon associated with alanine. In addition, its carbonyl is not significantly dephased by amide nitrogens, consistent with the expected microenvironment around teichoic acid.
Collapse
Affiliation(s)
- David M Rice
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford, CA 94305, USA
| | - Joseph A H Romaniuk
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford, CA 94305, USA
| | - Lynette Cegelski
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford, CA 94305, USA.
| |
Collapse
|
23
|
Kim SJ, Chang J, Singh M. Peptidoglycan architecture of Gram-positive bacteria by solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:350-62. [PMID: 24915020 PMCID: PMC4258515 DOI: 10.1016/j.bbamem.2014.05.031] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 10/25/2022]
Abstract
Peptidoglycan is an essential component of cell wall in Gram-positive bacteria with unknown architecture. In this review, we summarize solid-state NMR approaches to address some of the unknowns in the Gram-positive bacteria peptidoglycan architecture: 1) peptidoglycan backbone conformation, 2) PG-lattice structure, 3) variations in the peptidoglycan architecture and composition, 4) the effects of peptidoglycan bridge-length on the peptidoglycan architecture in Fem mutants, 5) the orientation of glycan strands with respect to the membrane, and 6) the relationship between the peptidoglycan structure and the glycopeptide antibiotic mode of action. Solid-state NMR analyses of Staphylococcus aureus cell wall show that peptidoglycan chains are surprisingly ordered and densely packed. The peptidoglycan disaccharide backbone adopts 4-fold screw helical symmetry with the disaccharide unit periodicity of 40Å. Peptidoglycan lattice in the S. aureus cell wall is formed by cross-linked PG stems that have parallel orientations. The structural characterization of Fem-mutants of S. aureus with varying lengths of bridge structures suggests that the PG-bridge length is an important determining factor for the PG architecture.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA.
| | - James Chang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| |
Collapse
|
24
|
Smith AJ, Ali FI, Soldatov DV. Glycine homopeptides: the effect of the chain length on the crystal structure and solid state reactivity. CrystEngComm 2014. [DOI: 10.1039/c4ce00630e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of linear oligoglycines has been studied to reveal the trends in their crystal structure, molecular conformation and thermally induced reactions.
Collapse
Affiliation(s)
- Aaron J. Smith
- Department of Chemistry
- University of Guelph
- Guelph, Canada
| | - Farukh I. Ali
- Department of Chemistry
- University of Guelph
- Guelph, Canada
| | | |
Collapse
|
25
|
Cegelski L. REDOR NMR for drug discovery. Bioorg Med Chem Lett 2013; 23:5767-75. [PMID: 24035486 PMCID: PMC4038398 DOI: 10.1016/j.bmcl.2013.08.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022]
Abstract
Rotational-echo double-resonance (REDOR) NMR is a powerful and versatile solid-state NMR measurement that has been recruited to elucidate drug modes of action and to drive the design of new therapeutics. REDOR has been implemented to examine composition, structure, and dynamics in diverse macromolecular and whole-cell systems, including taxol-bound microtubules, enzyme-cofactor-inhibitor ternary complexes, and antibiotic-whole-cell complexes. The REDOR approach involves the integrated design of specific isotopic labeling strategies and the selection of appropriate REDOR experiments. By way of example, this digest illustrates the versatility of the REDOR approach, with an emphasis on the practical considerations of experimental design and data interpretation.
Collapse
Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
26
|
Kim SJ, Tanaka KSE, Dietrich E, Rafai Far A, Schaefer J. Locations of the hydrophobic side chains of lipoglycopeptides bound to the peptidoglycan of Staphylococcus aureus. Biochemistry 2013; 52:3405-14. [PMID: 23607653 DOI: 10.1021/bi400054p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycopeptides whose aminosugars have been modified by attachment of hydrophobic side chains are frequently active against vancomycin-resistant microorganisms. We have compared the conformations of six such fluorinated glycopeptides (with side chains of varying length) complexed to cell walls labeled with d-[1-(13)C]alanine, [1-(13)C]glycine, and l-[ε-(15)N]lysine in whole cells of Staphylococcus aureus. The internuclear distances from (19)F of the bound drug to the (13)C and (15)N labels of the peptidoglycan, and to the natural abundance (31)P of lipid membranes and teichoic acids, were determined by rotational-echo double resonance NMR. The drugs did not dimerize, and their side chains did not form membrane anchors but instead became essential parts of secondary binding to pentaglycyl bridge segments of the cell-wall peptidoglycan.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | | | | | | | | |
Collapse
|
27
|
Kim SJ, Singh M, Wohlrab A, Yu TY, Patti GJ, O’Connor RD, VanNieuwenhze M, Schaefer J. The isotridecanyl side chain of plusbacin-A3 is essential for the transglycosylase inhibition of peptidoglycan biosynthesis. Biochemistry 2013; 52:1973-9. [PMID: 23421534 PMCID: PMC3628776 DOI: 10.1021/bi4000222] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plusbacin-A3 (pb-A3) is a cyclic lipodepsipeptide that exhibits antibacterial activity against multidrug-resistant Gram-positive pathogens. Plusbacin-A3 is thought not to enter the cell cytoplasm, and its lipophilic isotridecanyl side chain is presumed to insert into the membrane bilayer, thereby facilitating either lipid II binding or some form of membrane disruption. Analogues of pb-A3, [(2)H]pb-A3 and deslipo-pb-A3, were synthesized to test membrane insertion as a key to the mode of action. [(2)H]pb-A3 has an isotopically (2)H-labeled isopropyl subunit of the lipid side chain, and deslipo-pb-A3 is missing the isotridecanyl side chain. Both analogues have the pb-A3 core structure. The loss of antimicrobial activity in deslipo-pb-A3 showed that the isotridecanyl side chain is crucial for the mode of action of the drug. However, rotational-echo double-resonance nuclear magnetic resonance characterization of [(2)H]pb-A3 bound to [1-(13)C]glycine-labeled whole cells of Staphylococcus aureus showed that the isotridecanyl side chain does not insert into the lipid membrane but instead is found in the staphylococcal cell wall, positioned near the pentaglycyl cross-bridge of the cell-wall peptidoglycan. Addition of [(2)H]pb-A3 during the growth of S. aureus resulted in the accumulation of Park's nucleotide, consistent with the inhibition of the transglycosylation step of peptidoglycan biosynthesis.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Aaron Wohlrab
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Tsyr-Yan Yu
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | | | | | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130
| |
Collapse
|
28
|
Uniformity of glycyl bridge lengths in the mature cell walls of fem mutants of methicillin-resistant Staphylococcus aureus. J Bacteriol 2013; 195:1421-7. [PMID: 23335411 DOI: 10.1128/jb.01471-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Peptidoglycan (PG) composition in intact cells of methicillin-resistant Staphylococcus aureus (MRSA) and its isogenic Fem mutants has been characterized by measuring the glycine content of PG bridge structures by solid-state nuclear magnetic resonance (NMR). The glycine content estimated from integrated intensities (rather than peak heights) in the cell walls of whole cells was increased by approximately 30% for the FemA mutant and was reduced by 25% for the FemB mutant relative to expected values for homogeneous structures. In contrast, the expected compositions were observed in isolated cell walls of the same mutants. For FemA mutant whole cells, the increase was due to the presence of triglycyl bridge PG units (confirmed directly by mass spectrometric analysis), which constituted 10% of the total PG. These species were coalesced in some sort of a lattice or aggregate with spatial proximity to other PG bridges. This result suggests that the triglycyl-bridged PG units form a PG-like structure that is not incorporated into the mature cell wall.
Collapse
|
29
|
Zhou X, Cegelski L. Nutrient-dependent structural changes in S. aureus peptidoglycan revealed by solid-state NMR spectroscopy. Biochemistry 2012; 51:8143-53. [PMID: 22974326 DOI: 10.1021/bi3012115] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The bacterial cell wall is essential to cell survival and is a major target of antibiotics. The main component of the bacterial cell wall is peptidoglycan, a cage-like macromolecule that preserves cellular integrity and maintains cell shape. The insolubility and heterogeneity of peptidoglycan pose a challenge to conventional structural analyses. Here we use solid-state NMR combined with specific isotopic labeling to probe a key structural feature of the Staphylococcus aureus peptidoglycan quantitatively and nondestructively. We observed that both the cell-wall morphology and the peptidoglycan structure are functions of growth stage in S. aureus synthetic medium (SASM). Specifically, S. aureus cells at stationary phase have thicker cell walls with nonuniformly thickened septa compared to cells in exponential phase, and remarkably, 12% (±2%) of the stems in their peptidoglycan do not have pentaglycine bridges attached. Mechanistically, we determined that these observations are triggered by the depletion of glycine in the nutrient medium, which is coincident with the start of the stationary phase, and that the production of the structurally altered peptidoglycan can be prevented by the addition of excess glycine. We also demonstrated that the structural changes primarily arise within newly synthesized peptidoglycan rather than through the modification of previously synthesized peptidoglycan. Collectively, our observations emphasize the plasticity in bacterial cell-wall assembly and the possibility to manipulate peptidoglycan structure with external stimuli.
Collapse
Affiliation(s)
- Xiaoxue Zhou
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | |
Collapse
|
30
|
Sudiarta IP, Fukushima T, Sekiguchi J. Bacillus subtilis CwlP of the SP-{beta} prophage has two novel peptidoglycan hydrolase domains, muramidase and cross-linkage digesting DD-endopeptidase. J Biol Chem 2010; 285:41232-43. [PMID: 20980266 DOI: 10.1074/jbc.m110.156273] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
For bacteria and bacteriophages, cell wall digestion by hydrolases is a very important event. We investigated one of the proteins involved in cell wall digestion, the yomI gene product (renamed CwlP). The gene is located in the SP-β prophage region of the Bacillus subtilis chromosome. Inspection of the Pfam database indicates that CwlP contains soluble lytic transglycosylase (SLT) and peptidase M23 domains, which are similar to Escherichia coli lytic transglycosylase Slt70, and the Staphylococcus aureus Gly-Gly endopeptidase LytM, respectively. The SLT domain of CwlP exhibits hydrolytic activity toward the B. subtilis cell wall; however, reverse phase (RP)-HPLC and mass spectrometry revealed that the CwlP-SLT domain has only muramidase activity. In addition, the peptidase M23 domain of CwlP exhibited hydrolytic activity and could cleave d-Ala-diaminopimelic acid cross-linkage, a property associated with dd-endopeptidases. Remarkably, the M23 domain of CwlP possessed a unique Zn(2+)-independent endopeptidase activity; this contrasts with all other characterized M23 peptidases (and enzymes similar to CwlP), which are Zn(2+) dependent. Both domains of CwlP could hydrolyze the peptidoglycan and cell wall of B. subtilis. However, the M23 domain digested neither the peptidoglycans nor the cell walls of S. aureus or Streptococcus thermophilus. The effect of defined point mutations in conserved amino acid residues of CwlP is also determined.
Collapse
Affiliation(s)
- I Putu Sudiarta
- Interdisciplinary Graduate School of Science and Technology, Department of Life Sciences, Research Center for Human and Environmental Sciences, Shinshu University, Nagano 386-8567, Japan
| | | | | |
Collapse
|
31
|
Reid CW, Fulton KM, Twine SM. Never take candy from a stranger: the role of the bacterial glycome in host–pathogen interactions. Future Microbiol 2010; 5:267-88. [DOI: 10.2217/fmb.09.103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
With the comprehensive study and complete sequencing of the Haemophilus influenzae genome in 1995 came the term ‘genomics’ and the beginning of the ‘omics’ era. Since this time, several analogous fields, such as transcriptomics and proteomics, have emerged. While growth and advancement in these fields have increased understanding of microbial virulence, the study of bacterial glycomes is still in its infancy and little is known concerning their role in host–pathogen interactions. Bacterial glycomics is challenging owing to the diversity of glyco-conjugate molecules, vast array of unusual sugars and limited number of analytical approaches available. However, recent advances in glycomics technologies offer the potential for exploration and characterization of both the structures and functions of components of bacterial glycomes in a systematic manner. Such characterization is a prerequisite for discerning the role of bacterial glycans in the interaction between host defences and bacterial virulence factors.
Collapse
Affiliation(s)
- Christopher W Reid
- National Research Council – Institute for Biological Science, Ottawa, Ontario, K1A 0R6, Canada
| | - Kelly M Fulton
- National Research Council – Institute for Biological Science, Ottawa, Ontario, K1A 0R6, Canada
| | - Susan M Twine
- National Research Council – Institute for Biological Science, Ottawa, Ontario, K1A 0R6, Canada
| |
Collapse
|
32
|
Garimella R, Halye JL, Harrison W, Klebba PE, Rice CV. Conformation of the phosphate D-alanine zwitterion in bacterial teichoic acid from nuclear magnetic resonance spectroscopy. Biochemistry 2009; 48:9242-9. [PMID: 19746945 PMCID: PMC4196936 DOI: 10.1021/bi900503k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformation of d-alanine (d-Ala) groups of bacterial teichoic acid is a central, yet untested, paradigm of microbiology. The d-Ala binds via the C-terminus, thereby allowing the amine to exist as a free cationic NH(3)(+) group with the ability to form a contact ion pair with the nearby anionic phosphate group. This conformation hinders metal chelation by the phosphate because the zwitterion pair is charge neutral. To the contrary, the repulsion of cationic antimicrobial peptides (CAMPs) is attributed to the presence of the d-Ala cation; thus the ion pair does not form in this model. Solid-state nuclear magnetic resonance (NMR) spectroscopy has been used to measure the distance between amine and phosphate groups within cell wall fragments of Bacillus subtilis. The bacteria were grown on media containing (15)N d-Ala and beta-chloroalanine racemase inhibitor. The rotational-echo double-resonance (REDOR) pulse sequence was used to measure the internuclear dipolar coupling, and the results demonstrate (1) the metal-free amine-to-phosphate distance is 4.4 A and (2) the amine-to-phosphate distance increases to 5.4 A in the presence of Mg(2+) ions. As a result, the zwitterion exists in a nitrogen-oxygen ion pair configuration providing teichoic acid with a positive charge to repel CAMPs. Additionally, the amine of d-Ala does not prevent magnesium chelation in contradiction to the prevailing view of teichoic acids in metal binding. Thus, the NMR-based description of teichoic acid structure resolves the contradictory models, advances the basic understanding of cell wall biochemistry, and provides possible insight into the creation of new antibiotic therapies.
Collapse
Affiliation(s)
- Ravindranath Garimella
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - Jeffrey L. Halye
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - William Harrison
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - Phillip E. Klebba
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| | - Charles V. Rice
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019
| |
Collapse
|
33
|
Kim SJ, Singh M, Schaefer J. Oritavancin binds to isolated protoplast membranes but not intact protoplasts of Staphylococcus aureus. J Mol Biol 2009; 391:414-25. [PMID: 19538971 PMCID: PMC2747642 DOI: 10.1016/j.jmb.2009.06.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 06/04/2009] [Accepted: 06/11/2009] [Indexed: 11/19/2022]
Abstract
Solid-state NMR has been used to examine the binding of N'-4-[(4-fluorophenyl)benzyl)]chloroeremomycin, a fluorinated analogue of oritavancin, to isolated protoplast membranes and whole-cell sucrose-stabilized protoplasts of Staphylococcus aureus, grown in media containing [1(13)C]glycine and L-[epsilon-(15)N]lysine. Rotational-echo double-resonance NMR was used to characterize the binding by estimating internuclear distances from (19)F of oritavancin to (13)C and (15)N labels of the membrane-associated peptidoglycan and to the (31)P of the phospholipid bilayer of the membrane. In isolated protoplast membranes, both with and without 1 M sucrose added to the buffer, the nascent peptidoglycan was extended away from the membrane surface and the oritavancin hydrophobic side chain was buried deep in the exposed lipid bilayer. However, there was no N'-4-[(4-fluorophenyl)benzyl)]chloroeremomycin binding to intact sucrose-stabilized protoplasts, even though the drug bound normally to the cell walls of whole cells of S. aureus in the presence of 1 M sucrose. As shown by the proximity of peptidoglycan-bridge (13)C labels to phosphate (31)P, the nascent peptidoglycan of the intact protoplasts was confined to the membrane surface.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130
| |
Collapse
|
34
|
Sharif S, Singh M, Kim SJ, Schaefer J. Staphylococcus aureus peptidoglycan tertiary structure from carbon-13 spin diffusion. J Am Chem Soc 2009; 131:7023-30. [PMID: 19419167 DOI: 10.1021/ja808971c] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cell-wall peptidoglycan of Staphylococcus aureus is a heterogeneous, highly cross-linked polymer of unknown tertiary structure. We have partially characterized this structure by measuring spin diffusion from (13)C labels in pentaglycyl cross-linking segments to natural-abundance (13)C in the surrounding intact cell walls. The measurements were performed using a version of centerband-only detection of exchange (CODEX). The cell walls were isolated from S. aureus grown in media containing [1-(13)C]glycine. The CODEX spin diffusion rates established that the pentaglycyl bridge of one peptidoglycan repeat unit of S. aureus is within 5 A of the glycan chain of another repeat unit. This surprising proximity is interpreted in terms of a model for the peptidoglycan lattice in which all peptide stems in a plane perpendicular to the glycan mainchain are parallel to one another.
Collapse
Affiliation(s)
- Shasad Sharif
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | | | | | |
Collapse
|
35
|
Sharif S, Kim SJ, Labischinski H, Schaefer J. Characterization of peptidoglycan in fem-deletion mutants of methicillin-resistant Staphylococcus aureus by solid-state NMR. Biochemistry 2009; 48:3100-8. [PMID: 19309106 PMCID: PMC2785074 DOI: 10.1021/bi801750u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compositional analysis of the peptidoglycan (PG) of a wild-type methicillin-resistant Staphylococcus aureus and its fem-deletion mutants has been performed on whole cells and cell walls using stable-isotope labeling and rotational-echo double-resonance NMR. The labels included [1-(13)C,(15)N]glycine and l-[epsilon-(15)N]lysine (for a direct measure of the number of glycyl residues in the bridging segment), [1-(13)C]glycine and l-[epsilon-(15)N]lysine (concentration of bridge links), and d-[1-(13)C]alanine and [(15)N]glycine (concentrations of cross-links and wall teichoic acids). The bridging segment length changed from 5.0 glycyl residues (wild-type strain) to 2.5 +/- 0.1 (FemB) with modest changes in cross-link and bridge-link concentrations. This accurate in situ measurement for the FemB mutant indicates a heterogeneous PG structure with 25% monoglycyl and 75% triglycyl bridges. When the bridging segment was reduced to a single glycyl residue 1.0 +/- 0.1 (FemA), the level of cross-linking decreased by more than 20%, resulting in a high concentration of open N-terminal glycyl segments.
Collapse
Affiliation(s)
- Shasad Sharif
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Sung Joon Kim
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Harald Labischinski
- MerLion Pharmaceuticals GmbH, Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | - Jacob Schaefer
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| |
Collapse
|
36
|
Patti GJ, Chen J, Gross ML. Method revealing bacterial cell-wall architecture by time-dependent isotope labeling and quantitative liquid chromatography/mass spectrometry. Anal Chem 2009; 81:2437-45. [PMID: 19281243 PMCID: PMC2715431 DOI: 10.1021/ac802587r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular details of the biosynthesis and resulting architecture of the bacterial cell wall remain unclear but are essential to understanding the activity of glycopeptide antibiotics, the recognition of pathogens by hosts, and the processes of bacterial growth and division. Here we report a new strategy to elucidate bacterial cell-wall architecture based on time-dependent isotope labeling of bacterial cells quantified by liquid chromatography/accurate mass measurement mass spectrometry. The results allow us to track the fate of cell-wall precursors (which contain the vancomycin-binding site) in Enterococcus faecium, a leading antibiotic-resistant pathogen. By comparing isotopic enrichments of postinsertionally modified cell-wall precursors, we find that tripeptides and species without aspartic acid/asparagine (Asp/Asn, Asx) bridges are specific to mature cell wall. Additionally, we find that the sequence of cell-wall maturation varies throughout a cell cycle. We suggest that actively dividing E. faecium cells have three zones of unique peptidoglycan processing. Our results reveal new organizational characteristics of the bacterial cell wall that are important to understanding tertiary structure and designing novel drugs for antibiotic-resistant pathogens.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| |
Collapse
|
37
|
Matsuoka S, Inoue M. Application of REDOR NMR in natural product chemistry. Chem Commun (Camb) 2009:5664-75. [DOI: 10.1039/b910230b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
38
|
Yu TY, Schaefer J. REDOR NMR characterization of DNA packaging in bacteriophage T4. J Mol Biol 2008; 382:1031-42. [PMID: 18703073 PMCID: PMC2633174 DOI: 10.1016/j.jmb.2008.07.077] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/20/2008] [Accepted: 07/26/2008] [Indexed: 11/25/2022]
Abstract
Bacteriophage T4 is a large-tailed Escherichia coli virus whose capsid is 120x86 nm. ATP-driven DNA packaging of the T4 capsid results in the loading of a 171-kb genome in less than 5 min during viral infection. We have isolated 50-mg quantities of uniform (15)N- and [epsilon-(15)N]lysine-labeled bacteriophage T4. We have also introduced (15)NH(4)(+) into filled, unlabeled capsids from synthetic medium by exchange. We have examined lyo- and cryoprotected lyophilized T4 using (15)N{(31)P} and (31)P{(15)N} rotational-echo double resonance. The results of these experiments have shown that (i) packaged DNA is in an unperturbed duplex B-form conformation; (ii) the DNA phosphate negative charge is balanced by lysyl amines (3.2%), polyamines (5.8%), and monovalent cations (40%); and (iii) 11% of lysyl amines, 40% of -NH(2) groups of polyamines, and 80% of monovalent cations within the lyophilized T4 capsid are involved in the DNA charge balance. The NMR evidence suggests that DNA enters the T4 capsid in a charge-unbalanced state. We propose that electrostatic interactions may provide free energy to supplement the nanomotor-driven T4 DNA packaging.
Collapse
Affiliation(s)
- Tsyr-Yan Yu
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | | |
Collapse
|
39
|
Patti GJ, Chen J, Schaefer J, Gross ML. Characterization of structural variations in the peptidoglycan of vancomycin-susceptible Enterococcus faecium: understanding glycopeptide-antibiotic binding sites using mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1467-75. [PMID: 18692403 PMCID: PMC2613859 DOI: 10.1016/j.jasms.2008.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/20/2008] [Accepted: 06/21/2008] [Indexed: 05/23/2023]
Abstract
Enterococcus faecium, an opportunistic pathogen that causes a significant number of hospital-acquired infections each year, presents a serious clinical challenge because an increasing number of infections are resistant to the so-called antibiotic of last resort, vancomycin. Vancomycin and other new glycopeptide derivatives target the bacterial cell wall, thereby perturbing its biosynthesis. To help determine the modes of action of glycopeptide antibiotics, we have developed a bottom-up mass spectrometry approach complemented by solid-state nuclear magnetic resonance (NMR) to elucidate important structural characteristics of vancomycin-susceptible E. faecium peptidoglycan. Using accurate-mass measurements and integrating ion-current chromatographic peaks of digested peptidoglycan, we identified individual muropeptide species and approximated the relative amount of each. Even though the organism investigated is susceptible to vancomycin, only 3% of the digested peptidoglycan has the well-known D-Ala-D-Ala vancomycin-binding site. The data are consistent with a previously proposed template model of cell-wall biosynthesis where D-Ala-D-Ala stems that are not cross-linked are cleaved in mature peptidoglycan. Additionally, our mass-spectrometry approach allowed differentiation and quantification of muropeptide species seen as unresolved chromatographic peaks. Our method provides an estimate of the extent of muropeptides containing O-acetylation, amidation, hydroxylation, and the number of species forming cyclic imides. The varieties of muropeptides on which the modifications are detected suggest that significant processing occurs in mature peptidoglycan where several enzymes are active in editing cell-wall structure.
Collapse
Affiliation(s)
- Gary J Patti
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | | | | | |
Collapse
|
40
|
Kim SJ, Schaefer J. Hydrophobic side-chain length determines activity and conformational heterogeneity of a vancomycin derivative bound to the cell wall of Staphylococcus aureus. Biochemistry 2008; 47:10155-61. [PMID: 18759499 DOI: 10.1021/bi800838c] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disaccharide-modified glycopeptides with hydrophobic side chains are active against vancomycin-resistant enterococci and vancomycin-resistant Staphylococcus aureus. The activity depends on the length of the side chain. The benzyl side chain of N-(4-fluorobenzyl)vancomycin (FBV) has the minimal length sufficient for enhancement in activity against vancomycin-resistant pathogens. The conformation of FBV bound to the peptidoglycan in whole cells of S. aureus has been determined using rotational-echo double resonance NMR by measuring internuclear distances from the (19)F of FBV to (13)C and (15)N labels incorporated into the cell-wall peptidoglycan. The hydrophobic side chain and aglycon of FBV form a cleft around the pentaglycyl bridge. FBV binds heterogeneously to the peptidoglycan as a monomer with the (19)F positioned near the middle of the pentaglycyl bridge, approximately 7 A from the bridge link. This differs from the situation for N-(4-(4-fluorophenyl)benzyl)vancomycin complexed to the peptidoglycan where the (19)F is located at the end of pentaglycyl bridge, 7 A from the cross-link.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | |
Collapse
|
41
|
Patti GJ, Kim SJ, Schaefer J. Characterization of the peptidoglycan of vancomycin-susceptible Enterococcus faecium. Biochemistry 2008; 47:8378-85. [PMID: 18642854 DOI: 10.1021/bi8008032] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vancomycin and other antibacterial glycopeptide analogues target the cell wall and affect the enzymatic processes involved with cell-wall biosynthesis. Understanding the structure and organization of the peptidoglycan is the first step in establishing the mode of action of these glycopeptides. We have used solid-state NMR to determine the relative concentrations of stem-links (64%), bridge-links (61%), and cross-links (49%) in the cell walls of vancomycin-susceptible Enterococcus faecium (ATTC 49624). Furthermore, we have determined that in vivo only 7% of the peptidoglycan stems terminate in d-Ala- d-Ala, the well-known vancomycin-binding site. Presumably, d-Ala- d-Ala is cleaved from uncross-linked stems in mature peptidoglycan by an active carboxypeptidase. We believe that most of the few pentapeptide stems ending in d-Ala- d-Ala occur in the template and nascent peptidoglycan strands that are crucial for cell-wall biosynthesis.
Collapse
Affiliation(s)
- Gary J Patti
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130, USA
| | | | | |
Collapse
|
42
|
Kim SJ, Matsuoka S, Patti GJ, Schaefer J. Vancomycin derivative with damaged D-Ala-D-Ala binding cleft binds to cross-linked peptidoglycan in the cell wall of Staphylococcus aureus. Biochemistry 2008; 47:3822-31. [PMID: 18302341 PMCID: PMC2778263 DOI: 10.1021/bi702232a] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Des-N-methylleucyl-4-(4-fluorophenyl)benzyl-vancomycin (DFPBV) retains activity against vancomycin-resistant pathogens despite its damaged d-Ala-d-Ala binding cleft. Using solid-state nuclear magnetic resonance (NMR), a DFPBV binding site in the cell walls of whole cells of Staphylococcus aureus has been identified. The cell walls were labeled with d-[1-(13)C]alanine, [1-(13)C]glycine, and l-[epsilon-(15)N]lysine. Internuclear distances from (19)F of the DFPBV to the (13)C and (15)N labels of the cell-wall peptidoglycan were determined by rotational-echo double-resonance (REDOR) NMR. The (13)C{(19)F} and (15)N{(19)F} REDOR spectra show that, in situ, DFPBV binds to the peptidoglycan as a monomer with its vancosamine hydrophobic side chain positioned near a pentaglycyl bridge. This result suggests that the antimicrobial activity of other vancosamine-modified glycopeptides depends upon both d-Ala-d-Ala stem-terminus recognition (primary binding site) and stem-bridge recognition (secondary binding site).
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | | | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130
| |
Collapse
|
43
|
Kim SJ, Cegelski L, Stueber D, Singh M, Dietrich E, Tanaka KSE, Parr TR, Far AR, Schaefer J. Oritavancin exhibits dual mode of action to inhibit cell-wall biosynthesis in Staphylococcus aureus. J Mol Biol 2008; 377:281-93. [PMID: 18258256 DOI: 10.1016/j.jmb.2008.01.031] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 12/30/2007] [Accepted: 01/11/2008] [Indexed: 10/22/2022]
Abstract
Solid-state NMR measurements performed on intact whole cells of Staphylococcus aureus labeled selectively in vivo have established that des-N-methylleucyl oritavancin (which has antimicrobial activity) binds to the cell-wall peptidoglycan, even though removal of the terminal N-methylleucyl residue destroys the D-Ala-D-Ala binding pocket. By contrast, the des-N-methylleucyl form of vancomycin (which has no antimicrobial activity) does not bind to the cell wall. Solid-state NMR has also determined that oritavancin and vancomycin are comparable inhibitors of transglycosylation, but that oritavancin is a more potent inhibitor of transpeptidation. This combination of effects on cell-wall binding and biosynthesis is interpreted in terms of a recent proposal that oritavancin-like glycopeptides have two cell-wall binding sites: the well-known peptidoglycan D-Ala-D-Ala pentapeptide stem terminus and the pentaglycyl bridging segment. The resulting dual mode of action provides a structural framework for coordinated cell-wall assembly that accounts for the enhanced potency of oritavancin and oritavancin-like analogues against vancomycin-resistant organisms.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Kim SJ, Cegelski L, Preobrazhenskaya M, Schaefer J. Structures of Staphylococcus aureus cell-wall complexes with vancomycin, eremomycin, and chloroeremomycin derivatives by 13C{19F} and 15N{19F} rotational-echo double resonance. Biochemistry 2006; 45:5235-50. [PMID: 16618112 PMCID: PMC2504515 DOI: 10.1021/bi052660s] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-state NMR has been used to examine isolated cell walls and intact whole cells of Staphylococcus aureus complexed to five different vancomycin, eremomycin, and chloroeremomycin derivatives. The cell walls and whole cells were specifically labeled with d-[1-(13)C]alanine, or a combination of [1-(13)C]glycine and [epsilon-(15)N]lysine. Each of the bound glycopeptides had a (19)F-labeled substituent at either its C-terminus or its disaccharide position. The (13)C{(19)F} rotational-echo double-resonance (REDOR) dephasing for the cell-wall (13)C-labeled bridging pentaglycyl segment connecting a glycopeptide-complexed peptidoglycan stem with its neighboring stem indicates that the fluorine labels for all bound glycopeptides are positioned at one or the other end of the bridge. An exception is N'-(p-trifluoromethoxybenzyl)chloroeremomycin, whose hydrophobic substituent differs in length by one phenyl group compared to that of oritavancin, N'-4-[(4-chlorophenyl)benzyl)]chloroeremomycin. For this drug, the fluorine label is near the middle of the pentaglycyl segment. (15)N{(19)F} REDOR dephasing shows the proximity of the fluorine to the bridge-link site of the pentaglycyl bridge for C-terminus-substituted moieties and the cross-link site for disaccharide-substituted moieties. Full-echo REDOR spectra of cell-wall complexes from cells labeled by d-[1-(13)C]alanine (in the presence of an alanine racemase inhibitor) reveal three different carbonyl carbon chemical-shift environments, arising from the d-Ala-d-Ala binding site and the d-Ala-Gly-1 cross-link site. The REDOR results indicate a single fluorine dephasing center in each peptidoglycan complex. Molecular models of the mature cell-wall complexes that are consistent with internuclear distances obtained from (13)C{(19)F} and (15)N{(19)F} REDOR dephasing allow a correlation of structure and antimicrobial activity of the glycopeptides.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | | | | |
Collapse
|
45
|
Cegelski L, Steuber D, Mehta AK, Kulp DW, Axelsen PH, Schaefer J. Conformational and quantitative characterization of oritavancin-peptidoglycan complexes in whole cells of Staphylococcus aureus by in vivo 13C and 15N labeling. J Mol Biol 2006; 357:1253-62. [PMID: 16483598 DOI: 10.1016/j.jmb.2006.01.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 12/24/2005] [Accepted: 01/06/2006] [Indexed: 11/27/2022]
Abstract
Solid-state NMR has been used to examine the cell walls of intact whole cells of Staphyloccus aureus grown on media containing D-[1-(13)C]alanine, [(15)N]glycine, and the alanine racemase inhibitor, alaphosphin. The results of in situ site-selective, four-frequency NMR experiments show directly for the first time that (i) 54% of the cell-wall peptidoglycan stems have D-alanine termini and 46%, D-alanine-D-alanine termini; (ii) the molar ratio of stems ending in D-alanine to esterified alditol repeats of cell-wall teichoic and lipoteichoic acids is 3:2; and (iii) 50% of the mature cell-wall binding sites for a fluorinated oritavancin analogue consist of two nearest-neighbor peptide stems of different glycan strands. The drug is bound to the D-Ala-D-Ala terminus of one stem and is proximate to the bridging pentaglycyl segment that cross-links the two stems. Structural details of the binding site are revealed in a model of the glycopeptide-peptidoglycan interaction produced by molecular dynamics simulations with internuclear distance restraints determined by NMR.
Collapse
Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | | | | | | | | | | |
Collapse
|
46
|
Cegelski L, Rice CV, O'Connor RD, Caruano AL, Tochtrop GP, Cai ZY, Covey DF, Schaefer J. Mapping the locations of estradiol and potent neuroprotective analogues in phospholipid bilayers by REDOR. Drug Dev Res 2006. [DOI: 10.1002/ddr.20048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
47
|
Sinha N, Hong M. X–1H rotational-echo double-resonance NMR for torsion angle determination of peptides. Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.09.088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
48
|
Mehta AK, Cegelski L, O'Connor RD, Schaefer J. REDOR with a relative full-echo reference. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 163:182-187. [PMID: 12852922 DOI: 10.1016/s1090-7807(03)00078-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
REDOR and REDOR-like 13C[19F] and 2H[19F] NMR experiments have been performed on lyophilized whole cells of Staphylococcus aureus. The bacteria were grown to maturity on media containing L-[13C(3)]alanine or L-[methyl-d(3)]alanine, and then complexed with the 4-fluorobiphenyl derivative of chloroeremomycin, an analogue of the widely used antibiotic, vancomycin. The position of the 19F of the drug bound in the bacterial cell wall was determined relative to L-alanine 13C and 2H labels in the peptidoglycan peptide stem that was closest to the fluorinated biphenyl moiety of the drug. These determinations were made by dipolar recoupling methods that do not require an absolute measurement of the REDOR full echo (the signal observed without rotor-synchronized dephasing pulses) of the labels in the peptide stem.
Collapse
Affiliation(s)
- Anil K Mehta
- Department of Chemistry, Washington University, One Brookings Dr., Campus Box 1134, St. Louis, MO 63130, USA
| | | | | | | |
Collapse
|
49
|
Ridley BL, O'Neill MA, Mohnen D. Pectins: structure, biosynthesis, and oligogalacturonide-related signaling. PHYTOCHEMISTRY 2001; 57:929-67. [PMID: 11423142 DOI: 10.1016/s0031-9422(01)00113-3] [Citation(s) in RCA: 1133] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pectin is a family of complex polysaccharides present in all plant primary cell walls. The complicated structure of the pectic polysaccharides, and the retention by plants of the large number of genes required to synthesize pectin, suggests that pectins have multiple functions in plant growth and development. In this review we summarize the current level of understanding of pectin primary and tertiary structure, and describe new methods that may be useful to study localized pectin structure in the plant cell wall. We also discuss progress in our understanding of how pectin is biosynthesized and review the biological activities and possible modes of action of pectic oligosaccharides referred to as oligogalacturonides. We present our view of critical questions regarding pectin structure, biosynthesis, and function that need to be addressed in the coming decade. As the plant community works towards understanding the functions of the tens of thousands of genes expressed by plants, a large number of those genes are likely to be involved in the synthesis, turnover, biological activity, and restructuring of pectin. A combination of genetic, molecular, biochemical and chemical approaches will be necessary to fully understand the function and biosynthesis of pectin.
Collapse
Affiliation(s)
- B L Ridley
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, 220 Riverbend Road, Athens, GA 30602-4712, USA
| | | | | |
Collapse
|
50
|
Protein and peptide interactions with lipids: Structure, membrane function and new methods. Curr Opin Colloid Interface Sci 1998. [DOI: 10.1016/s1359-0294(98)80024-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|