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Khaykelson D, Asor R, Zhao Z, Schlicksup CJ, Zlotnick A, Raviv U. Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis. Biochemistry 2024; 63:1543-1552. [PMID: 38787909 PMCID: PMC11191408 DOI: 10.1021/acs.biochem.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.
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Affiliation(s)
- Daniel Khaykelson
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Asor
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zhongchao Zhao
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher John Schlicksup
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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Peng R, Chen X, Xu F, Hailstone R, Men Y, Du K. Pneumatic nano-sieve for CRISPR-based detection of drug-resistant bacteria. NANOSCALE HORIZONS 2023; 8:1677-1685. [PMID: 37877474 PMCID: PMC11162761 DOI: 10.1039/d3nh00365e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieved an on-chip concentration factor of ∼15-fold for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU mL-1. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.
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Affiliation(s)
- Ruonan Peng
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA.
| | - Xinye Chen
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA.
- Department of Microsystems Engineering, Rochester Institute of Technology, 1 Lomb Memorial Dr, Rochester, NY 14623, USA
| | - Fengjun Xu
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA.
| | - Richard Hailstone
- Center for Imaging Science, Rochester Institute of Technology, 1 Lomb Memorial Dr, Rochester, NY 14623, USA
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA.
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA.
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Peng R, Chen X, Xu F, Hailstone R, Men Y, Du K. Pneumatic Nano-Sieve for CRISPR-based Detection of Drug-resistant Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553737. [PMID: 37645720 PMCID: PMC10462146 DOI: 10.1101/2023.08.17.553737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieve an on-chip concentration factor of 15 for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU/mL. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.
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Affiliation(s)
- Ruonan Peng
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Xinye Chen
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
- Department of Microsystems Engineering, Rochester Institute of Technology, 1 Lomb Memorial Dr, Rochester, NY 14623, USA
| | - Fengjun Xu
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Richard Hailstone
- Center for Imaging Science, Rochester Institute of Technology, 1 Lomb Memorial Dr, Rochester, NY 14623, USA
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
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Apo-metallothionein-3 cooperatively forms tightly compact structures under physiological conditions. J Biol Chem 2023; 299:102899. [PMID: 36639030 PMCID: PMC9930159 DOI: 10.1016/j.jbc.2023.102899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Metallothioneins (MTs) are essential mammalian metal chaperones. MT isoform 1 (MT1) is expressed in the kidneys and isoform 3 (MT3) is expressed in nervous tissue. For MTs, the solution-based NMR structure was determined for metal-bound MT1 and MT2, and only one X-ray diffraction structure on a crystallized mixed metal-bound MT2 has been reported. The structure of solution-based metalated MT3 is partially known using NMR methods; however, little is known about the fluxional de novo apo-MT3 because the structure cannot be determined by traditional methods. Here, we used cysteine modification coupled with electrospray ionization mass spectrometry, denaturing reactions with guanidinium chloride, stopped-flow methods measuring cysteine modification and metalation, and ion mobility mass spectrometry to reveal that apo-MT3 adopts a compact structure under physiological conditions and an extended structure under denaturing conditions, with no intermediates. Compared with apo-MT1, we found that this compact apo-MT3 binds to a cysteine modifier more cooperatively at equilibrium and 0.5 times the rate, providing quantitative evidence that many of the 20 cysteines of apo-MT3 are less accessible than those of apo-MT1. In addition, this compact apo-MT3 can be identified as a distinct population using ion mobility mass spectrometry. Furthermore, proposed structural models can be calculated using molecular dynamics methods. Collectively, these findings provide support for MT3 acting as a noninducible regulator of the nervous system compared with MT1 as an inducible scavenger of trace metals and toxic metals in the kidneys.
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Restrepo-Pineda, Rosiles-BecerrilVargas-Castillo D, Ávila-Barrientos LP, Luviano A, Sánchez-Puig N, García-Hernández E, Pérez NO, Trujillo-Roldán MA, Valdez-Cruz NA. Induction temperature impacts the structure of recombinant HuGM-CSF inclusion bodies in thermoinducible E. coli. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Ganguly P, Shea JE. Distinct and Nonadditive Effects of Urea and Guanidinium Chloride on Peptide Solvation. J Phys Chem Lett 2019; 10:7406-7413. [PMID: 31721587 DOI: 10.1021/acs.jpclett.9b03004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using enhanced-sampling replica exchange fully atomistic molecular dynamics simulations, we show that, individually, urea and guanidinium chloride (GdmCl) denature the Trpcage protein, but remarkably, the helical segment 1NLYIQWL7 of the protein is stabilized in mixed denaturant solutions. GdmCl induces protein denaturation via a combination of direct and indirect effects involving dehydration of the protein and destabilization of stabilizing salt bridges. In contrast, urea denatures the protein through favorable protein-urea preferential interactions, with peptide-specific indirect effects of urea on the water structure around the protein. In the case of the helical segment of Trpcage, urea "oversolvates" the peptide backbone by reorganizing water molecules from the peptide side chains to the peptide backbone. An intricate nonadditive thermodynamic balance between GdmCl-induced dehydration of the peptide and the urea-induced changes in solvation structure triggers partial counteraction to urea denaturation and stabilization of the helix.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
- Department of Physics , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
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Muttathukattil AN, Srinivasan S, Halder A, Reddy G. Role of Guanidinium-Carboxylate Ion Interaction in Enzyme Inhibition with Implications for Drug Design. J Phys Chem B 2019; 123:9302-9311. [DOI: 10.1021/acs.jpcb.9b06130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aswathy N. Muttathukattil
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sriraksha Srinivasan
- Department of Chemistry, St. Joseph’s College, Bangalore, Karnataka 560027, India
| | - Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Su Z, Mahmoudinobar F, Dias CL. Effects of Trimethylamine-N-oxide on the Conformation of Peptides and its Implications for Proteins. PHYSICAL REVIEW LETTERS 2017; 119:108102. [PMID: 28949191 DOI: 10.1103/physrevlett.119.108102] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 05/16/2023]
Abstract
To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. The effects of TMAO on the backbone and charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins, which accounts for hydrophobic swelling, backbone collapse, and stabilization of charge-charge interactions. These mechanisms are observed in Trp cage.
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Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Farbod Mahmoudinobar
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
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Williams C, Dougherty ML, Makaroff K, Stapleton J, Konkolewicz D, Berberich JA, Page RC. Strategies for Biophysical Characterization of Protein–Polymer Conjugates. Methods Enzymol 2017; 590:93-114. [DOI: 10.1016/bs.mie.2016.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model. Biophys J 2016; 110:1510-1522. [PMID: 27074677 DOI: 10.1016/j.bpj.2016.02.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
Conformational states of the metastable drkN SH3 domain were characterized using single-molecule fluorescence techniques. Under nondenaturing conditions, two Förster resonance energy transfer (FRET) populations were observed that corresponded to a folded and an unfolded state. FRET-estimated radii of gyration and hydrodynamic radii estimated by fluorescence correlation spectroscopy of the two coexisting conformations are in agreement with previous ensemble x-ray scattering and NMR measurements. Surprisingly, when exposed to high concentrations of urea and GdmCl denaturants, the protein still exhibits two distinct FRET populations. The dominant conformation is expanded, showing a low FRET efficiency, consistent with the expected behavior of a random chain with excluded volume. However, approximately one-third of the drkN SH3 conformations showed high, nearly 100%, FRET efficiency, which is shown to correspond to denaturation-induced looped conformations that remain stable on a timescale of at least 100 μs. These loops may contain interconverting conformations that are more globally collapsed, hairpin-like, or circular, giving rise to the observed heterogeneous broadening of this population. Although the underlying mechanism of chain looping remains elusive, FRET experiments in formamide and dimethyl sulfoxide suggest that interactions between hydrophobic groups in the distal regions may play a significant role in the formation of the looped state.
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11
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Maneeruttanarungroj C, Incharoensakdi A. Rapid method for DNA isolation from a tough cell wall green alga Tetraspora sp. CU2551. World J Microbiol Biotechnol 2016; 32:99. [DOI: 10.1007/s11274-016-2055-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 03/18/2016] [Indexed: 01/04/2023]
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12
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Meuzelaar H, Panman MR, Woutersen S. Guanidinium-Induced Denaturation by Breaking of Salt Bridges. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Meuzelaar H, Panman MR, Woutersen S. Guanidinium-Induced Denaturation by Breaking of Salt Bridges. Angew Chem Int Ed Engl 2015; 54:15255-9. [DOI: 10.1002/anie.201508601] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 11/11/2022]
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