1
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Hackett JC, Krueger S, Urban VS, Zárate-Pérez F. Small angle scattering reveals the orientation of cytochrome P450 19A1 in lipoprotein nanodiscs. J Inorg Biochem 2024; 257:112579. [PMID: 38703512 DOI: 10.1016/j.jinorgbio.2024.112579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
Human aromatase (CYP19A1), the cytochrome P450 enzyme responsible for conversion of androgens to estrogens, was incorporated into lipoprotein nanodiscs (NDs) and interrogated by small angle X-ray and neutron scattering (SAXS/SANS). CYP19A1 was associated with the surface and centered at the edge of the long axis of the ND membrane. In the absence of the N-terminal anchor, the amphipathic A'- and G'-helices were predominately buried in the lipid head groups, with the possibly that their hydrophobic side chains protrude into the hydrophobic, aliphatic tails. The prediction is like that for CYP3A4 based on SAXS employing a similar modeling approach. The orientation of CYP19A1 in a ND is consistent with our previous predictions based on molecular dynamics simulations and lends additional credibility to the notion that CYP19A1 captures substrates from the membrane.
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Affiliation(s)
- John C Hackett
- Department of Chemistry and Biochemistry and the Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States.
| | - Susan Krueger
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, MD 20899, United States; Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Francisco Zárate-Pérez
- Department of Chemistry and Biochemistry and the Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
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2
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Thomas GM, Wu Y, Leite W, Pingali SV, Weiss KL, Grant AJ, Diggs MW, Schmidt-Krey I, Gutishvili G, Gumbart JC, Urban VS, Lieberman RL. SANS reveals lipid-dependent oligomerization of an intramembrane aspartyl protease from H. volcanii. Biophys J 2024:S0006-3495(24)00378-3. [PMID: 38824390 DOI: 10.1016/j.bpj.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/05/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024] Open
Abstract
Reactions that occur within the lipid membrane involve, at minimum, ternary complexes among the enzyme, substrate, and lipid. For many systems, the impact of the lipid in regulating activity or oligomerization state is poorly understood. Here, we used small-angle neutron scattering (SANS) to structurally characterize an intramembrane aspartyl protease (IAP), a class of membrane-bound enzymes that use membrane-embedded aspartate residues to hydrolyze transmembrane segments of biologically relevant substrates. We focused on an IAP ortholog from the halophilic archaeon Haloferax volcanii (HvoIAP). HvoIAP purified in n-dodecyl-β-D-maltoside (DDM) fractionates on size-exclusion chromatography (SEC) as two fractions. We show that, in DDM, the smaller SEC fraction is consistent with a compact HvoIAP monomer. Molecular dynamics flexible fitting conducted on an AlphaFold2-generated monomer produces a model in which loops are compact alongside the membrane-embedded helices. In contrast, SANS data collected on the second SEC fraction indicate an oligomer consistent with an elongated assembly of discrete HvoIAP monomers. Analysis of in-line SEC-SANS data of the HvoIAP oligomer, the first such experiment to be conducted on a membrane protein at Oak Ridge National Lab (ORNL), shows a diversity of elongated and spherical species, including one consistent with the tetrameric assembly reported for the Methanoculleusmarisnigri JR1 IAP crystal structure not observed previously in solution. Reconstitution of monomeric HvoIAP into bicelles increases enzyme activity and results in the assembly of HvoIAP into a species with similar dimensions as the ensemble of oligomers isolated from DDM. Our study reveals lipid-mediated HvoIAP self-assembly and demonstrates the utility of in-line SEC-SANS in elucidating oligomerization states of small membrane proteins.
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Affiliation(s)
- Gwendell M Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Wellington Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Arshay J Grant
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Monneh W Diggs
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Ingeborg Schmidt-Krey
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | - James C Gumbart
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia; School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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3
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Hayes DG, Barth BA, Pingali SV. Effect of equilibration time on the structural gradient in the vertical direction for bicontinuous microemulsions in Winsor-III and -IV systems. SOFT MATTER 2024. [PMID: 38651769 DOI: 10.1039/d3sm01741a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Bicontinuous microemulsions (BMEs), self-assembly systems consisting of oil and water nanodomains separated by surfactant monolayers, have many applications. However, changes in structure and properties of BMEs in the vertical direction can affect BMEs' utility. This study's objective was to determine the effect of equilibration time (τeq) on structural changes in the vertical direction for bicontinuous phases of Winsor-III (WIII) systems in situ or after being isolated, for D2O + H2O/1-dodecane/sodium dodecyl sulfate (SDS)/1-pentanol/NaCl at 22 °C. Small-angle neutron scattering (SANS) measurements were performed using a vertical stage sample environment that precisely aligned samples in the neutron beam. SANS data were fitted by the Teubner-Strey (TS) model and changes in TS-derived parameter values were observed. For 10 min ≤ τeq ≤ 4 h, the effective activity of the bicontinuous phase's surfactant monolayers increased with time at all vertical positions. At short equilibration (τeq = 10 min), small but significant amounts of water and oil were transiently emulsified near the WIII upper liquid-liquid interface. WIII systems underwent a relaxation process after being transferred to narrow 1 mm pathlength cells, resulting in a decrease of surfactant activity for the top half of the bicontinuous phase. For isolated bicontinuous phases, results suggest that SDS was desorbed from the BMEs by quartz near the bottom, while near the top, the water concentration near was relatively high. The results suggest that WIII systems should equilibrate for at least 4 hours after being prepared and transferred to a container that differs in cross sectional area and surfactant behavior in BMEs can change near interfaces.
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Affiliation(s)
- Douglas G Hayes
- Department of Biosystems Engineering and Soil Science, University of Tennessee, 2506 E.J. Chapman Drive, Knoxville, TN 37996-4531, USA.
| | - Brian A Barth
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr, Knoxville, TN 37996, USA.
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4
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Joseph N, Mirzamani M, Abudiyah T, Al-Antaki AHM, Jellicoe M, Harvey DP, Crawley E, Chuah C, Whitten AE, Gilbert EP, Qian S, He L, Michael MZ, Kumari H, Raston CL. Vortex fluidic regulated phospholipid equilibria involving liposomes down to sub-micelle size assemblies. NANOSCALE ADVANCES 2024; 6:1202-1212. [PMID: 38356632 PMCID: PMC10863723 DOI: 10.1039/d3na01080e] [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: 12/06/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
Conventional channel-based microfluidic platforms have gained prominence in controlling the bottom-up formation of phospholipid based nanostructures including liposomes. However, there are challenges in the production of liposomes from rapidly scalable processes. These have been overcome using a vortex fluidic device (VFD), which is a thin film microfluidic platform rather than channel-based, affording ∼110 nm diameter liposomes. The high yielding and high throughput continuous flow process has a 45° tilted rapidly rotating glass tube with an inner hydrophobic surface. Processing is also possible in the confined mode of operation which is effective for labelling pre-VFD-prepared liposomes with fluorophore tags for subsequent mechanistic studies on the fate of liposomes under shear stress in the VFD. In situ small-angle neutron scattering (SANS) established the co-existence of liposomes ∼110 nm with small rafts, micelles, distorted micelles, or sub-micelle size assemblies of phospholipid, for increasing rotation speeds. The equilibria between these smaller entities and ∼110 nm liposomes for a specific rotational speed of the tube is consistent with the spatial arrangement and dimensionality of topological fluid flow regimes in the VFD. The prevalence for the formation of ∼110 nm diameter liposomes establishes that this is typically the most stable structure from the bottom-up self-assembly of the phospholipid and is in accord with dimensions of exosomes.
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Affiliation(s)
- Nikita Joseph
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
| | - Marzieh Mirzamani
- James L. Winkle College of Pharmacy, University of Cincinnati Cincinnati OH 45267-0004 USA
| | - Tarfah Abudiyah
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
| | - Ahmed Hussein Mohammed Al-Antaki
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
- Department of Chemistry, Faculty of Science, University of Kufa Najaf 54001 Iraq
| | - Matt Jellicoe
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
| | - David P Harvey
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
| | - Emily Crawley
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
| | - Clarence Chuah
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation (ANSTO) Lucas Heights NSW 2234 Australia
| | - Elliot Paul Gilbert
- Australian Nuclear Science and Technology Organisation (ANSTO) Lucas Heights NSW 2234 Australia
| | - Shuo Qian
- The Second Target Station Project of SNS, Oak Ridge National Laboratory Oak Ridge TN 37830 USA
| | - Lilin He
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37830 USA
| | - Michael Z Michael
- Flinders Centre for Innovation in Cancer (FCIC), Flinders Medical Centre (FMC) Bedford Park SA 5042 Australia
| | - Harshita Kumari
- James L. Winkle College of Pharmacy, University of Cincinnati Cincinnati OH 45267-0004 USA
| | - Colin L Raston
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University Bedford Park SA 5042 Australia
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5
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Thelen JL, Leite W, Urban VS, O'Neill HM, Grishaev AV, Curtis JE, Krueger S, Castellanos MM. Morphological Characterization of Self-Amplifying mRNA Lipid Nanoparticles. ACS NANO 2024; 18:1464-1476. [PMID: 38175970 DOI: 10.1021/acsnano.3c08014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The mRNA technology has emerged as a rapid modality to develop vaccines during pandemic situations with the potential to protect against endemic diseases. The success of mRNA in producing an antigen is dependent on the ability to deliver mRNA to the cells using a vehicle, which typically consists of a lipid nanoparticle (LNP). Self-amplifying mRNA (SAM) is a synthetic mRNA platform that, besides encoding for the antigen of interest, includes the replication machinery for mRNA amplification in the cells. Thus, SAM can generate many antigen encoding mRNA copies and prolong expression of the antigen with lower doses than those required for conventional mRNA. This work describes the morphology of LNPs containing encapsulated SAM (SAM LNPs), with SAM being three to four times larger than conventional mRNA. We show evidence that SAM changes its conformational structure when encapsulated in LNPs, becoming more compact than the free SAM form. A characteristic "bleb" structure is observed in SAM LNPs, which consists of a lipid-rich core and an aqueous RNA-rich core, both surrounded by a DSPC-rich lipid shell. We used SANS and SAXS data to confirm that the prevalent morphology of the LNP consists of two-core compartments where components are heterogeneously distributed between the two cores and the shell. A capped cylinder core-shell model with two interior compartments was built to capture the overall morphology of the LNP. These findings provide evidence that bleb two-compartment structures can be a representative morphology in SAM LNPs and highlight the need for additional studies that elucidate the role of spherical and bleb morphologies, their mechanisms of formation, and the parameters that lead to a particular morphology for a rational design of LNPs for mRNA delivery.
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Affiliation(s)
- Jacob L Thelen
- GSK, Rockville Center for Vaccines Research, 14200 Shady Grove Road, Rockville, Maryland 20850, United States
| | - Wellington Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Alexander V Grishaev
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Maria Monica Castellanos
- GSK, Rockville Center for Vaccines Research, 14200 Shady Grove Road, Rockville, Maryland 20850, United States
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6
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Keller MJ, Zhang Q, Qian S, Sanders BC, O'Neill HM, Hettich RL. Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization. Anal Chem 2024; 96:212-219. [PMID: 38150504 DOI: 10.1021/acs.analchem.3c03750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.
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Affiliation(s)
- Matthew J Keller
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- The Second Target Station Project of SNS, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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7
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Donnelly RB, Pingali SV, Heroux L, Brinson RG, Wagner NJ, Liu Y. Hydrogen-Deuterium Exchange Dynamics of NISTmAb Measured by Small Angle Neutron Scattering. Mol Pharm 2023; 20:6358-6367. [PMID: 37961914 DOI: 10.1021/acs.molpharmaceut.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Understanding protein dynamics and conformational stability holds great significance in biopharmaceutical research. Hydrogen-deuterium exchange (HDX) is a quantitative methodology used to examine these fundamental properties of proteins. HDX involves measuring the exchange of solvent-accessible hydrogens with deuterium, which yields valuable insights into conformational fluctuations and conformational stability. While mass spectrometry is commonly used to measure HDX on the peptide level, we explore a different approach using small-angle neutron scattering (SANS). In this work, SANS is demonstrated as a complementary and noninvasive HDX method (HDX-SANS). By assessing subtle changes in the tertiary and quaternary structure during the exchange process in deuterated buffer, along with the influence of added electrolytes on protein stability, SANS is validated as a complementary HDX technique. The HDX of a model therapeutic antibody, NISTmAb, an IgG1κ, is monitored by HDX-SANS over many hours using several different formulations, including salts from the Hofmeister series of anions, such as sodium perchlorate, sodium thiocyanate, and sodium sulfate. The impact of these formulation conditions on the thermal stability of NISTmAb is probed by differential scanning calorimetry. The more destabilizing salts led to heightened conformational dynamics in mAb solutions even at temperatures significantly below the denaturation point. HDX-SANS is demonstrated as a sensitive and noninvasive technique for quantifying HDX kinetics directly in mAb solution, providing novel information about mAb conformational fluctuations. Therefore, HDX-SANS holds promise as a potential tool for assessing protein stability in formulation.
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Affiliation(s)
- Róisín B Donnelly
- Department of Biomedical Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Luke Heroux
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland 20850, United States
| | - Norman J Wagner
- Department of Biomedical Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Yun Liu
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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8
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Larison T, Pingali SV, Stefik M. New approach for SANS measurement of micelle chain mixing during size and morphology transitions. SOFT MATTER 2023; 19:3487-3495. [PMID: 37133391 DOI: 10.1039/d3sm00157a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chain exchange in amphiphilic block polymer micelles is measurable with time-resolved small-angle neutron scattering (TR-SANS) where contrast-matched conditions reveal chain mixing as reduced intensity. However, analyzing chain mixing on short time scales e.g. during micelle transformations remains challenging. SANS model fitting can quantify chain mixing during size and morphology changes, however short acquisition times lead to lower data statistics (higher error). Such data are unsuitable for form factor fitting, especially with polydisperse and/or multimodal scenarios. An integrated-reference approach, R(t), is compatible with such data by using fixed reference patterns for the unmixed and fully mixed states that are each integrated to improve data statistics (lower error). Although the R(t) approach is tolerant of low data statistics, it remains incompatible with size and morphology changes. A new shifting references relaxation approach, SRR(t), is proposed where reference patterns are acquired at each time point to enable mixed state calculations regardless of short acquisition times. The additional experimental measurements needed are described which provide these time-varying reference patterns. The use of reference patterns makes the SRR(t) approach size/morphology-agnostic, allowing for the extent of micelle mixing to be directly calculated without this knowledge. SRR(t) is thus compatible with arbitrary levels of complexity and can provide accurate assessment of the mixed state which could support future model analysis. Calculated scattering datasets were used to demonstrate the SRR(t) approach during multiple size, morphology, and solvent conditions (scenarios 1-3). The mixed state calculated from the SRR(t) approach is shown to be accurate for all three scenarios.
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Affiliation(s)
- Taylor Larison
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Morgan Stefik
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
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9
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Gurumoorthy V, Shrestha UR, Zhang Q, Pingali SV, Boder ET, Urban VS, Smith JC, Petridis L, O'Neill H. Disordered Domain Shifts the Conformational Ensemble of the Folded Regulatory Domain of the Multidomain Oncoprotein c-Src. Biomacromolecules 2023; 24:714-723. [PMID: 36692364 DOI: 10.1021/acs.biomac.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
c-Src kinase is a multidomain non-receptor tyrosine kinase that aberrantly phosphorylates several signaling proteins in cancers. Although the structural properties of the regulatory domains (SH3-SH2) and the catalytic kinase domain have been extensively characterized, there is less knowledge about the N-terminal disordered region (SH4UD) and its interactions with the other c-Src domains. Here, we used domain-selective isotopic labeling combined with the small-angle neutron scattering contrast matching technique to study SH4UD interactions with SH3-SH2. Our results show that in the presence of SH4UD, the radius of gyration (Rg) of SH3-SH2 increases, indicating that it has a more extended conformation. Hamiltonian replica exchange molecular dynamics simulations provide a detailed molecular description of the structural changes in SH4UD-SH3-SH2 and show that the regulatory loops of SH3 undergo significant conformational changes in the presence of SH4UD, while SH2 remains largely unchanged. Overall, this study highlights how a disordered region can drive a folded region of a multidomain protein to become flexible, which may be important for allosteric interactions with binding partners. This may help in the design of therapeutic interventions that target the regulatory domains of this important family of kinases.
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Affiliation(s)
- Viswanathan Gurumoorthy
- UT/ORNL Graduate School of Genome and Science Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Utsab R Shrestha
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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10
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Kangarlou B, Hoy D, Scott HL, Pingali SV, Khalil N, Chung B, Katsaras J, Nieh MP. Water Content in Nanoparticles Determined by Small-Angle Neutron Scattering and Light Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:227-235. [PMID: 36580910 DOI: 10.1021/acs.langmuir.2c02420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The amount of water in therapeutic nanoparticles (NPs) is of great importance to the pharmaceutical industry, as water content reflects the volume occupied by the solid components. For example, certain biomolecules, such as mRNA, can undergo conformational change or degradation when exposed to water. Using static light scattering (SLS) and dynamic light scattering (DLS), we estimated the water content of NPs, including extruded liposomes of two different sizes and polystyrene (PS) Latex NPs. In addition, we used small-angle neutron scattering (SANS) to independently access the water content of the samples. The water content of NPs estimated by SLS/DLS was systematically higher than that from SANS. The discrepancy is most likely attributed to the larger radius determined by DLS, in contrast to the SANS-derived radius observed by SANS. However, because of low accessibility to the neutron facilities, we validate the combined SLS/DLS to be a reasonable alternative to SANS for determining the water (or solvent) content of NPs.
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Affiliation(s)
- Behrad Kangarlou
- Materials Science Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut06269, United States
| | - Donyeil Hoy
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut06269, United States
| | - Haden L Scott
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Nora Khalil
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut06269, United States
| | - Benjamin Chung
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut06269, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Mu-Ping Nieh
- Materials Science Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut06269, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut06269, United States
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut06269, United States
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut06269, United States
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11
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Leite WC, Wu Y, Pingali SV, Lieberman RL, Urban VS. Change in Morphology of Dimyristoylphosphatidylcholine/Bile Salt Derivative Bicelle Assemblies with Dodecylmaltoside in the Disk and Ribbon Phases. J Phys Chem Lett 2022; 13:9834-9840. [PMID: 36250687 DOI: 10.1021/acs.jpclett.2c02445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bicelles, composed of a mixture of long and short chain lipids, form nanostructured molecular assemblies that are attractive lipid-membrane mimics for in vitro studies of integral membrane proteins. Here we study the effect of a third component, the single chain detergent n-dodecyl-β-d-maltoside (DDM) on the morphology of bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) below (10 °C) and above (38 °C) the phase transition. In the absence of DDM, bicelles convert from ellipsoidal disks at 10 °C to extended ribbon-like structures at 38 °C. The addition of DDM reshapes the ellipsoidal disc to a circular one and the flattened ribbon to a circular-cylinder worm-like micelle. Knowledge of the influence of the single chain detergent DDM on bicelle nanoscale morphology contributes toward comprehending lipid membrane self-organization and to the goal of optimizing lipid mimics for membrane biology research.
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Affiliation(s)
- Wellington C Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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12
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How neutron scattering techniques benefit investigating structures and dynamics of monoclonal antibody. Biochim Biophys Acta Gen Subj 2022; 1866:130206. [PMID: 35872327 DOI: 10.1016/j.bbagen.2022.130206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022]
Abstract
Over the past several decades, great progresses have been made for the pharmaceutical industry of monoclonal antibody (mAb). More and more mAb products were approved for human therapeutics. This review describes the state of art of utilizing neutron scattering to investigate mAbs, in the aspects of structures, dynamics, physicochemical stability, functionality, etc. Firstly, brief histories of mAbs and neutron scattering, as well as some basic knowledges and principles of neutron scattering were introduced. Then specific examples were demonstrated. For the structure and structural evolution investigation of in dilute and concentrated mAbs solution, in situ small angle neutron scattering (SANS) was frequently utilized. Neutron reflectometry (NR) is powerful to probe the absorption behaviors of mAbs on various surfaces and interfaces. While for dynamic investigation, quasi-elastic scattering techniques such as neutron spin echo (NSE) demonstrate the capabilities. With this review, how to utilize and take advantages of neutron scattering on investigating structures and dynamics of mAbs were demonstrated and discussed.
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13
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Qian S, Heller W, Chen WR, Christianson A, Do C, Wang Y, Lin JYY, Huegle T, Jiang C, Boone C, Hart C, Graves V. CENTAUR-The small- and wide-angle neutron scattering diffractometer/spectrometer for the Second Target Station of the Spallation Neutron Source. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:075104. [PMID: 35922314 DOI: 10.1063/5.0090527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
CENTAUR has been selected as one of the eight initial instruments to be built at the Second Target Station (STS) of the Spallation Neutron Source at Oak Ridge National Laboratory. It is a small-angle neutron scattering (SANS) and wide-angle neutron scattering (WANS) instrument with diffraction and spectroscopic capabilities. This instrument will maximally leverage the high brightness of the STS source, the state-of-the-art neutron optics, and a suite of detectors to deliver unprecedented capabilities that enable measurements over a wide range of length scales with excellent resolution, measurements on smaller samples, and time-resolved investigations of evolving structures. Notably, the simultaneous WANS and diffraction capability will be unique among neutron scattering instruments in the United States. This instrument will provide much needed capabilities for soft matter and polymer sciences, geology, biology, quantum condensed matter, and other materials sciences that need in situ and operando experiments for kinetic and/or out-of-equilibrium studies. Beam polarization and a high-resolution chopper will enable detailed structural and dynamical investigations of magnetic and quantum materials. CENTAUR's excellent resolution makes it ideal for low-angle diffraction studies of highly ordered large-scale structures, such as skyrmions, shear-induced ordering in colloids, and biomembranes. Additionally, the spectroscopic mode of this instrument extends to lower momentum transfers than are currently possible with existing spectrometers, thereby providing a unique capability for inelastic SANS studies.
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Affiliation(s)
- Shuo Qian
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - William Heller
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Wei-Ren Chen
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | | | - Changwoo Do
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Yangyang Wang
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Jiao Y Y Lin
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Thomas Huegle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Chenyang Jiang
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Cristina Boone
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Cameron Hart
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Van Graves
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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14
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Copp SM, Hamblin RL, Swingle K, Rai D, Urban VS, Ivanov SA, Montaño GA. Complex pH-Dependent Interactions between Weak Polyelectrolyte Block Copolymer Micelles and Molecular Fluorophores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2038-2045. [PMID: 35119286 DOI: 10.1021/acs.langmuir.1c02889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amphiphilic block copolymers with weak polyelectrolyte blocks can assemble stimulus-responsive nanostructures and interfaces. Applications of these materials in drug delivery, biomimetics, and sensing largely rely on the well-understood swelling of polyelectrolyte chains upon deprotonation, often induced by changes in pH or ionic strength. This deprotonation can also tune interfacial interactions between the polyelectrolyte blocks and surrounding solution, an effect which is less studied than morphological swelling of polyelectrolytes but can be just as critical for intended function. Here, we investigate whether the pH-driven morphological response of polyelectrolyte-bearing nanostructures also affects the interactions of these nanostructures with molecules in solution, using micelles of a short-chain polybutadiene-block-poly(acrylic acid) (pBd-pAA) as a model system. We introduce a Förster resonance energy transfer (FRET) approach to probe interactions between micelles and fluorescent molecular solutes as a function of solution pH. As expected, the pAA corona of these pBd-pAA micelles increases in thickness monotonically as a function of pH. However, FRET efficiency, which provides a metric of the spatial proximity of fluorescently labeled micelles and freely diffusing fluorophores, exhibits complex nonmonotonic behavior as a function of pH, indicating that the average separation of micelles and acceptor fluorophores is not strictly correlated with micelle swelling. Dialysis experiments quantify the affinity of fluorophores for micelles as a function of pH, confirming that changes in FRET are driven almost entirely by the pH-dependent affinity of the pAA block for the investigated molecular fluorophores, not simply by a shape change of the pAA corona. This study provides key insights into the interfacial interactions between weak-polyelectrolyte-bearing nanostructures and molecular solutes, of importance for the development of their stimulus-responsive applications.
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Affiliation(s)
- Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2585, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697-4575, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-2580, United States
| | - Ryan L Hamblin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
| | - Kirstie Swingle
- Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
| | - Durgesh Rai
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sergei A Ivanov
- Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
| | - Gabriel A Montaño
- Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, Arizona 86011, United States
- Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, Arizona 86011, United States
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15
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Qian S, Zolnierczuk PA. Interaction of a Short Antimicrobial Peptide on Charged Lipid Bilayer: A Case Study on Aurein 1.2 Peptide. BBA ADVANCES 2022; 2:100045. [PMID: 37082600 PMCID: PMC10074906 DOI: 10.1016/j.bbadva.2022.100045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 12/27/2022] Open
Abstract
Aurein 1.2 (aurein) is a short but active α-helical antimicrobial peptide discovered in Australian tree frogs (Litoria aurea). It shows inhibition on a broad spectrum of bacteria and cancer cells. With well-defined helicity, amphipathicity, and cationic charges, it readily binds to membranes and causes membrane change and disruption. This study provides details on how aurein interacts with charged lipid membranes by using neutron membrane diffraction (NMD) and neutron spin echo (NSE) spectroscopy on complex peptide-membrane systems. NMD provides higher resolution lipid bilayer structures than solution scattering. NMD revealed the peptide is mostly associated in the lipid headgroup region. Even at moderately high concentrations (e.g., peptide:lipid ratio of 1:30), aurein is located at the acyl chain-headgroup region without deep penetration into the hydrophobic acyl chain. However, it does reduce the elasticity of the membrane at that concentration, which was corroborated by the NSE results. Furthermore, NSE shows that aurein first softens the membrane, like many other α-helical peptides at low concentration, but then makes the membrane much more rigid, even without membrane pore formation. Combining our previous studies, the evidence shows that aurein at relatively low concentrations still modifies lipid distribution significantly and can cause membrane thinning and lateral segregation of charged lipids. At the same time, the membrane's mechanical properties are modified with much slower lipid diffusion. This suggests that aurein can attack the microbial membrane without the need to form membrane pores or disintegrate membranes; instead, it promotes the formation of domains at low concentration.
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Affiliation(s)
- Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
- Corresponding author.
| | - Piotr A. Zolnierczuk
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
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16
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Martel A, Gabel F. Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines. Methods Enzymol 2022; 677:263-290. [DOI: 10.1016/bs.mie.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Incorporation of Membrane Proteins Into Bicontinuous Microemulsions Through
Winsor‐III System‐Based
Extraction. J SURFACTANTS DETERG 2021. [DOI: 10.1002/jsde.12500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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18
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Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication. Biophys J 2021; 120:3152-3165. [PMID: 34197805 PMCID: PMC8238635 DOI: 10.1016/j.bpj.2021.06.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/27/2021] [Accepted: 06/04/2021] [Indexed: 01/18/2023] Open
Abstract
The replication transcription complex (RTC) from the virus SARS-CoV-2 is responsible for recognizing and processing RNA for two principal purposes. The RTC copies viral RNA for propagation into new virus and for ribosomal transcription of viral proteins. To accomplish these activities, the RTC mechanism must also conform to a large number of imperatives, including RNA over DNA base recognition, basepairing, distinguishing viral and host RNA, production of mRNA that conforms to host ribosome conventions, interfacing with error checking machinery, and evading host immune responses. In addition, the RTC will discontinuously transcribe specific sections of viral RNA to amplify certain proteins over others. Central to SARS-CoV-2 viability, the RTC is therefore dynamic and sophisticated. We have conducted a systematic structural investigation of three components that make up the RTC: Nsp7, Nsp8, and Nsp12 (also known as RNA-dependent RNA polymerase). We have solved high-resolution crystal structures of the Nsp7/8 complex, providing insight into the interaction between the proteins. We have used small-angle x-ray and neutron solution scattering (SAXS and SANS) on each component individually as pairs and higher-order complexes and with and without RNA. Using size exclusion chromatography and multiangle light scattering-coupled SAXS, we defined which combination of components forms transient or stable complexes. We used contrast-matching to mask specific complex-forming components to test whether components change conformation upon complexation. Altogether, we find that individual Nsp7, Nsp8, and Nsp12 structures vary based on whether other proteins in their complex are present. Combining our crystal structure, atomic coordinates reported elsewhere, SAXS, SANS, and other biophysical techniques, we provide greater insight into the RTC assembly, mechanism, and potential avenues for disruption of the complex and its functions.
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19
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Leite W, Weiss KL, Phillips G, Zhang Q, Qian S, Tsutakawa SE, Coates L, O’Neill H. Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein. J Phys Chem Lett 2021; 12:5608-5615. [PMID: 34110168 PMCID: PMC8204754 DOI: 10.1021/acs.jpclett.1c00831] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
Papain-like protease (PLpro) from SARS-CoV-2 plays essential roles in the replication cycle of the virus. In particular, it preferentially interacts with and cleaves human interferon-stimulated gene 15 (hISG15) to suppress the innate immune response of the host. We used small-angle X-ray and neutron scattering combined with computational techniques to study the mechanism of interaction of SARS-CoV-2 PLpro with hISG15. We showed that hISG15 undergoes a transition from an extended to a compact state after binding to PLpro, a conformation that has not been previously observed in complexes of SARS-CoV-2 PLpro with ISG15 from other species. Furthermore, computational analysis showed significant conformational flexibility in the ISG15 N-terminal domain, suggesting that it is weakly bound to PLpro and supports a binding mechanism that is dominated by the C-terminal ISG15 domain. This study fundamentally improves our understanding of the SARS-CoV-2 deISGylation complex that will help guide development of COVID-19 therapeutics targeting this complex.
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Affiliation(s)
- Wellington
C. Leite
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Kevin L. Weiss
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Gwyndalyn Phillips
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Shuo Qian
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Susan E. Tsutakawa
- Molecular
Biophysics and Integrated Bioimaging, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leighton Coates
- Second
Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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20
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Chen P, Li Y, Nishiyama Y, Pingali SV, O’Neill HM, Zhang Q, Berglund LA. Small Angle Neutron Scattering Shows Nanoscale PMMA Distribution in Transparent Wood Biocomposites. NANO LETTERS 2021; 21:2883-2890. [PMID: 33734720 PMCID: PMC8050824 DOI: 10.1021/acs.nanolett.0c05038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/08/2021] [Indexed: 05/25/2023]
Abstract
Transparent wood biocomposites based on PMMA combine high optical transmittance with excellent mechanical properties. One hypothesis is that despite poor miscibility the polymer is distributed at the nanoscale inside the cell wall. Small-angle neutron scattering (SANS) experiments are performed to test this hypothesis, using biocomposites based on deuterated PMMA and "contrast-matched" PMMA. The wood cell wall nanostructure soaked in heavy water is quantified in terms of the correlation distance d between the center of elementary cellulose fibrils. For wood/deuterated PMMA, this distance d is very similar as for wood/heavy water (correlation peaks at q ≈ 0.1 Å-1). The peak disappears when contrast-matched PMMA is used, indeed proving nanoscale polymer distribution in the cell wall. The specific processing method used for transparent wood explains the nanocomposite nature of the wood cell wall and can serve as a nanotechnology for cell wall impregnation of polymers in large wood biocomposite structures.
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Affiliation(s)
- Pan Chen
- Beijing
Engineering Research Centre of Cellulose and Its Derivatives, School
of Materials Science and Engineering, Beijing
Institute of Technology, 100081, Beijing, P.R. China
| | - Yuanyuan Li
- Department
of Fibre and Polymer Technology, Wallenberg Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56, 10044 Stockholm, Sweden
| | | | - Sai Venkatesh Pingali
- Neutron
Scattering Division and Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh M. O’Neill
- Neutron
Scattering Division and Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron
Scattering Division and Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Lars A. Berglund
- Department
of Fibre and Polymer Technology, Wallenberg Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56, 10044 Stockholm, Sweden
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21
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Yuan Y, Li H, Leite W, Zhang Q, Bonnesen PV, Labbé JL, Weiss KL, Pingali SV, Hong K, Urban VS, Salmon S, O'Neill H. Biosynthesis and characterization of deuterated chitosan in filamentous fungus and yeast. Carbohydr Polym 2021; 257:117637. [PMID: 33541662 DOI: 10.1016/j.carbpol.2021.117637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/29/2020] [Accepted: 01/09/2021] [Indexed: 10/22/2022]
Abstract
Deuterated chitosan was produced from the filamentous fungus Rhizopus oryzae, cultivated with deuterated glucose in H2O medium, without the need for conventional chemical deacetylation. After extraction and purification, the chemical composition and structure were determined by Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and small-angle neutron scattering (SANS). 13C NMR experiments provided additional information about the position of the deuterons in the glucoseamine backbone. The NMR spectra indicated that the deuterium incorporation at the non-exchangeable hydrogen positions of the aminoglucopyranosyl ring in the C3 - C5 positions was at least 60-80 %. However, the C2 position was deuterated at a much lower level (6%). Also, SANS showed that the structure of deuterated chitosan was very similar compared to the non-deuterated counterpart. The most abundant radii of the protiated and deuterated chitosan fibers were 54 Å and 60 Å, respectively, but there is a broader distribution of fiber radii in the protiated chitosan sample. The highly deuterated, soluble fungal chitosan described here can be used as a model material for studying chitosan-enzyme complexes for future neutron scattering studies. Because the physical behavior of non-deuterated fungal chitosan mimicked that of shrimp shell chitosan, the methods presented here represent a new approach to producing a high quality deuterated non-animal-derived aminopolysaccharide for studying the structure-function association of biocomposite materials in drug delivery, tissue engineering and other bioactive chitosan-based composites.
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Affiliation(s)
- Yue Yuan
- Department of Textile Engineering, Chemistry and Science, Wilson College of Textiles, North Carolina State University, Raleigh, NC, 27606, USA
| | - Hui Li
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Leite
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Qiu Zhang
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Peter V Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jessy L Labbé
- Fungal Systems Genetics and Biology Lab, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sai Venkatesh Pingali
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kunlun Hong
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Volker S Urban
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sonja Salmon
- Department of Textile Engineering, Chemistry and Science, Wilson College of Textiles, North Carolina State University, Raleigh, NC, 27606, USA.
| | - Hugh O'Neill
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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22
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Gupta K, Allen A, Giraldo C, Eilers G, Sharp R, Hwang Y, Murali H, Cruz K, Janmey P, Bushman F, Van Duyne GD. Allosteric HIV Integrase Inhibitors Promote Formation of Inactive Branched Polymers via Homomeric Carboxy-Terminal Domain Interactions. Structure 2021; 29:213-225.e5. [PMID: 33357410 PMCID: PMC7935764 DOI: 10.1016/j.str.2020.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/04/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
The major effect of allosteric HIV integrase (IN) inhibitors (ALLINIs) is observed during virion maturation, where ALLINI treatment interrupts IN-RNA interactions via drug-induced IN aggregation, leading to the formation of aberrant virions. To understand the structural changes that accompany drug-induced aggregation, we determined the soft matter properties of ALLINI-induced IN aggregates. Using small-angle neutron scattering, SEM, and rheology, we have discovered that the higher-order aggregates induced by ALLINIs have the characteristics of weak three-dimensional gels with a fractal-like character. Their formation is inhibited by the host factor LEDGF/p75, as well as ex vivo resistance substitutions. Mutagenesis and biophysical analyses reveal that homomeric carboxy-terminal domain interactions are required to achieve the branched-polymer nature of the ALLINI-induced aggregates. These studies provide key insight into the mechanisms of ALLINI action and resistance in the context of the crowded virion environment where ALLINIs exert their effect.
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 809C Stellar-Chance Building, 422 Curie Boulevard, Philadelphia, PA 19105-6059, USA
| | - Audrey Allen
- Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
| | - Carolina Giraldo
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 809C Stellar-Chance Building, 422 Curie Boulevard, Philadelphia, PA 19105-6059, USA
| | - Grant Eilers
- Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
| | - Robert Sharp
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 809C Stellar-Chance Building, 422 Curie Boulevard, Philadelphia, PA 19105-6059, USA
| | - Young Hwang
- Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
| | - Hemma Murali
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 809C Stellar-Chance Building, 422 Curie Boulevard, Philadelphia, PA 19105-6059, USA
| | - Katrina Cruz
- Department of Physiology, and Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104-6383, USA
| | - Paul Janmey
- Department of Physiology, and Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104-6383, USA
| | - Frederic Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA.
| | - Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 809C Stellar-Chance Building, 422 Curie Boulevard, Philadelphia, PA 19105-6059, USA.
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23
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Rai DK, Gillilan RE, Huang Q, Miller R, Ting E, Lazarev A, Tate MW, Gruner SM. High-pressure small-angle X-ray scattering cell for biological solutions and soft materials. J Appl Crystallogr 2021; 54:111-122. [PMID: 33841059 PMCID: PMC7941318 DOI: 10.1107/s1600576720014752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
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Affiliation(s)
- Durgesh K. Rai
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Robert Miller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Edmund Ting
- Pressure BioSciences Inc., South Easton, MA 02375, USA
| | | | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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De Mel JU, Gupta S, Perera RM, Ngo L, Zolnierczuk P, Bleuel M, Pingali SV, Schneider GJ. Influence of External NaCl Salt on Membrane Rigidity of Neutral DOPC Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9356-9367. [PMID: 32672981 DOI: 10.1021/acs.langmuir.0c01004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sodium chloride (NaCl) is a very common molecule in biotic and abiotic aqueous environments. In both cases, variation of ionic strength is inevitable. In addition to the osmotic variation posed by such perturbations, the question of whether the interactions of monovalent ions Na+ and Cl-, especially with the neutral head groups of phospholipid membranes are impactful enough to change the membrane rigidity, is still not entirely understood. We investigated the dynamics of 1,2-di-(octadecenoyl)-sn-glycero-3-phosphocholine (DOPC) vesicles with zwitterionic neutral head groups in the fluid phase with increasing external salt concentration. At higher salt concentrations, we observe an increase in bending rigidity from neutron spin echo (NSE) spectroscopy and an increase in bilayer thickness from small-angle X-ray scattering (SAXS). We compared different models to distinguish membrane undulations, lipid tail motions, and the translational diffusion of the vesicles. All of the models indicate an increase in bending rigidity by a factor of 1.3-3.6. We demonstrate that even down to t > 10 ns and for Q > 0.07 Å-1, the observed NSE relaxation spectra are influenced by translational diffusion of the vesicles. For t < 5 ns, the lipid tail motion dominates the intermediate dynamic structure factor. As the salt concentration increases, this contribution diminishes. We introduced a time-dependent analysis for the bending rigidity that highlights only a limited Zilman-Granek time window in which the rigidity is physically meaningful.
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Affiliation(s)
- Judith U De Mel
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sudipta Gupta
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Rasangi M Perera
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Ly Ngo
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Piotr Zolnierczuk
- Jülich Centre for Neutron Science (JCNS), Outstation at SNS, POB 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Markus Bleuel
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, United States
| | - Sai Venkatesh Pingali
- Neutron Sciences Directorate, Oak Ridge National Laboratory (ORNL), POB 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Gerald J Schneider
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Department of Physics & Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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25
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Smith CJ, Wagle DV, Bhawawet N, Gehrke S, Hollóczki O, Pingali SV, O’Neill H, Baker GA. Combined Small-Angle Neutron Scattering, Diffusion NMR, and Molecular Dynamics Study of a Eutectogel: Illuminating the Dynamical Behavior of Glyceline Confined in Bacterial Cellulose Gels. J Phys Chem B 2020; 124:7647-7658. [DOI: 10.1021/acs.jpcb.0c04916] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chip J. Smith
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Durgesh V. Wagle
- Department of Chemistry and Physics, Florida Gulf Coast University, 10501 FGCU Boulevard, Fort Myers, Florida 33965, United States
| | - Nakara Bhawawet
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Sascha Gehrke
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4+6, Bonn 53115, Germany
| | - Oldamur Hollóczki
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4+6, Bonn 53115, Germany
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Gary A. Baker
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
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26
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Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces. Proc Natl Acad Sci U S A 2020; 117:16776-16781. [PMID: 32636260 PMCID: PMC7382264 DOI: 10.1073/pnas.1922883117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of plant biomass for the production of fuels and chemicals is of critical economic and environmental importance, but has posed a formidable challenge, due to the recalcitrance of biomass to deconstruction. We report direct experimental and computational evidence of a simple physical chemical principle that explains the success of mixing an organic cosolvent, tetrahydrofuran, with water to overcome this recalcitrance. The hydrophilic and hydrophobic biomass surfaces are solvated by single-component nanoclusters of complementary polarity. This principle can serve as a guide for designing even more effective technologies for solubilizing and fractionating biomass. The results further highlight the role of nanoscale fluctuations of molecular solvents in driving changes in the structure of the solutes. A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 °C) cellulose disruption occurs only above 150 °C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (Rg ∼ 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent water-rich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.
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Astner AF, Hayes DG, Pingali SV, O’Neill HM, Littrell KC, Evans BR, Urban VS. Effects of soil particles and convective transport on dispersion and aggregation of nanoplastics via small-angle neutron scattering (SANS) and ultra SANS (USANS). PLoS One 2020; 15:e0235893. [PMID: 32692771 PMCID: PMC7373282 DOI: 10.1371/journal.pone.0235893] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/24/2020] [Indexed: 11/18/2022] Open
Abstract
Terrestrial nanoplastics (NPs) pose a serious threat to agricultural food production systems due to the potential harm of soil-born micro- and macroorganisms that promote soil fertility and ability of NPs to adsorb onto and penetrate into vegetables and other crops. Very little is known about the dispersion, fate and transport of NPs in soils. This is because of the challenges of analyzing terrestrial NPs by conventional microscopic techniques due to the low concentrations of NPs and absence of optical transparency in these systems. Herein, we investigate the potential utility of small-angle neutron scattering (SANS) and Ultra SANS (USANS) to probe the agglomeration behavior of NPs prepared from polybutyrate adipate terephthalate, a prominent biodegradable plastic used in agricultural mulching, in the presence of vermiculite, an artificial soil. SANS with the contrast matching technique was used to study the aggregation of NPs co-dispersed with vermiculite in aqueous media. We determined the contrast match point for vermiculite was 66% D2O / 33% H2O. At this condition, the signal for vermiculite was ~50–100%-fold lower that obtained using neat H2O or D2O as solvent. According to SANS and USANS, smaller-sized NPs (50 nm) remained dispersed in water and did not undergo size reduction or self-agglomeration, nor formed agglomerates with vermiculite. Larger-sized NPs (300–1000 nm) formed self-agglomerates and agglomerates with vermiculite, demonstrating their significant adhesion with soil. However, employment of convective transport (simulated by ex situ stirring of the slurries prior to SANS and USANS analyses) reduced the self-agglomeration, demonstrating weak NP-NP interactions. Convective transport also led to size reduction of the larger-sized NPs. Therefore, this study demonstrates the potential utility of SANS and USANS with contrast matching technique for investigating behavior of terrestrial NPs in complex soil systems.
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Affiliation(s)
- Anton F. Astner
- Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Douglas G. Hayes
- Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (DGH); (SVP)
| | - Sai Venkatesh Pingali
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail: (DGH); (SVP)
| | - Hugh M. O’Neill
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Kenneth C. Littrell
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Barbara R. Evans
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Volker S. Urban
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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Mechanism of heat-induced gelation for ovalbumin under acidic conditions and the effect of peptides. Polym J 2020. [DOI: 10.1038/s41428-020-0382-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer. J Biol Chem 2020; 295:1105-1119. [PMID: 31836666 PMCID: PMC6983858 DOI: 10.1074/jbc.ra119.010934] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/10/2019] [Indexed: 12/28/2022] Open
Abstract
Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS-mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography-multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.
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Affiliation(s)
- Mukul Sherekar
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Sae-Won Han
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Puneet Juneja
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia 30322
| | - Hugh O'Neill
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | | | | | | | - Sriram Subramaniam
- Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
- Department of Biochemistry, Life Sciences Center, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
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30
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Meilleur F, Kovalevsky A, Myles DAA. IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor. Methods Enzymol 2020; 634:69-85. [PMID: 32093843 DOI: 10.1016/bs.mie.2019.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of <1mm3 and unit cell edges of <150Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0×3.2mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.
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Affiliation(s)
- Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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31
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Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49919-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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32
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Puster LO, Stanley CB, Uversky VN, Curtis JE, Krueger S, Chu Y, Peterson CB. Characterization of an Extensive Interface on Vitronectin for Binding to Plasminogen Activator Inhibitor-1: Adoption of Structure in an Intrinsically Disordered Region. Biochemistry 2019; 58:5117-5134. [PMID: 31793295 DOI: 10.1021/acs.biochem.9b00605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Small-angle neutron scattering (SANS) measurements were pursued to study human vitronectin, a protein found in tissues and the circulation that regulates cell adhesion/migration and proteolytic cascades that govern hemostasis and pericellular proteolysis. Many of these functions occur via interactions with its binding partner, plasminogen activator inhibitor-1 (PAI-1), the chief inhibitor of proteases that lyse and activate plasminogen. We focused on a region of vitronectin that remains uncharacterized from previous X-ray scattering, nuclear magnetic resonance, and computational modeling approaches and which we propose is involved in binding to PAI-1. This region, which bridges the N-terminal somatomedin B (SMB) domain with a large central β-propeller domain of vitronectin, appears unstructured and has characteristics of an intrinsically disordered domain (IDD). The effect of osmolytes was evaluated using circular dichroism and SANS to explore the potential of the IDD to undergo a disorder-to-order transition. The results suggest that the IDD favors a more ordered structure under osmotic pressure; SANS shows a smaller radius of gyration (Rg) and a more compact fold of the IDD upon addition of osmolytes. To test whether PAI-1 binding is also coupled to folding within the IDD structure, a set of SANS experiments with contrast variation were performed on the complex of PAI-1 with a vitronectin fragment corresponding to the N-terminal 130 amino acids (denoted the SMB-IDD because it contains the SMB domain and IDD in linear sequence). Analysis of the SANS data using the Ensemble Optimization Method confirms that the SMB-IDD adopts a more compact configuration when bound to PAI-1. Calculated structures for the PAI-1:SMB-IDD complex suggest that the IDD provides an interaction surface outside of the primary PAI-1-binding site located within the SMB domain; this binding is proposed to lead to the assembly of higher-order structures of vitronectin and PAI-1 commonly found in tissues.
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Affiliation(s)
- Letitia O Puster
- Department of Biochemistry and Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , United States.,Laboratory of New Methods in Biology , Institute for Biological Instrumentation, Russian Academy of Sciences , Pushchino , Moscow region 142290 , Russia
| | - Joseph E Curtis
- National Institute of Standards and Technology Center for Neutron Research , Gaithersburg , Maryland 20899 , United States
| | - Susan Krueger
- National Institute of Standards and Technology Center for Neutron Research , Gaithersburg , Maryland 20899 , United States
| | - Yuzhuo Chu
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Cynthia B Peterson
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
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Rai DK, Gurusaran M, Urban V, Aran K, Ma L, Li P, Qian S, Narayanan TN, Ajayan PM, Liepmann D, Sekar K, Álvarez-Cao ME, Escuder-Rodríguez JJ, Cerdán ME, González-Siso MI, Viswanathan S, Paulmurugan R, Renugopalakrishnan V. Structural determination of Enzyme-Graphene Nanocomposite Sensor Material. Sci Rep 2019; 9:15519. [PMID: 31664095 PMCID: PMC6820869 DOI: 10.1038/s41598-019-51882-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022] Open
Abstract
State-of-the-art ultra-sensitive blood glucose-monitoring biosensors, based on glucose oxidase (GOx) covalently linked to a single layer graphene (SLG), will be a valuable next generation diagnostic tool for personal glycemic level management. We report here our observations of sensor matrix structure obtained using a multi-physics approach towards analysis of small-angle neutron scattering (SANS) on graphene-based biosensor functionalized with GOx under different pH conditions for various hierarchical GOx assemblies within SLG. We developed a methodology to separately extract the average shape of GOx molecules within the hierarchical assemblies. The modeling is able to resolve differences in the average GOx dimer structure and shows that treatment under different pH conditions lead to differences within the GOx at the dimer contact region with SLG. The coupling of different analysis methods and modeling approaches we developed in this study provides a universal approach to obtain detailed structural quantifications, for establishing robust structure-property relationships. This is an essential step to obtain an insight into the structure and function of the GOx-SLG interface for optimizing sensor performance.
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Affiliation(s)
- Durgesh K Rai
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York, 14853, USA.
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne-NE1 7RU, UK
| | - Volker Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA.
| | - Kiana Aran
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94709, USA
| | - Lulu Ma
- Department of Mechanical Engineering and Materials Science, Rice University, Houston, Texas, 77005, USA
| | - Pingzuo Li
- Center for Life Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Tharangattu N Narayanan
- Tata Institute of Fundamental Research - Center for Interdisciplinary Sciences, Hyderabad, 500107, India
| | - Pulickel M Ajayan
- Department of Mechanical Engineering and Materials Science, Rice University, Houston, Texas, 77005, USA
| | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94709, USA
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - María-Efigenia Álvarez-Cao
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - Juan-José Escuder-Rodríguez
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - María-Esperanza Cerdán
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - María-Isabel González-Siso
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - Sowmya Viswanathan
- Newton Wellesley Hospital/Partners Healthcare System, Newton, Massachusetts, 02462, USA
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Dept. of Radiology, Stanford University School of Medicine, 3155 Porter Drive, Suite 2236, Palo Alto, California, 94304, USA
| | - Venkatesan Renugopalakrishnan
- Center for Life Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115, USA.
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Sharma VK, Nagao M, Rai DK, Mamontov E. Membrane softening by nonsteroidal anti-inflammatory drugs investigated by neutron spin echo. Phys Chem Chem Phys 2019; 21:20211-20218. [PMID: 31486459 DOI: 10.1039/c9cp03767e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In spite of their well-known side effects, the nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly prescribed medications for their antipyretic and anti-inflammatory actions. Interaction of NSAIDs with the plasma membrane plays a vital role in their therapeutic actions and defines many of their side effects. In the present study, we investigate the effects of three NSAIDs, aspirin, ibuprofen, and indomethacin, on the structure and dynamics of a model plasma membrane using a combination of small angle neutron scattering (SANS) and neutron spin echo (NSE) techniques. The SANS and NSE measurements were carried out on a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane, with and without NSAIDs, at two different temperatures, 11 °C and 37 °C, where the DMPC membrane is in the gel and fluid phase, respectively. SANS data analysis shows that incorporation of NSAIDs leads to bilayer thinning of the membrane in both the phases. The dynamic properties of the membrane are represented by the intermediate scattering functions for NSE data, which are successfully described by the Zilman and Granek model. NSE data analysis shows that in both gel and fluid phases, addition of NSAIDs results in a decrease in the bending rigidity and compressibility modulus of the membrane, which is more prominent when the membrane is in the gel phase. The magnitude of the effect of NSAIDs on the bending rigidity and compressibility modulus of the membrane in the gel phase follows an order of ibuprofen > aspirin > indomethacin, whereas in the fluid phase, it is in the order of aspirin > ibuprofen > indomethacin. We find that the interaction between NSAIDs and phospholipid membranes is strongly dependent on the chemical structure of the drugs and physical state of the membrane. Mechanical properties of the membrane can be quantified by the membrane's bending rigidity. Hence, the present study reveals that incorporation of NSAIDs modulates the mechanical properties of the membrane, which may affect several physiological processes, particularly those linked to the membrane curvature.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
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Garg S, Liu Y, Perez-Salas U, Porcar L, Butler PD. Anomalous inter-membrane cholesterol transport in fluid phase phosphoserine vesicles driven by headgroup ordered to disordered entropic transition. Chem Phys Lipids 2019; 223:104779. [PMID: 31153912 PMCID: PMC11132670 DOI: 10.1016/j.chemphyslip.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
Abstract
POPS is highly enriched in the inner leaflet of the plasma membrane. Here we present measurements of inter-membrane cholesterol transport rates in POPS vesicles. We find that the cholesterol transport kinetics are not only an order of magnitude slower than in POPC lipids at near physiological temperatures, they exhibit a surprising discontinuous Arrhenius behavior around 48 °C. Moreover, thermodynamic analysis suggests that for biologically relevant temperatures, below the discontinuity, the exchange of cholesterol is entropically dominated while it is enthalpically driven, as is the case in POPC vesicles, above that discontinuity. Using the polar fluorescent probe Laurdan we found that POPS fluid membranes retain a large degree of order in the headgroup region for temperatures below the discontinuity but undergo an order-to-disorder transition in the region coinciding with the discontinuity in the transport of cholesterol in POPS membranes providing an explanation not only for the discontinuity but for the entropic dominance at physiological temperatures.
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Affiliation(s)
- Sumit Garg
- Physics Department, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yangmingyue Liu
- Physics Department, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ursula Perez-Salas
- Physics Department, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Lionel Porcar
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Paul D Butler
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-6102, USA
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Influence of Chemically Disrupted Photosynthesis on Cyanobacterial Thylakoid Dynamics in Synechocystis sp. PCC 6803. Sci Rep 2019; 9:5711. [PMID: 30952892 PMCID: PMC6450941 DOI: 10.1038/s41598-019-42024-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022] Open
Abstract
The photosynthetic machinery of the cyanobacterium Synechocystis sp. PCC 6803 resides in flattened membrane sheets called thylakoids, situated in the peripheral part of the cellular cytoplasm. Under photosynthetic conditions these thylakoid membranes undergo various dynamical processes that could be coupled to their energetic functions. Using Neutron Spin Echo Spectroscopy (NSE), we have investigated the undulation dynamics of Synechocystis sp. PCC 6803 thylakoids under normal photosynthetic conditions and under chemical treatment with DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea), an herbicide that disrupts photosynthetic electron transfer. Our measurements show that DCMU treatment has a similar effect as dark conditions, with differences in the undulation modes of the untreated cells compared to the chemically inhibited cells. We found that the disrupted membranes are 1.5-fold more rigid than the native membranes during the dark cycle, while in light they relax approximately 1.7-fold faster than native and they are 1.87-fold more flexible. The strength of the herbicide disruption effect is characterized further by the damping frequency of the relaxation mode and the decay rate of the local shape fluctuations. In the dark, local thicknesses and shape fluctuations relax twice as fast in native membranes, at 17% smaller mode amplitude, while in light the decay rate of local fluctuations is 1.2-fold faster in inhibited membranes than in native membranes, at 56% higher amplitude. The disrupted electron transfer chain and the decreased proton motive force within the lumenal space partially explain the variations observed in the mechanical properties of the Synechocystis membranes, and further support the hypothesis that the photosynthetic process is tied to thylakoid rigidity in this type of cyanobacterial cell.
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Murthy NS, Wang W, Kamath Y. Structure of intermediate filament assembly in hair deduced from hydration studies using small-angle neutron scattering. J Struct Biol 2019; 206:295-304. [PMID: 30951823 DOI: 10.1016/j.jsb.2019.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 11/27/2022]
Abstract
Intermediate filaments (IFs) are ubiquitous in biological structures including hair. Small-angle neutron scattering (SANS) data from hydrated samples were used in this study to investigate the distribution of water in hair, and model the structure of the IF assembly. A main diffraction peak at a d-spacing of ∼90 Å, and two weaker reflections show that IFs are arranged in a ∼105 Å quasi-hexagonal lattice. Changes in the diffraction peaks show that only a small fraction of the water absorbed by hair enters between the IFs, and little water diffuses into the core of the IFs. The amount of water in the IF assembly increases rapidly up to 10% relative humidity (RH), and then slowly with further increase in RH. Most of the water appears to reside outside the IF assembly, in the voids and at the interfaces, and contribute to the central diffuse scattering. The IF assembly in the decuticled hair absorbs more water and is more ordered than that the native hair. This suggests that cuticle acts as a barrier, and might constrain the structure by compressing the cortex radially. Treatments with oils that are hydrophobic, heat treatment, and reduction of the S-S linkages that opens up the matrix by disulfide bond cleavage, all affect structure and water permeability. Coconut oil was found to impede hydration more than the soybean oil because of its ability to penetrate deeper into hair. A new model for the IF assembly that is sterically more favorable than the previous models is proposed.
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Affiliation(s)
- N Sanjeeva Murthy
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ 08854, USA.
| | - Wenjie Wang
- Ames Laboratory, Iowa State University, Ames, IA 50011, USA
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He L, Li C, Hamilton WA, Hong T, Tong X, Winn BL, Crow L, Bailey K, Gallego NC. Anomalous neutron scattering `halo' observed in highly oriented pyrolytic graphite. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719001110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Highly oriented pyrolytic graphite (HOPG) has been used as monochromators, analyzers and filters at neutron and X-ray scattering facilities for more than half a century. Interesting questions remain. In this work, the first observation of anomalous neutron `halo' scattering of HOPG is reported. The scattering projects a ring onto the detector with a half-cone angle of 12.4°, which surprisingly persists to incident neutron wavelengths far beyond the Bragg cutoff for graphite (6.71 Å). At longer wavelengths the ring is clearly a doublet with a splitting roughly proportional to wavelength. Sample tilting leads to the shift of the ring, which is wavelength dependent with longer wavelengths providing a smaller difference between the ring shift and the sample tilting. The ring broadens and weakens with decreasing HOPG quality. The lattice dynamics of graphite play a role in causing the scattering ring, as shown by the fact that the ring vanishes once the sample is cooled to 30 K. A possible interpretation by multiple scattering including elastic and inelastic processes is proposed.
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Sharma VK, Qian S. Effect of an Antimicrobial Peptide on Lateral Segregation of Lipids: A Structure and Dynamics Study by Neutron Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4152-4160. [PMID: 30720281 DOI: 10.1021/acs.langmuir.8b04158] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Antimicrobial peptides are one of the most promising classes of antibiotic agents for drug-resistant bacteria. Although the mechanisms of their action are not fully understood, many of them are found to interact with the target bacterial membrane, causing different degrees of perturbations. In this work, we directly observed that a short peptide disturbs membranes by inducing lateral segregation of lipids without forming pores or destroying membranes. Aurein 1.2 (aurein) is a 13-amino acid antimicrobial peptide discovered in the frog Litoria genus that exhibits high antibiotic efficacy. Being cationic and amphiphilic, it binds spontaneously to a membrane surface with or without charged lipids. With a small-angle neutron scattering contrast matching technique that is sensitive to lateral heterogeneity in membrane, we found that aurein induces significant lateral segregation in an initially uniform lipid bilayer composed of zwitterionic lipid and anionic lipid. More intriguingly, the lateral segregation was similar to the domain formed below the order-disorder phase-transition temperature. To our knowledge, this is the first direct observation of lateral segregation caused by a peptide. With quasi-elastic neutron scattering, we indeed found that the lipid lateral motion in the fluid phase was reduced even at low aurein concentrations. The reduced lateral mobility makes the membrane prone to additional stresses and defects that change membrane properties and impede membrane-related biological processes. Our results provide insights into how a short peptide kills bacteria at low concentrations without forming pores or destroying membranes. With a better understanding of the interaction, more effective and economically antimicrobial peptides may be designed.
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Affiliation(s)
- Veerendra K Sharma
- Solid State Physics Division , Bhabha Atomic Research Centre , Mumbai 400085 , India
| | - Shuo Qian
- Neutron Scattering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
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Naing SH, Oliver RC, Weiss KL, Urban VS, Lieberman RL. Solution Structure of an Intramembrane Aspartyl Protease via Small Angle Neutron Scattering. Biophys J 2019; 114:602-608. [PMID: 29414706 DOI: 10.1016/j.bpj.2017.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/04/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022] Open
Abstract
Intramembrane aspartyl proteases (IAPs) comprise one of four families of integral membrane proteases that hydrolyze substrates within the hydrophobic lipid bilayer. IAPs include signal peptide peptidase, which processes remnant signal peptides from nascent polypeptides in the endoplasmic reticulum, and presenilin, the catalytic component of the γ-secretase complex that processes Notch and amyloid precursor protein. Despite their broad biomedical reach, basic structure-function relationships of IAPs remain active areas of research. Characterization of membrane-bound proteins is notoriously challenging due to their inherently hydrophobic character. For IAPs, oligomerization state in solution is one outstanding question, with previous proposals for monomer, dimer, tetramer, and octamer. Here we used small angle neutron scattering (SANS) to characterize n-dodecyl-β-D-maltopyranoside (DDM) detergent solutions containing and absent a microbial IAP ortholog. A unique feature of SANS is the ability to modulate the solvent composition to mask all but the enzyme of interest. The signal from the IAP was enhanced by deuteration and, uniquely, scattering from DDM and buffers were matched by the use of both tail-deuterated DDM and D2O. The radius of gyration calculated for IAP and the corresponding ab initio consensus model are consistent with a monomer. The model is slightly smaller than the crystallographic IAP monomer, suggesting a more compact protein in solution compared with the crystal lattice. Our study provides direct insight into the oligomeric state of purified IAP in surfactant solution, and demonstrates the utility of fully contrast-matching the detergent in SANS to characterize other intramembrane proteases and their membrane-bound substrates.
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Affiliation(s)
- Swe-Htet Naing
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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Mahieu E, Gabel F. Biological small-angle neutron scattering: recent results and development. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:715-726. [DOI: 10.1107/s2059798318005016] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023]
Abstract
Small-angle neutron scattering (SANS) has increasingly been used by the structural biology community in recent years to obtain low-resolution information on solubilized biomacromolecular complexes in solution. In combination with deuterium labelling and solvent-contrast variation (H2O/D2O exchange), SANS provides unique information on individual components in large heterogeneous complexes that is perfectly complementary to the structural restraints provided by crystallography, nuclear magnetic resonance and electron microscopy. Typical systems studied include multi-protein or protein–DNA/RNA complexes and solubilized membrane proteins. The internal features of these systems are less accessible to the more broadly used small-angle X-ray scattering (SAXS) technique owing to a limited range of intra-complex and solvent electron-density variation. Here, the progress and developments of biological applications of SANS in the past decade are reviewed. The review covers scientific results from selected biological systems, including protein–protein complexes, protein–RNA/DNA complexes and membrane proteins. Moreover, an overview of recent developments in instruments, sample environment, deuterium labelling and software is presented. Finally, the perspectives for biological SANS in the context of integrated structural biology approaches are discussed.
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Hayes DG, Pingali SV, O'Neill HM, Urban VS, Ye R. Observation of a structural gradient in Winsor-III microemulsion systems. SOFT MATTER 2018; 14:5270-5276. [PMID: 29892769 DOI: 10.1039/c8sm00322j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We demonstrate here for the first time via small-angle neutron scattering (SANS) that the middle, bicontinuous microemulsion (BμE) phase of Winsor-III systems undergoes a gradual change of structure and composition in the vertical direction, contrary to the commonly held belief of uniform structure and composition. A vertical stage was deployed to enable precise alignment of a custom-designed rectangular cell containing the WIII system with respect to the neutron beam, allowing for several different vertical positions to be analyzed. For the water/AOT/CK-2,13 (two-tailed alkyl ethoxylate containing a 1,3-dioxolane linkage)/heptane Winsor-III system, the quasi-periodic repeat distance (d) and correlation length (ξ), obtained from the Teubner-Strey model applied to the SANS data, decreased and the surface area per volume of the surfactant monolayer (via Porod analysis) increased in the downward direction, trends that reflect an increase of surfactant concentration, consistent with the ultralow interfacial tension that often occurs for the lower liquid-liquid interface of many WIII systems. The water/sodium dodecyl sulfate (SDS)/1-pentanol/dodecane system shared the same trend with regard to d as observed for AOT/CK-2,13. In contrast, for SDS/pentanol, ξ increased and the amphiphilicity factor (fa) decreased in the downward direction, trends consistent with a decrease of cosurfactant (pentanol) concentration in the downward direction. Non-uniformity in the vertical direction has implications in the transport of solutes between WIII phases during the extractive purification of proteins or the removal of heavy metals and pollutants from wastewater, or the deposition of BμEs onto hydrophilic vs. hydrophobic surfaces as thin coatings.
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Affiliation(s)
- Douglas G Hayes
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996-4531, USA.
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Bodenheimer AM, O'Dell WB, Oliver RC, Qian S, Stanley CB, Meilleur F. Structural investigation of cellobiose dehydrogenase IIA: Insights from small angle scattering into intra- and intermolecular electron transfer mechanisms. Biochim Biophys Acta Gen Subj 2018; 1862:1031-1039. [DOI: 10.1016/j.bbagen.2018.01.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/18/2017] [Accepted: 01/23/2018] [Indexed: 01/08/2023]
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Sparks S, Temel DB, Rout MP, Cowburn D. Deciphering the "Fuzzy" Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering. Structure 2018; 26:477-484.e4. [PMID: 29429880 PMCID: PMC5929991 DOI: 10.1016/j.str.2018.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 10/27/2017] [Accepted: 01/12/2018] [Indexed: 11/16/2022]
Abstract
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism that enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interacting with TFs. To selectively characterize conformational changes in FG Nups induced by TFs we performed small-angle neutron scattering (SANS) with contrast matching. Conformational-ensembles derived from SANS data indicated an increase in the overall size of FG Nups is associated with TF interaction. Moreover, the organization of the FG motif in the interacting state is consistent with prior experimental analyses defining that FG motifs undergo conformational restriction upon interacting with TFs. These results provide structural insights into a highly dynamic interaction and illustrate how functional disorder imparts rapid and selective FG Nup-TF interactions.
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Affiliation(s)
- Samuel Sparks
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deniz B Temel
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY, USA
| | - David Cowburn
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA.
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Heller WT, Cuneo M, Debeer-Schmitt L, Do C, He L, Heroux L, Littrell K, Pingali SV, Qian S, Stanley C, Urban VS, Wu B, Bras W. The suite of small-angle neutron scattering instruments at Oak Ridge National Laboratory. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718001231] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Oak Ridge National Laboratory is home to the High Flux Isotope Reactor (HFIR), a high-flux research reactor, and the Spallation Neutron Source (SNS), the world's most intense source of pulsed neutron beams. The unique co-localization of these two sources provided an opportunity to develop a suite of complementary small-angle neutron scattering instruments for studies of large-scale structures: the GP-SANS and Bio-SANS instruments at the HFIR and the EQ-SANS and TOF-USANS instruments at the SNS. This article provides an overview of the capabilities of the suite of instruments, with specific emphasis on how they complement each other. A description of the plans for future developments including greater integration of the suite into a single point of entry for neutron scattering studies of large-scale structures is also provided.
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Sawada D, Kalluri UC, O’Neill H, Urban V, Langan P, Davison B, Pingali SV. Tension wood structure and morphology conducive for better enzymatic digestion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:44. [PMID: 29467822 PMCID: PMC5815229 DOI: 10.1186/s13068-018-1043-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Tension wood is a type of reaction wood in response to bending or leaning stem as a corrective growth process. Tension wood is formed by both natural and man-made processes. Most attractively, tension wood contains higher glucan content and undergoes higher enzymatic conversion to fermentable sugars. Here, we have employed structural techniques, small-angle neutron scattering (SANS) and wide-angle X-ray diffraction (WAXD) to elucidate structural and morphological aspects of tension wood conducive to higher sugar yields. RESULTS Small-angle neutron scattering data exhibited a tri-modal distribution of the fibril cross-sectional dimension. The smallest size, 22 Å observed in all samples concurred with the WAXD results of the control and opposite side samples. This smallest and the most abundant occurring size was interpreted as the cellulose elementary microfibril diameter. The intermediate size of 45 Å, which is most pronounced in the tension side sample and consistent with WAXD results for tension side sample, indicates association of neighboring elementary microfibrils to form larger crystallite bundles. The largest size 61 Å observed by SANS was however not observed by WAXD and therefore associated to mesopores. CONCLUSIONS Structure and morphology of tension wood is different from control wood. Cellulose crystallinity increases, lignin content is lower and the appearance of mesopores with 61 Å diameter is observed. Despite the presence of higher crystalline cellulose content in tension side, the lower lignin content and may be combined with the abundance of mesopores, substantially improves enzyme accessibility leading to higher yields in cellulose digestion.
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Affiliation(s)
- Daisuke Sawada
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Udaya C. Kalluri
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Hugh O’Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Volker Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Brian Davison
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831 USA
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Oliver RC, Pingali SV, Urban VS. Designing Mixed Detergent Micelles for Uniform Neutron Contrast. J Phys Chem Lett 2017; 8:5041-5046. [PMID: 28960995 DOI: 10.1021/acs.jpclett.7b02149] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Micelle-forming detergents provide an amphipathic environment that mimics lipid bilayers and are important tools used to solubilize and stabilize membrane proteins in solution for in vitro structural investigations. Small-angle neutron scattering (SANS) at the neutron contrast match point of detergent molecules allows observing the signal from membrane proteins unobstructed by contributions from the detergent. However, we show that even for a perfectly average-contrast matched detergent there arises significant core-shell scattering from the contrast difference between aliphatic detergent tails and hydrophilic head groups. This residual signal interferes with interpreting structural data of membrane proteins. This complication is often made worse by the presence of excess empty (protein-free) micelles. We present an approach for the rational design of mixed micelles containing a deuterated detergent analog, which eliminates neutron contrast between core and shell and allows the micelle scattering to be fully contrast-matched to unambiguously resolve membrane protein structure using solution SANS.
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Affiliation(s)
- Ryan C Oliver
- Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, MS 6475, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, MS 6475, Oak Ridge, Tennessee 37831, United States
| | - Volker S Urban
- Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, MS 6475, Oak Ridge, Tennessee 37831, United States
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Abstract
Interactions of water with cellulose are of both fundamental and technological importance. Here, we characterize the properties of water associated with cellulose using deuterium labeling, neutron scattering and molecular dynamics simulation. Quasi-elastic neutron scattering provided quantitative details about the dynamical relaxation processes that occur and was supported by structural characterization using small-angle neutron scattering and X-ray diffraction. We can unambiguously detect two populations of water associated with cellulose. The first is "non-freezing bound" water that gradually becomes mobile with increasing temperature and can be related to surface water. The second population is consistent with confined water that abruptly becomes mobile at ~260 K, and can be attributed to water that accumulates in the narrow spaces between the microfibrils. Quantitative analysis of the QENS data showed that, at 250 K, the water diffusion coefficient was 0.85 ± 0.04 × 10-10 m2sec-1 and increased to 1.77 ± 0.09 × 10-10 m2sec-1 at 265 K. MD simulations are in excellent agreement with the experiments and support the interpretation that water associated with cellulose exists in two dynamical populations. Our results provide clarity to previous work investigating the states of bound water and provide a new approach for probing water interactions with lignocellulose materials.
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50
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Abstract
Aurein 1.2 is a potent antimicrobial peptide secreted by frog Litoria aurea. As a short membrane-active peptide with only 13 amino acids in sequence, it has been found to be residing on the surface of lipid bilayer and permeabilizing bacterial membranes at high concentration. However, the detail at the molecular level is largely unknown. In this study, we investigated the action of Aurein 1.2 in charged lipid bilayers composed of DMPC/DMPG. Oriented Circular Dichroism results showed that the peptide was on the surface of lipid bilayer regardless of the charged lipid ratio. Only at a very high peptide-to-lipid ratio (~1/10), the peptide became perpendicular to the bilayer, however no pore was detected by neutron in-plane scattering. To further understand how it interacted with charged lipid bilayers, we employed Small Angle Neutron Scattering to probe lipid distribution across bilayer leaflets in lipid vesicles. The results showed that Aurein 1.2 interacted strongly with negatively charged DMPG, causing strong asymmetry in lipid bilayer. At high concentration, while the vesicles were intact, we found additional structure feature on the bilayer. Our study provides a glimpse into how Aurein 1.2 disturbs anionic lipid-containing membranes without pore formation.
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