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Article ; Online: Planning, executing and assessing the validity of SANS contrast variation experiments.

Krueger, Susan

2022 Volume 677, Page(s) 127–155

Abstract: Small angle neutron scattering (SANS) along with contrast variation (CV) can provide key information that is used to determine the shape and structure of biological complexes in solution. The successful SANS CV experiment is usually a result of judicious ...

Abstract	Small angle neutron scattering (SANS) along with contrast variation (CV) can provide key information that is used to determine the shape and structure of biological complexes in solution. The successful SANS CV experiment is usually a result of judicious planning, careful execution and meticulous scrutiny of the resultant SANS data. A workflow for planning, executing and, importantly, assessing the validity of SANS CV data is presented here, along with tips to follow in order to perform a successful SANS CV experiment. Some knowledge of the basics of small angle scattering is assumed, including data reduction and standard analysis to obtain model independent parameters such as the radius of gyration and forward scattering intensity, and SANS CV theory is not covered in detail. Rather, the focus is on the SANS CV workflow from in silico experiment planning and execution to obtaining the SANS CV data, assessing its validity, and determining a model structure or ensemble of structures using the SANS CV data as constraints.
MeSH term(s)	Neutrons ; Scattering, Small Angle ; Workflow
Language	English
Publishing date	2022-09-21
Publishing country	United States
Document type	Journal Article
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2022.08.023
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Article ; Online: Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs.

Krueger, Susan

Current opinion in structural biology

2022 Volume 74, Page(s) 102375

Abstract: Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron ... ...

Abstract	Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron instrumentation and complementary techniques such as small-angle x-ray scattering (SAXS), cryo-EM, NMR and x-ray crystallography, along with the availability of more powerful structure prediction algorithms and computational resources has made SANS more important than ever as a means to obtain unique information on the structure of biological complexes in solution. In particular, the contrast variation (CV) technique, which requires a large commitment in both sample preparation and measurement time, has become more practical with the advent of these improved resources. Here, challenges and recent triumphs as well as future prospects are discussed.
MeSH term(s)	Crystallography, X-Ray ; Neutron Diffraction/methods ; Neutrons ; Scattering, Small Angle ; X-Ray Diffraction
Language	English
Publishing date	2022-04-28
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2022.102375
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Article ; Online: Small angle scattering reveals the orientation of cytochrome P450 19A1 in lipoprotein nanodiscs.

Hackett, John C / Krueger, Susan / Urban, Volker S / Zárate-Pérez, Francisco

Journal of inorganic biochemistry

2024 Volume 257, Page(s) 112579

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 ...

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.
Language	English
Publishing date	2024-05-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	162843-4
ISSN	1873-3344 ; 0162-0134
ISSN (online)	1873-3344
ISSN	0162-0134
DOI	10.1016/j.jinorgbio.2024.112579
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Article: Designing and Performing Biological Solution Small-Angle Neutron Scattering Contrast Variation Experiments on Multi-component Assemblies.

Krueger, Susan

Advances in experimental medicine and biology

2017 Volume 1009, Page(s) 65–85

Abstract: Solution small-angle neutron scattering (SANS) combined with contrast variation provides information about the size and shape of individual components of a multi-component biological assembly, as well as the spatial arrangements between the components. ... ...

Abstract	Solution small-angle neutron scattering (SANS) combined with contrast variation provides information about the size and shape of individual components of a multi-component biological assembly, as well as the spatial arrangements between the components. The large difference in the neutron scattering properties between hydrogen and deuterium is key to the method. Isotopic substitution of deuterium for some or all of the hydrogen in either the molecule or the solvent can greatly alter the scattering properties of the biological assembly, often with little or no change to its biochemical properties. Thus, SANS with contrast variation provides unique information not easily obtained using other experimental techniques.If used correctly, SANS with contrast variation is a powerful tool for determining the solution structure of multi-component biological assemblies. This chapter discusses the principles of SANS theory that are important for contrast variation, essential considerations for experiment design and execution, and the proper approach to data analysis and structure modeling. As sample quality is extremely important for a successful contrast variation experiment, sample issues that can affect the outcome of the experiment are discussed as well as procedures used to verify the sample quality. The described methodology is focused on two-component biological complexes. However, examples of its use for multi-component assemblies are also discussed.
MeSH term(s)	Computer Simulation ; Data Accuracy ; Deuterium/chemistry ; Deuterium Exchange Measurement/methods ; Humans ; Hydrogen/chemistry ; Models, Molecular ; Molecular Conformation ; Neutron Diffraction/instrumentation ; Neutron Diffraction/methods ; Nucleic Acids/chemistry ; Nucleic Acids/ultrastructure ; Proteins/chemistry ; Proteins/ultrastructure ; Research Design ; Scattering, Small Angle
Chemical Substances	Nucleic Acids ; Proteins ; Hydrogen (7YNJ3PO35Z) ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-981-10-6038-0_5
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Article ; Online: Synthesis of Polymer Nanoweb via a Lipid Template.

Liu, Chung-Hao / Krueger, Susan / Nieh, Mu-Ping

ACS macro letters

2023 Volume 12, Issue 7, Page(s) 993–998

Abstract: We report a generalized platform for synthesizing a polymer nanoweb with a high specific surface area via a bicellar template, composed of 1,2-dipalmitoyl phosphocholine (DPPC), 1,2-dihexanoyl phosphocholine (DHPC), and 1,2-dipalmitoyl phosphoglycerol ( ... ...

Abstract	We report a generalized platform for synthesizing a polymer nanoweb with a high specific surface area via a bicellar template, composed of 1,2-dipalmitoyl phosphocholine (DPPC), 1,2-dihexanoyl phosphocholine (DHPC), and 1,2-dipalmitoyl phosphoglycerol (DPPG). The pristine bicelle (in the absence of monomer or polymer) yields a variety of well-defined structures, including disc, vesicle, and perforated lamella. The addition of styrene monomers in the mixture causes bicelles to transform into lamellae. Monomers are miscible with DPPC and DPPG initially, while polymerization drives polymers to the DHPC-rich domain, resulting in a polymer nanoweb supported by the outcomes of small angle neutron scattering, differential scanning calorimetry, and transmission electron microscopy.
Language	English
Publishing date	2023-07-05
Publishing country	United States
Document type	Journal Article
ISSN	2161-1653
ISSN (online)	2161-1653
DOI	10.1021/acsmacrolett.3c00255
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Article ; Online: Enabling Efficient Design of Biological Formulations Through Advanced Characterization.

Sonje, Jayesh / Thakral, Seema / Krueger, Susan / Suryanarayanan, Raj

Pharmaceutical research

2023 Volume 40, Issue 6, Page(s) 1459–1477

Abstract: The present review summarizes the use of differential scanning calorimetry (DSC) and scattering techniques in the context of protein formulation design and characterization. The scattering techniques include wide angle X-ray diffractometry (XRD), small- ... ...

Abstract	The present review summarizes the use of differential scanning calorimetry (DSC) and scattering techniques in the context of protein formulation design and characterization. The scattering techniques include wide angle X-ray diffractometry (XRD), small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS). While DSC is valuable for understanding thermal behavior of the excipients, XRD provides critical information about physical state of solutes during freezing, annealing and in the final lyophile. However, as these techniques lack the sensitivity to detect biomolecule-related transitions, complementary characterization techniques such as small-angle scattering can provide valuable insights.
MeSH term(s)	Scattering, Small Angle ; X-Ray Diffraction
Language	English
Publishing date	2023-03-23
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	843063-9
ISSN	1573-904X ; 0724-8741 ; 0739-0742
ISSN (online)	1573-904X
ISSN	0724-8741 ; 0739-0742
DOI	10.1007/s11095-023-03495-z
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Article ; Online: Temperature-induced DNA density transition in phage λ capsid revealed with contrast-matching SANS.

Villanueva Valencia, José Ramón / Tsimtsirakis, Efthymios / Krueger, Susan / Evilevitch, Alex

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 45, Page(s) e2220518120

Abstract: Structural details of a genome packaged in a viral capsid are essential for understanding how the structural arrangement of a viral genome in a capsid controls its release dynamics during infection, which critically affects viral replication. We ... ...

Abstract	Structural details of a genome packaged in a viral capsid are essential for understanding how the structural arrangement of a viral genome in a capsid controls its release dynamics during infection, which critically affects viral replication. We previously found a temperature-induced, solid-like to fluid-like mechanical transition of packaged λ-genome that leads to rapid DNA ejection. However, an understanding of the structural origin of this transition was lacking. Here, we use small-angle neutron scattering (SANS) to reveal the scattering form factor of dsDNA packaged in phage λ capsid by contrast matching the scattering signal from the viral capsid with deuterated buffer. We used small-angle X-ray scattering and cryoelectron microscopy reconstructions to determine the initial structural input parameters for intracapsid DNA, which allows accurate modeling of our SANS data. As result, we show a temperature-dependent density transition of intracapsid DNA occurring between two coexisting phases-a hexagonally ordered high-density DNA phase in the capsid periphery and a low-density, less-ordered DNA phase in the core. As the temperature is increased from 20 °C to 40 °C, we found that the core-DNA phase undergoes a density and volume transition close to the physiological temperature of infection (~37 °C). The transition yields a lower energy state of DNA in the capsid core due to lower density and reduced packing defects. This increases DNA mobility, which is required to initiate rapid genome ejection from the virus capsid into a host cell, causing infection. These data reconcile our earlier findings of mechanical DNA transition in phage.
MeSH term(s)	Bacteriophage lambda/genetics ; Capsid/chemistry ; Temperature ; Cryoelectron Microscopy ; DNA, Viral/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/analysis
Chemical Substances	DNA, Viral ; Capsid Proteins
Language	English
Publishing date	2023-10-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2220518120
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Article ; Online: Protein-Surfactant and Protein-Protein Interactions During Freeze and Thaw: A Small-Angle Neutron Scattering Study of Lysozyme Solutions with Polysorbate and Poloxamer.

Yuan, Xiaoda / Krueger, Susan / Shalaev, Evgenyi

Journal of pharmaceutical sciences

2022 Volume 112, Issue 1, Page(s) 76–82

Abstract: Protein structural changes during freezing and subsequent thawing are of great importance to a variety of biopharmaceutical applications. In this work, we studied the influence of non-ionic surfactants (polysorbate 20 and poloxamer 188) on protein ... ...

Abstract	Protein structural changes during freezing and subsequent thawing are of great importance to a variety of biopharmaceutical applications. In this work, we studied the influence of non-ionic surfactants (polysorbate 20 and poloxamer 188) on protein structural changes during freeze and thaw using lysozyme as a model protein. Small-angle neutron scattering was employed to characterize protein structures in both liquid and frozen solution states. The results show minimal impact of polysorbate 20 on lysozyme structures during freeze and thaw using practically relevant concentrations. Polysorbate 20 used at 0.04% (w/w) completely prevents freeze-induced aggregation of lysozyme. Poloxamer 188 seems to interact with lysozyme; when applied at high concentrations (10% w/w), such interaction prevents protein crowding or close packing typically associated with freeze concentration. Despite such interactions, lysozyme aggregation is observed with 10% (w/w) of poloxamer 188 during freezing, although the aggregation is reversed upon thawing.
MeSH term(s)	Polysorbates ; Poloxamer/chemistry ; Surface-Active Agents/chemistry ; Freezing ; Muramidase/chemistry ; Scattering, Small Angle ; Proteins
Chemical Substances	Polysorbates ; Poloxamer (106392-12-5) ; Surface-Active Agents ; Muramidase (EC 3.2.1.17) ; Proteins
Language	English
Publishing date	2022-08-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	3151-3
ISSN	1520-6017 ; 0022-3549
ISSN (online)	1520-6017
ISSN	0022-3549
DOI	10.1016/j.xphs.2022.08.017
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Article ; Online: Morphological Characterization of Self-Amplifying mRNA Lipid Nanoparticles.

Thelen, Jacob L / Leite, Wellington / Urban, Volker S / O'Neill, Hugh M / Grishaev, Alexander V / Curtis, Joseph E / Krueger, Susan / Castellanos, Maria Monica

ACS nano

2024 Volume 18, Issue 2, Page(s) 1464–1476

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 ... ...

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.
MeSH term(s)	RNA, Messenger/chemistry ; Scattering, Small Angle ; X-Ray Diffraction ; Nanoparticles/chemistry ; Lipids/chemistry ; RNA, Small Interfering/chemistry ; Liposomes
Chemical Substances	Lipid Nanoparticles ; RNA, Messenger ; Lipids ; RNA, Small Interfering ; Liposomes
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Journal Article
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.3c08014
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Article ; Online: Reversible Self-Association in Lactate Dehydrogenase during Freeze-Thaw in Buffered Solutions Using Neutron Scattering.

Sonje, Jayesh / Thakral, Seema / Krueger, Susan / Suryanarayanan, Raj

Molecular pharmaceutics

2021 Volume 18, Issue 12, Page(s) 4459–4474

Abstract: The aims of this work were to evaluate the effect of freezing and thawing stresses on lactate dehydrogenase (LDH) stability under three conditions. (i) In a solution buffered with sodium phosphate (NaP; 10 and 100 mM). The selective crystallization of ... ...

Abstract	The aims of this work were to evaluate the effect of freezing and thawing stresses on lactate dehydrogenase (LDH) stability under three conditions. (i) In a solution buffered with sodium phosphate (NaP; 10 and 100 mM). The selective crystallization of disodium hydrogen phosphate during freezing caused a pronounced pH shift. (ii) In a solution buffered with histidine, where there was no pH shift due to buffer salt crystallization. (iii) At different concentrations of LDH so as to determine the self-stabilizing ability of LDH. The change in LDH tetrameric conformation was measured by small-angle neutron scattering (SANS). The pH of the phosphate buffer solutions was monitored as a function of temperature to quantify the pH shift. The conditions of buffer component crystallization from solution were identified using low-temperature X-ray diffractometry. Dynamic light scattering (DLS) enabled us to determine the effect of freeze-thawing on the protein aggregation behavior. LDH, at a high concentration (1000 μg/mL; buffer concentration 10 mM), has a pronounced self-stabilizing effect and did not aggregate after five freeze-thaw cycles. At lower LDH concentrations (10 and 100 μg/mL), only with the selection of an appropriate buffer, irreversible aggregation could be avoided. While SANS provided qualitative information with respect to protein conformation, the insights from DLS were quantitative with respect to the particle size of the aggregates. SANS is the only technique which can characterize the protein both in the frozen and thawed states.
MeSH term(s)	Buffers ; Enzyme Stability ; Freezing ; Hydrogen-Ion Concentration ; L-Lactate Dehydrogenase/chemistry ; Neutron Diffraction ; Protein Aggregates ; Protein Conformation ; Protein Multimerization ; Scattering, Small Angle ; Solutions
Chemical Substances	Buffers ; Protein Aggregates ; Solutions ; L-Lactate Dehydrogenase (EC 1.1.1.27)
Language	English
Publishing date	2021-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2138405-8
ISSN	1543-8392 ; 1543-8384
ISSN (online)	1543-8392
ISSN	1543-8384
DOI	10.1021/acs.molpharmaceut.1c00666
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