Article
Chemistry, Analytical
Katherine T. Peter, Allison L. Phillips, Ann M. Knolhoff, Piero R. Gardinali, Carlos A. Manzano, Kelsey E. Miller, Manuel Pristner, Lyne Sabourin, Mark W. Sumarah, Benedikt Warth, Jon R. Sobus
Summary: Non-targeted analysis (NTA) workflows using mass spectrometry are becoming increasingly popular in various disciplines, but there is still a lack of universally accepted reporting standards. To address this issue, researchers have developed the NTA Study Reporting Tool (SRT), which has been shown to be effective in guiding study design, manuscript writing, and evaluating NTA reporting quality through analysis of published articles.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Takahide Yamaguchi, Kouhei Akao, Alexandros Koutsioubas, Henrich Frielinghaus, Takamitsu Kohzuma
Summary: The dynamic structure changes of Cyt c & PRIME;, including unfolding, dimerization, and transition to an open-bundle structure, were investigated by small-angle neutron scattering experiment. The transition from compactly folded to an open-bundle structure at higher pH was confirmed through numerical analysis and ab initio modeling.
Review
Chemistry, Analytical
Seema Thakral, Kyungtae Kim
Summary: Small-angle scattering (SAS) is a versatile analytical technique that provides detailed structural information at the nanometer scale. It has diverse applications in pharmaceutical material characterization, including identification of liquid-crystalline mesophase of drugs, study of excipient microstructure influence, and optimization of solid dispersions and protein-based therapeutics formulations.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Abigail Barclay, Birthe B. Kragelund, Lise Arleth, Martin Cramer Pedersen
Summary: Recent advances in protein expression protocols have allowed for the investigation of structurally complex and disordered biomolecules using small-angle scattering experiments. A modeling scheme has been developed that combines classical form factor based modeling with spherical harmonics-based formulation to accurately calculate scattering profiles from these complex samples. The scheme can account for flexible domains and other structurally elaborate components, and we demonstrate its utility through a case study on a growth hormone receptor membrane protein. We also explore how the scattering profiles vary under different contrasts and discuss the implications for data modeling.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biology
F. Emil Thomasen, Matthew J. Cuneo, Tanja Mittag, Kresten Lindorff-Larsen
Summary: Speckle-type POZ protein (SPOP) is a key protein in the ubiquitin proteasome system, with important roles in cell-cycle control, development, and cancer pathogenesis. This study combines small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations to characterize the conformational ensembles and oligomeric states of SPOP. The results suggest that SPOP oligomers behave as rigid, helical structures with flexible substrate-binding domains.
Article
Polymer Science
Zhen Liu, Xin Li, Ruike Zou, Zekun Zhou, Qianyun Ma, Peng Zhang
Summary: The structure of PEDOT:PSS and its relationship with conductivity and device performance were investigated in this study. It was found that PEDOT:PSS formed a conductive network in the aqueous dispersion due to its quaternary structure, and secondary doping with lithium bis(trifluoromethanesulfonyl)imide salt changed the structure and enhanced the conductivity. In situ analysis of the structure change and resistance during solvent evaporation provided fundamental knowledge for understanding the structure-property correlations.
Article
Chemistry, Multidisciplinary
Charlotte E. Conn, Liliana de Campo, Andrew E. Whitten, Christopher J. Garvey, Anwen M. Krause-Heuer, Leonie Van't Hag
Summary: This perspective discusses the progress in determining membrane protein structures in lipid bilayers using small-angle neutron scattering, highlighting the use of differentially labeled detergents with homogeneous scattering length density for contrast matching. It also explores the limitations of using detergent micelles and deuterated vesicles, as well as the potential of contrast-matching in distinguishing different membrane protein conformations within the lipid bilayer. Time-resolved studies using SANS illustrate the complex phase behavior in lyotropic liquid crystalline systems and emphasize the significance of this development for advancing biological and pharmaceutical applications related to membrane-associated proteins.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Physical
Rasmus Palm, Riinu Harmas, Eneli Hark, Ben Kent, Heisi Kurig, Miriam Koppel, Margarita Russina, Indrek Tallo, Tavo Romann, Jitendra Mata, Kenneth Tuul, Enn Lust
Summary: The study explored the impact of synthesis conditions on the formation of porous and graphitic structures of carbon materials, showing that lower synthesis temperatures result in predominantly nano-scale cylindrical geometries, while higher temperatures promote the formation of slit-like structures.
Article
Chemistry, Physical
Meltem Bayrak, Jitendra Mata, Jared K. Raynes, Mark Greaves, Jacinta White, Charlotte E. Conn, Juliane Floury, Amy Logan
Summary: This study investigated the structural devolution of RG and TG gels during simulated gastric digestion, finding that gel firmness and disintegration behavior are closely related. Gel firmness and brittleness were greater in D2O samples compared to H2O.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Fernando T. Tanouye, Jozismar R. Alves, Francesco Spinozzi, Rosangela Itri
Summary: In this study, protein interactions were investigated using in-solution small angle X-Ray scattering (SAXS) experiments and Monte Carlo (MC) simulations under different conditions. The analysis of experimental data using the HSDY/RPA model combined with MC simulations showed limitations in describing the protein-protein pair potential for highly concentrated systems at low ionic strength. SAXS/MC results revealed that lysozyme concentrations between 2 and 20 mg/mL exhibited similar protein-protein pair potentials, with a surface net charge of around 7 e, protein diameter of 28 Å, attractive well potential decay range of 3 Å, and a depth varying from 1 to 5 kBT depending on temperature and salt addition. Additionally, a novel method combining SAXS with MC simulations was proposed to overcome the limitations of closure relationships in analyzing interacting protein SAXS data.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Health Care Sciences & Services
Michael M. Schlussel, Melissa K. Sharp, Jennifer A. de Beyer, Shona Kirtley, Patricia Logullo, Paula Dhiman, Angela MacCarthy, Anna Koroleva, Benjamin Speich, Garrett S. Bullock, David Moher, Gary S. Collins
Summary: This study investigated the developing methods of reporting guidelines in the EQUATOR Network's database. The findings show that the number of reporting guidelines has increased over the past 30 years, and developers should use existing guidance and an evidence-based approach during the development process.
JOURNAL OF CLINICAL EPIDEMIOLOGY
(2023)
Article
Medicine, Research & Experimental
Dileep Urimi, Maja Hellsing, Najet Mahmoudi, Christopher Soderberg, Ronja Widenbring, Lars Gedda, Katarina Edwards, Thorsteinn Loftsson, Nicolaas Schipper
Summary: Lipid nanocapsules (LNCs) with core-shell structure were studied using various techniques, and it was found that drug loading does not alter the overall structure of LNCs. However, the presence of the drug leads to an increase in the thickness of the shell while the core size remains unchanged.
MOLECULAR PHARMACEUTICS
(2022)
Article
Biochemical Research Methods
Jill Trewhella, Patrice Vachette, Jan Bierma, Clement Blanchet, Emre Brookes, Srinivas Chakravarthy, Leonie Chatzimagas, Thomas E. Cleveland, Nathan Cowieson, Ben Crossett, Anthony P. Duff, Daniel Franke, Frank Gabel, Richard E. Gillilan, Melissa Graewert, Alexander Grishaev, J. Mitchell Guss, Michal Hammel, Jesse Hopkins, Qingqui Huang, Jochen S. Hub, Greg L. Hura, Thomas C. Irving, Cy Michael Jeffries, Cheol Jeong, Nigel Kirby, Susan Krueger, Anne Martel, Tsutomu Matsui, Na Li, Javier Perezt, Lionel Porcar, Thierry Prange, Ivan Rajkovic, Mattia Rocco, Daniel J. Rosenberg, Timothy M. Ryan, Soenke Seifert, Hiroshi Sekiguchi, Dmitri Svergun, Susana Teixeira, Aurelien Thureaut, Thomas M. Weiss, Andrew E. Whitten, Kathleen Wood, Xiaobing Zuo
Summary: By collecting SAXS and SANS measurements, consensus scattering profiles for proteins were obtained, which were consistent with theoretical predictions. Optimization of sample purification methods and measurement conditions can improve the quality and precision of the data.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Flavio Carsughi
Summary: In this research, a simplified polydispersion analysis (SPA) method is proposed for analyzing small-angle scattering (SAS) data. By straightforward interpolation of SAS data, the size distribution function (SDF) of polydisperse inhomogeneities can be determined without advanced computational skills. The method is tested against simulated and experimental data with excellent results, offering new opportunities for scientists to investigate polydisperse systems using SAS technique.
APPLIED SCIENCES-BASEL
(2022)
Review
Crystallography
Maksym Golub, Adrian Kolsch, Artem Feoktystov, Athina Zouni, Jorg Pieper
Summary: High-resolution structures of photosynthetic pigment-protein complexes are typically determined using crystallography or cryo-electron microscopy, which have limitations in studying proteins in aqueous solution at physiological temperatures. Small-angle neutron and X-ray scattering offer a solution by providing structural information for proteins in solution at room temperature. Studies on phycocyanin and Photosystem I revealed discrepancies in their solution structures compared to crystal structures, possibly due to protein dynamics at physiological temperatures.
Article
Chemistry, Multidisciplinary
Derrick Lau, James C. Walsh, Amir Mousapasandi, Nicholas Ariotti, Vaibhav B. Shah, Stuart Turville, David A. Jacques, Till Boecking
Article
Biology
Richard J. Miles, Claire Kerridge, Laura Hilditch, Christopher Monit, David A. Jacques, Greg J. Towers
Article
Immunology
Mehdi Moustaqil, Emma Ollivier, Hsin-Ping Chiu, Sarah Van Tol, Paulina Rudolffi-Soto, Christian Stevens, Akshay Bhumkar, Dominic J. B. Hunter, Alexander N. Freiberg, David Jacques, Benhur Lee, Emma Sierecki, Yann Gambin
Summary: The study revealed that the proteases NSP3 and NSP5 of SARS-CoV-2 can cleave proteins involved in host immune responses, shedding light on the mechanisms behind enhanced inflammatory responses in COVID-19 patients. The direct cleavage of specific proteins by these proteases provides insights into the pathophysiology of the disease.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Chemistry, Analytical
Derrick Lau, James C. Walsh, Claire F. Dickson, Andrew Tuckwell, Jeffrey H. Stear, Dominic J. B. Hunter, Akshay Bhumkar, Vaibhav Shah, Stuart G. Turville, Emma Sierecki, Yann Gambin, Till Bocking, David A. Jacques
Summary: The study developed a fluorescence analysis method using HIV capsid as bait to screen for fluorescence-labeled binding molecules. By using a scanning stage, rapid detection was achieved without compromising sensitivity, providing a new approach for screening potential interactors.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Jingwei Zeng, Ana Filipa Santos, Aamir S. Mukadam, Mariana Osswald, David A. Jacques, Claire F. Dickson, Stephen H. McLaughlin, Christopher M. Johnson, Leo Kiss, Jakub Luptak, Nadine Renner, Marina Vaysburd, William A. McEwan, Eurico Morais-de-Sa, Dean Clift, Leo C. James
Summary: The article explains the working principle of Trim-Away, a new technology that utilizes TRIM21's ubiquitination activity for protein degradation, promoting virus neutralization or targeting disease-causing proteins. The study expands the understanding of TRIM21 and broadens the application of Trim-Away.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Microbiology
Nadine Renner, Donna L. Mallery, K. M. Rifat Faysal, Wang Peng, David A. Jacques, Till Boecking, Leo C. James
Summary: HIV protects its RNA genome while copying it into DNA by constructing a capsid with highly charged pores that can import nucleotides, preventing host sensing and allowing DNA synthesis. The metabolite IP6 plays a crucial role in coordinating positively charged residues in the capsid, and mutations in K25 affect HIV infectivity and DNA synthesis.
Article
Chemistry, Multidisciplinary
Jill Trewhella
Summary: Small-angle scattering emerged as a tool for studying noncrystalline structures in the early 1930s. Andre' Guinier emphasized the value of the technique in studying submicroscopical inhomogeneities in his summary findings from the first Conference on Small Angle Scattering in 1958. Since 1965, a successful series of Small-Angle Scattering (SAS) meetings have been held approximately every three years, with many of them publishing their proceedings in the IUCr Journal of Applied Crystallography. In the early 2000s, the international SAS community and the IUCr have strengthened their relationship through formal cooperation and collaboration in various activities that have supported the growth and health of the field and the organization.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Review
Biochemistry & Molecular Biology
Jill Trewhella
Summary: Applications of small-angle scattering (SAS) in structural biology have been enhanced by advancements in instrumentation, data analysis tools, modeling capabilities, data presentation standards, and data archiving. These capabilities have allowed SAS to contribute to breakthroughs in the study of biomolecular complexes and assemblies, including whole cells, membrane proteins in lipid environments, and dynamic systems across various time scales.
Correction
Chemistry, Multidisciplinary
Jill Trewhella
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Review
Biophysics
Margaret J. Zhang, Jeffrey H. Stear, David A. Jacques, Till Bocking
Summary: This review explores the limitations in our understanding of the uncoating process of HIV and presents recently developed techniques that aim to understand the mechanisms behind this essential aspect of HIV infection.
BIOPHYSICAL REVIEWS
(2022)
Biographical-Item
Chemistry, Multidisciplinary
Dmitri Svergun, Jill Trewhella
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2022)
Article
Biochemical Research Methods
Jill Trewhella, Patrice Vachette, Jan Bierma, Clement Blanchet, Emre Brookes, Srinivas Chakravarthy, Leonie Chatzimagas, Thomas E. Cleveland, Nathan Cowieson, Ben Crossett, Anthony P. Duff, Daniel Franke, Frank Gabel, Richard E. Gillilan, Melissa Graewert, Alexander Grishaev, J. Mitchell Guss, Michal Hammel, Jesse Hopkins, Qingqui Huang, Jochen S. Hub, Greg L. Hura, Thomas C. Irving, Cy Michael Jeffries, Cheol Jeong, Nigel Kirby, Susan Krueger, Anne Martel, Tsutomu Matsui, Na Li, Javier Perezt, Lionel Porcar, Thierry Prange, Ivan Rajkovic, Mattia Rocco, Daniel J. Rosenberg, Timothy M. Ryan, Soenke Seifert, Hiroshi Sekiguchi, Dmitri Svergun, Susana Teixeira, Aurelien Thureaut, Thomas M. Weiss, Andrew E. Whitten, Kathleen Wood, Xiaobing Zuo
Summary: By collecting SAXS and SANS measurements, consensus scattering profiles for proteins were obtained, which were consistent with theoretical predictions. Optimization of sample purification methods and measurement conditions can improve the quality and precision of the data.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Microbiology
Lorena Zuliani-Alvarez, Morten L. Govasli, Jane Rasaiyaah, Chris Monit, Stephen O. Perry, Rebecca P. Sumner, Simon McAlpine-Scott, Claire Dickson, K. M. Rifat Faysal, Laura Hilditch, Richard J. Miles, Frederic Bibollet-Ruche, Beatrice H. Hahn, Till Boecking, Nikos Pinotsis, Leo C. James, David A. Jacques, Greg J. Towers
Summary: Innate immune evasion is crucial for the evolution of the pandemic lineage of HIV. The pandemic HIV-1(M) exhibits better replication and evasion of immune response compared to non-pandemic HIV strains.
NATURE MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Jill Trewhella, Cy M. Jeffries, Andrew E. Whitten
Summary: Guidelines were published in 2017 for reporting small-angle scattering (SAS) data from biomolecules in solution, introducing best-practice documentation of experiments and analysis. The IUCr biology journals now require the deposition of SAS data into a public archive, along with adherence to the 2017 reporting guidelines. Updated reporting templates have been developed based on feedback from the SAS community, providing standard descriptions for proteins, glycosylated proteins, DNA and RNA, as well as specialized templates for SAS contrast-variation experiments.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Emre Brookes, Mattia Rocco, Patrice Vachette, Jill Trewhella
Summary: The artificial intelligence program AlphaFold (AF) has a significant impact on structural biology by providing predicted protein structures from nearly all known protein sequences. However, challenges still exist in predicting unstructured regions and arranging potentially flexible linkers connecting structured domains.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2023)
